Open access peer-reviewed chapter

Barley (Hordeum vulgare L.) Improvement Past, Present and Future

Written By

Nermin Gozukirmizi and Elif Karlik

Submitted: 18 November 2016 Reviewed: 07 March 2017 Published: 19 July 2017

DOI: 10.5772/intechopen.68359

From the Edited Volume

Brewing Technology

Edited by Makoto Kanauchi

Chapter metrics overview

2,412 Chapter Downloads

View Full Metrics


Barley has been cultivated for more than 10,000 years. Barley improvement studies always have the privilege of the breeders and scientists. This review is expected to provide a resource for researchers interested in barley improvement research in terms of mutation breeding, tissue culture, gene transfers, gene editing, molecular markers, transposons, epigenetic, genomic studies and system biology. We aimed to discuss some important and/or recent studies and improvements about barley for understanding the factors responsible for converting barley plants into the superior cereals, which occurred through gene transfers, gene editing and molecular breeding, which is important and could help us enhance the current pool of cultivated barley species to provide enough material for the future.


  • barley improvement
  • Hordeum vulgare L.
  • genetic research
  • genomics research
  • complex trait

1. Introduction

Cultivated barley (Hordeum vulgare L.) is the fourth important annual cereal crop from the family of Poaceae after wheat, rice, maize and is consumed as feed for livestock and, food—either pure or combined with other cereals in the form of porridge, sattu (roasted barley), breakfast foods and chapattis [1] and, most importantly, is also used for brewing malts. Barley, which is also an excellent model plant for biochemists, physiologists, geneticists and molecular biologists, is one of the world’s earliest domesticated and most important crop plants [2]. According to world statistics, its production in 2015 was 148.78 million tons, where Turkey’s contribution was 4,750,000 metric tons [3]. Barley is a self-pollinating diploid with 2n = 2x = 14 chromosomes. Moreover, it has two-rowed and six-rowed types, according to spike morphology [4]. The barley genome project is completed by the International Barley Genome Sequencing Consortium [5]. It has 26,159 genes and large haploid genome of 5.1 gigabases (Gb), approximately 84% of the genome is comprised of mobile elements or other repeated structures. Ease of growth under laboratory conditions, and tissue cultures facilitate the development of gene transfer and gene editing technologies, although research on barley genome and system biology is progressing.

Barley has been cultivated for more than 10,000 years [6]. In former times, the Sumerian and Babylonian cultures utilized barley grains as currency. Barley improvement studies always have the privilege of the breeders and scientists. Barley is a short season, early maturing grain with a high-yield potential, and may be found on the fringes of agriculture in widely varying environments, often on the fringes of deserts and steppes or at high elevations in the tropics, receiving modest or no inputs [7]. Wide genetic variation of barley has generated cultivars that are tolerant to stress environments such as cold, salinity, drought and alkaline soil [8]. It is possible to cultivate barley in extensive ecological range. This adaptive genetic diversity against abiotic and biotic stresses indicates the potential of barley to develop stress resistant cultivars. The main objective of barley breeding programmes is enriching yield and grain quality. Improvement studies are also based on producing varieties resistant to biotic (pathogens, fungal, viral and other organisms) and abiotic stresses (e.g. drought, salt, cold and heat) [9]. Identifying and understanding the genetics basis of stress tolerance mechanisms in crops is fundamental to develop new varieties with more stress tolerant characters [10].

Barley is an economically important crop plant, the fourth cereal worldwide in terms of the planting area, utilized almost 60% as animal feed, around 30% for malt production, 7% for seed production and only 3% for human food [11, 12]. In recent years, the malt derived from the germinated barley is the key material for the malting which represents the most economically favourable application for beer brewing [13]. However, to enhance the germination and malting quality of barley, addition of malting additivives during the malting is strictly controlled cause of food safety and environmenal pollution. Improvement of barley cultivars for the malting may be the most economical approach to improve malt quality. As a result, identifying and understanding the genetics basis of barley is fundamental to develop new varieties with more properties [14]. Also nowadays, barley has numerous advantages in food industry due to its high content of bioactive compounds such as β-d-glucan, tocopherols, tocotrienols and phenolics such as benzoic and cinnamic acid derivatives, proanthocyanidins, quinones, flavonols, chalcones and flavones [15, 16]. The studies showed that β-d-glucan is regarded as a significant function of preventing various diseases such as diabetes, cardiovascular diseases, hypertension and others [17].

Barley is one of the most genetically diverse cereals which is categorized as spring or winter types, two-rowed six row, hulled or hulless by the presence or absence of hull tightly adhering to the grain, and malting or feed by end-use type. Therefore, breeding programmes depend on high level of genetic diversity which provides a significant opportunity for achieving progress. Specific traits may be introgressed in back-crossing studies by hybridisations between high-yielding cultivars and wild barley in conventional breeding programmes [18]. However, mutation breeding is also important for widening variation to develop new cultivars. Herman Nilsson-Ehle and Ake Gustafsson, and even L. J. Stadler have performed induced mutation studies on barley, and then Stadler have published his data in 1928. In 1953, the ‘Group for theoretical and applied mutation research’ was established by the Swedish Government. The aim of their study was the investigation of basic research problems in order to effect and improve methods for breeding programmes [19]. Both radiation and chemical mutagenesis have been separately used to increase the numbers of barley cultivars which may have desirable traits. ‘Golden promise’, which is the most popular malting barley, was produced by radiation mutagenesis [20]. In Turkey, mutation breeding programme has been started by Bilge et al. with collaboration of Agricultural Research Institutes [21, 22]. They treated barley seeds with radiations (X and gamma rays) and chemical (ethyl alcohol, streptomycin, terramycin, penicillin G, sodium cyanide and ethyl methane sulfonate solutions) mutagens and observed different traits such as chlorophyll deficiency, large-eared, high-yielding, thick-stemmed, dwarf and early-heading in M1. Today, use of mutation breeding generally continuing at targeted level will be discussed by new technologies.

In this review, we summarize the history of barley improvement research in terms of mutation breeding, tissue culture, gene transfers, gene editing, molecular markers, transposons, epigenetic, genomic studies and system biology. We aimed to discuss some important and/or recent studies and improvements about barley for understanding the factors responsible for converting barley plants into the superior cereals, which occurred through gene transfers, gene editing and molecular breeding, which is important and could help us enhance the current pool of cultivated barley species to provide enough material for the future.


2. Barley molecular markers

Plant breeders have been used with phenotypic traits for selection of desirable traits due to habits, disease resistance, yield or quality to develop new cultivars. Two major strategies have been utilized to select desirable traits which are classical breeding and molecular breeding. The development and use of molecular markers for the detection and exploitation of polymorphism have been playing a significant role in plant breeding studies. Molecular plant breeding utilizes two major approaches, marker-assisted selection (MAS) and genetic transformation, to produce new varieties with desirable characteristics [23, 24]. MAS is a process that uses molecular markers to increase crop yield, quality and tolerance to biotic or abiotic stresses [25]. The choice of marker systems is a significant part of plant breeding cause of the requirements according to the conditions and resources. In the last two decades, molecular markers such as restricted fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs), simple sequence repeats(SSR), inter-simple sequence repeats (ISSR), expressed sequence tags (ESTs) and single-nucleotide polymorphisms (SNPs), transposon-based markers (IRAP, iPBS) have been used as genetic markers for measuring the genetic differences existing in the genomes [2630]. Development of next-generation sequencing technologies opened new opportunities for the development of sequence-based markers. Today, we have new markers which are not fragment-based but are sequence-based. Medium and high density arrays are available for barley. The choice of utilized marker methods has shifted from the first and second generation markers such as RFLPs, RAPDs, microsatellite and AFLPs to third and fourth generation markers including DArTs, TAMs, RADs and CNVs/PAVs which are demonstrated in Table 1 [3134]. Next-generation breeding technologies are now effectively used for the establishment of genotypic and phenotypic relations [35]. Future barley varieties are designed with crop model ensemble [36].

Marker types usedAimResultsReference
RFLPConstruction of an RFLP map of barleyGenetic and physical mapping achieved[37, 38]
RAPDAnalyses genetic variations in barleyCultivar certification achieved[56]
Cultivar discriminationCultivar and hybrid certification achieved[57]
AFLPAFLP markers linked to water stress tolerant and sensitive bulbs of barleyAFLP markers was identified in two barley genotypes (tolerant and sensitive)[41]
SSRConstruction of a SSR consensus map of barley149 mapped SSR markers on Australian varieties are presented in the form of a consensus map, SSRs proved to be adaptable to several technologies[44, 45]
IRAP and iPBSCallus age and retrotransposonTissue culture conditions and callus age affected Sukkula retrotransposon movements, and all individuals did not present the same effect[51]
SNPUtilization of the BOPA1 assay to explore SNPs in geographically matched landraces and wild accessions collectedOf the 1536 SNPs represented on BOPA1, 1301 mapped SNPs[58]
CAPSComparison of SNP and CAPS markers application in genetic research in wheat and barleyResults supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley[59]
CNVThe prevalence of copy number variation (CNV) and its role in phenotypic variation in domesticated barley cultivars and wild barleysLevels of CNV in the wild accessions were found to be higher than cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV[55]
cDNA-AFLPDevelopment of molecular markers linked to barley heterosisFive transcript-derived fragments (TDFs) showed significant effects on heterosis[60]
DArT94 Czech malting barley cultivars identificationDArT-based dendrogram was established[61]
Genome-wide association studies of agronomic and quality traits in a set of German winter barley (Hordeum vulgare L.) cultivars using DArTA set of about 100 winter barley (Hordeum vulgare L.) cultivars, comprising diverse and economically important German barley elite germplasm was analysed[62]
QTL loci effecting kernel lengthLEN-3H and LEN-4H could be used for improve kernel length[63]
SLAF-seq and whole-genome shotgunsemi-dwarf gene ari-e from Golden PromiseSpecific-length amplified fragment sequencing (SLAF-seq) with bulked Segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region[64]
Restriction site associated DNA (RAD) sequencingSNP-based high density genetic map and mapping of btwd1 dwarfing gene in barleyThe SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped[65]
InDel markersDevelopment of InDel markersHigh-density InDel markers with specific genome locations were developed with 6976 molecular markers (SSRs, DArTs, SNPs and InDels) integrated into single barley genetic map[66]

Table 1.

Molecular markers used in barley research.

Restriction fragment length polymorphism (RFLP) marker system has been used as a measure of genetic diversity for mapping studies in barley [37, 38]. Genetic relationships among 21 barley accessions (17 of H. bulbosum L. and 4 of H. vulgare L.) have been investigated by Okumus and Uzun [39] have successfully produced 111 RAPD markers. Combination of bulked segregant analysis and RAPD primers has been used to identify molecular markers linked to crown rust resistance gene Rpc1 in barley [40]. Another molecular marker technique AFLP has been utilized for linkage studies and evolution of barley [4143]. 149 simple sequence repeats (SSRs) or microsatellite markers have been constructed in the form of a consensus map by using 12 barley populations [44, 45]. SSR markers have been utilized for the selection of Rym4/Rym5 locus conferring resistance to the barley mosaic virus complex in barley. The polymorphic SSR marker QLB1 was found to be co-segregated with Rym4/Rym5 locus which also used to develop for the high-resolution map [46]. Other marker methods used in plant breeding are transposable elements-based marker systems such as inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and inter-primer binding site amplification (iPBS) to identify retrotransposon markers linked to traits. Our group has been using IRAP and iPBS marker techniques to determine retrotransposon insertion patterns, movements of transposons, somaclonal variations, and callus aging. Our results showed that callus culture conditions have activated BARE-1 and Nikita elements [4750]. Movements of the non-autonomous retrotransposon Sukkula were investigated by Kartal-Alacam et al. [51] in barley. Recently, IRAP technique is also utilized to assess the genotoxicity of some drugs such as epirubicin [52] and amiprophos-methyl [53].

Genome- and chromosomal-level genetic structures are really important for the investigation of the evolution, adaptation and spread of the crops. Therefore, single-nucleotide polymorphism (SNP) platforms, which are used to assess the evolution of barley, are a key tool in the development of farming. Russell et al. [54] utilized the barley oligonucleotide pool assay 1 platform (BOPA1, composed of 1536 SNPs) to compare 448 accessions genome-level genetic structures, 317 of landrace material and 131 of wild barley, and observed that significant chromosome-level differences diversity between landrace and wild barley types was around genes known to be involved in the evolution of cultivars. Fourteen barley genotypes (eight cultivars and six wild barleys) have been utilized to explore copy number variations (CNV) by using comparative genomic hybridization. The study showed that CNVs were enriched near the ends of all chromosomes except 4H and affected 9.5% of the coding sequences represented on the array [55].


3. Barley tissue cultures and gene transfers systems

Plant tissue culture, which provides convenience for plant propagation and manipulation, is based on growing plant cells, tissues or organs isolated from the mother plant, on artificial media [67]. It is required to regenerate in vitro whole transgenic plants by using cells, tissues or a single cell cultured on a nutrient medium in a sterile environment [68]. Regeneration ability in barley depends on the donor plant material, genotype, media and environment [6971]. One significant limitation of barley transformation is still the poor regeneration potential of modern cultivars. However, several studies have been conducted to improve tissue culture techniques to increase regeneration rates [72]. From past to today, various tissue culture protocols have been developed by using immature embryos [7380], mature embryos [8187], apical meristems [8890], anthers [9194], microspores [9597], ovaries [98, 99], cell suspensions [100104], protoplasts [105], coleoptile tissue [106] and leaf base segments [90, 107].

The improvement of barley through genetic transformation and in vitro methods requires the development of reliable, efficient and reproducible plant regeneration systems (Table 2) [70, 108, 109]. The plant regeneration capacity is affected by the genotype of donor plants, growth characteristics of induced calluses, the composition of the media, including growth regulators [110, 111]. Tissue cultures of barley are mainly based on the optimization of callus induction [112], regeneration [71, 113] and transformation [99], understanding of tissue culture response [114], detection, evaluation and elimination of somaclonal variation [81, 94, 115118]. The use of mature embryos has a great advantage compared to other systems such as protoplast and cell suspensions. For barley tissue culture, mature embryos represent ideal system because of higher germination and regeneration rates by somatic embryogenesis from cultured mature embryos of barley [87]. Phytohormones are also crucial to setting optimal tissue culture conditions to produce undifferentiated callus tissue from differentiated tissues such as an embryo [119].

Culture typeAimResultsReference
Immature embryosTissue culture and plant regeneration from immature embryo explantsRegeneration of plantlets was obtained for 19 of the 20 genotypes approximately 4 months after culture initiation[75]
Evaluation 9 barley cultivar for in vitro culture responseFor each character, there were significant differences between genotypes, between 2,4-D concentrations and also significant genotype × medium interactions[136]
Evaluation of 10 Canadian barley genotypes for in vitro culture responseFertile plants were regenerated[137]
Callus induction and regeneration at Czech cultivarsThe callus formation frequency and number of green regenerants were influenced significantly both by genotype and auxin[123]
Callus induction and regeneration at Nordic cultivarsRegeneration of many plants from the same callus over long periods of time and makes available highly efficient regeneration protocols[138]
Mature embryosTissue culture establishment and plantlet regenerationPlantlets regenerated both via organogenesis and somatic embryogenesis[139]
Tissue culture and plant regeneration at Indian cultivarsMultiple shoot induction and plantlet regeneration in Indian cultivar of barley[140]
Anther culturePossible effect of copper during anther culture in barleyThe positive influence of copper sulphate was characterized by an increase of microspore survival during anther culture[141]

Table 2.

Tissue culture and plant regeneration studies in barley.

Callus formation, which is a dedifferentiation of single cells or tissue explants, offers the great opportunity for investigation of in vitro selection production of genetic variations [120124]. The regeneration of plants from callus of barley has a great potential to produce new lines in breeding improved barley cultivars [125, 126]. The type of auxin, 2,4-dichlorophenoxyacetic acid (2,4-D), is the most used growth regulator for callus induction [123, 127, 128]. 2,4-D have been utilized to induce embryogenic callus together with or without cytokinins such as zeatin or 6-benzylaminopurine (6-BAP). Moreover, the influences of 2,4-D, Dicamba (3,6-dichloro-O-anisic acid), Picloram (4-amino-3,5,6-trichloropicolinic acid) or 2,4,5-T (2,4,5-trichlorophenoxyacetic acid) have been investigated on the induction of embryogenic callus. It was found that Dicamba significantly increased the regeneration through somatic embryogenesis [78, 111, 129131]. However, callus quality depends on barley genotypes [125, 132]. And also, it has been reported that the most barley cultivars produced friable and translucent callus [122, 125].

Somatic embryogenesis, which is defined as a process by which haploid or diploid somatic cells develop into structure that resembles zygotic embryo, is an important tool for large scale vegetative propagation. Somatic embryos are bipolar structures without any vascular connection with the parental tissue and these structures can differentiate either directly from the explants without an intervening callus phase or indirectly after a callus phase. Immature embryos have a great potential to produce somatic embryos through embryogenic callus [133]. Marthe et al. [134] have investigated transformation efficiency for more than 20 barley cultivars by using immature barley embryos, and they found that the transformation efficiency of cv ‘Golden Promise’ was still higher than any other cultivar tested. Another study conducted by Hisano et al. [135] showed that callus derived from immature embryos of ‘Golden Promise’ had the highest ratio of regeneration of green shoots comparing with ‘Haruna Nijo’ and ‘Morex’.

Since 1990s, genetic engineering of plants is a powerful research tool for gene discovery and function to investigate genetically that controlled traits have provided great opportunities to introduce agronomically useful traits. The first report on stable barley transformation via direct DNA-transfer methods has been established by Lazzeri et al. [105]. Tingay et al. [142] were first reported Agrobacterium-mediated gene transfer protocol to barley using immature embryos (IEs). Since then, numerous protocols for barley transformation have been developed with the contribution of technical improvements based on immature embryos or androgenetic pollen cultures or isolated ovules as gene transfer targets [99, 143146]. Gurel and Gozukirmizi [147] optimized the transformation parameters for efficient and successful genetic transformation of mature barley embryos. They defined the optimal combination of electroporation and electroporated mature embryos with β-glucuronidase (Gus) and neomycin phosphotransferase II (nptII) genes. The frequency of transformants was generally not very high between 1.7 and 7.0% of the immature embryos infected via Agrobacterium. On the other hand, it has been recently reported that the frequency is around 25% or higher [148150]. Although the transformation frequency is lower, immature embryos still remain the target tissue of choice in barley [148, 151].

The most of barley transformation studies have been performed to confer biotic (fungal and viral resistance) and abiotic (herbicide, drought and salinity, etc.) resistance, to facilitate brewing and digestibility, to alter protein composition and for molecular pharming [152]. Some of those methods have been established in Table 3. Yeo et al. [153] developed 'Golden SusPtrit' which is a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise. They generated a double haploid (DH) mapping population (n=122) by crossing SusPtrit with Golden Promise to develop the ‘Golden SusPtrit’. SG062N was found the most efficiently transformed DH line with 11–17 transformants per 100 immature embryos. To protect barley from the effects of stress-produced reactive carbonyls, which is accumulated by reactive oxygen species in the plant cells, an Agrobacterium-mediated transformation was carried out using the Medicago sativa al dose reductase (MsALR) gene by Nagy et al. [154]. Their results demonstrated that this technique could be applied for the detection of cellular stress, and also found that targeting of MsALR into the chloroplast has also resulted in increased stress tolerance. In addition to these studies, Han et al. [155] reported that a construct containing full-length of HvGlb2 cDNA encoding barley (1,3;1,4)-β-glucanase isoenzymes EII under the control of a promoter of barley D-Hordein gene Hor3-1 was introduced into barley cultivar Golden Promise via Agrobacterium-mediated transformation. High content of (1,3;1,4)-β-D-glucan of barley grains is considered as an undesirable factor effecting malting potential, brewing yield and feed utilization. They showed that over-expression of (1,3;1,4)-β-glucanase led to an increase in the thousand grain weight. Also, manipulating expression of (1,3;1,4)-β-glucanase EII could control the β-glucan content in grain with no apparent harmful effects on grain quality.

Gene transfer typeAimResultsReferences
Biolistic transformation systemTarget tissues such as immature embryos, embryos derived callus and microspore derived callusSuccessful transformation[156]
Immature embryos and microspore-derived culturesSuccessful transformation[157]
Transformation of recalcitrant speciesSuccessful transformation[158]
Pre cultured immature embryosMolecular analysis of T1 generation plantlets revealed the amplification of selectable marker hptII gene in the progeny[159]
Agrobacterium-mediated transformationImmature embryosSuccessful transformation[142]
Shoot apicesSuccessful transformation[160]
Optimization of gene transfer immature embryosTransformation efficiencies 2.6–6.7%[145]
Young ovulesSuccessful transformation[161]
MicrosporesSuccessful transformation[147]
Optimization of gene transfer immature embryos25 % transformation efficiency[148]
Mature scutellumSuccessful transformation[162]
Immature embryo-derived callus culturesImprove T-DNA transfer in monocotyledon transformation procedures[163]
Mature embryosSuccessful transformation[164]
Tissue electroporationDNA transfer into mature embryos of barley via electroporationSuccessful transformation[147]

Table 3.

Gene transfer research on barley.


4. Genomic studies on barley

The genetic revolution of the past decade has greatly improved our understanding of the relationships between genetic and phenotypic diversity with a resolution that has never been reached before. The development of next generation sequencing (NGS) technologies has increased accuracy and decreased costs. Sequencing or re-sequencing of reference genomes and also new varieties allow the identification of numerous numbers of markers, allelic diversities and have changed our insight of genome organization and evolution. The sequencing of crop genomes provided evidences for plant origin and evolution; genome duplications, re-arrangements; adaptations and functional modulations [165]. The full genome sequence is essential to provide knowledge for understanding natural genetic variations and development for breeding programs.

Recently, novel high-throughput sequencing strategies have revealed the structure of barley genome [166, 167]. Existence of 26,159 barley genes was confirmed by a systematic synteny analysis with model species from the Poaceae family (rice, maize, sorghum and Brachypodium) which have already had annotation of their genomes. Also, up to 80% of the 5.1 Gb genome of barley contains repetitive DNA, making the fully sequencing complicated [5]. Full annotations and a sequence-rich physical map of the barley genome, which is based on the genomic information contained in bacterial artificial chromosomes (BACs) developed for the Morex variety [168, 169], are available on public databases ( [167]. The first single nucleotide polymorphisms (SNPs) genotyping approach, based on the illumina oligo pool assays (OPAs), allowed the examination of 4596 markers in sets of 1536 SNPs [58]. Although declining cost of NGS technologies, thousands to million SNPs have been discovered via re-sequencing, providing greater detail for high density genetic maps [170]. Currently, array-based genotyping platform Infinium iSelect allows the simultaneous testing of 7842 SNPs [171]. Takahagi et al. [172], performed deep transcriptome sequencing, identified 38,729–79,949 SNPs in the 19 domesticated accessions and 55,403 SNPs in the wild barley. However, the complete sequences of the 525,599 bp mitochondrial genomes of wild and cultivated barley have been determined by Hisano et al. [135]. The mitochondrial genome of barley consists of 33 protein-coding genes, three ribosomal RNAs, 16 transfer RNAs, 188 new ORFs, six major repeat sequences and several types of transposable elements. The mitochondrial genomes of these wild and cultivated barley lines have been found to be almost identical in terms of both nucleotide sequence and genome structure, only three SNPs detected between haplotypes [135].

Several techniques, including linkage (or QTL mapping) mapping, association mapping (GWAS) and high-throughput omic techniques, such as transcriptomics, ionomics, proteomics and metabolomics analysis, have been used to identify a single gene or multi-genes corresponding to gene regulation networks of development, flowering, vernalization and biotic and abiotic stress conditions [173]. Next generation sequencing approaches (e.g. RNA-Seq) were carried out within 5 years and enlarged our knowledge about gene regulation networks of stress conditions. Especially, RNA-seq approach has been widely utilized due to low background noise, high sensitivity and reproducibility, great dynamic range of expression and base-pair resolution for transcription profiling [174]. Transcriptomic analyses of more than 28 plant species have revealed thousands of genes that are differentially regulated under drought stress conditions [175]. During last few years, an increasing number of these genes have been characterized and their function under drought conditions has been shown by the analysis of loss-of-function mutants or over expressing lines. Most of these functional characterization studies have been performed in the model species Arabidopsis thaliana and in the grass Oryza sativa. However, production of desired drought-tolerant crop species has required the identification of orthologous genes in each species. Transcriptome and whole-genome sequencing of different plant species lead to identify orthologous genes across several model and crop species [176].

Transcriptome profiling of barley under low nitrogen (LN) conditions have been determined by using RNA-seq approach. 1469 differentially expressed genes were identified between tolerant and sensitive barley varieties under LN. Differences between tolerant and sensitive genotypes involved transporters, transcription factors, kinases, antioxidant stress and hormone signalling related genes. However, DEGs were classified in amino acid metabolism, starch and sucrose metabolism, secondary metabolism [177]. Up to today, transcription dynamic of hulless barley grain development was not well understood. Tang et al. [178] have conducted comparative transcriptome approach to investigate changes during grain development. 38 DEGs were determined co-modulated in two barley landraces with the differential seed starch synthesis traits. The results showed that these 38 DEGs encoded proteins such as alpha-amylase-related proteins, lipid-transfer protein, homeodomain leucine zipper (HD-Zip), Nuclear Factor-Y, subunit B (NFYBs), as well as MYB transcription factors. Also, they found that two genes Hvulgare_GLEAN_10012370 and Hvulgare_GLEAN_10021199 encoding SuSy, AGPase (Hvulgare_GLEAN_10033640 and Hvulgare_GLEAN_10056301), as well as SBE2b (Hvulgare_GLEAN_10018352) were significantly contributed to the regulatory mechanism during grain development in both genotypes.

Numerous numbers of studies have been performed to understand biotic and abiotic stress tolerance mechanisms. For this purpose, RNA-seq approach or microarray have a valuable potential to define stress mechanisms. One of the studies has been conducted by Tombuloglu et al. [179] to discover the properties underlying the boron tolerance mechanism. By using transcriptome-wide approach, 256,847 unigenes were generated and, 16 and 17% of the transcripts were found to be differentially regulated in root and leaf tissues, respectively, according to gene expression analysis. Most of these unigenes were found to be involved in cell wall, stress response, membrane, protein kinase and transporter mechanisms [179]. Also, physiological and biochemical analysis have provided valuable insights towards a novel integrated molecular mechanism of stress tolerance mechanisms in barley. A genome-wide transcriptome analysis was performed to identify the mechanisms of cadmium (Cd) tolerance in two barley genotypes with distinct Cd tolerance by using microarray approach. Microarray expression profiling revealed that novel genes may play important roles in Cd tolerance which were mainly via producing protectants such as catalase against reactive oxygen species, Cd compartmentalization (e.g. phytochelatin-synthase and vacuolar ATPase) and defence response and DNA replication (e.g. chitinase and histones) [180]. Another study to understand abiotic stress was the sequencing of young leaves RNAs of wild barley treated with salt (500 mM NaCl) at four different time intervals. Differential expression profiles have been classified into nine clusters by two-dimensional hierarchical clustering. The most important groups were assigned to ‘response to external stimulus’ and ‘electron-carrier activity’ which means that the highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis and reactive oxygen species (ROS) scavenging, ethylene production, signalling network and protein refolding [181]. Hulless barley, also called naked barley, often suffered from drought stress during growth and development. Therefore, Zeng et al. [182] have investigated co-regulated mRNAs expression patterns under early well water, later water deficit and finally water recovery treatments, and to identify mRNAs specific to water limiting conditions. The results showed that 853 DEGs were determined and categorized into nine clusters. The up-regulated genes were found to be relevant to abiotic stress responses in abscisic acid (ABA) dependent and independent signalling pathway, including NCED, PYR/PYL/RCAR, SnRK2, ABF, MYB/MYC, AP2/ERF family, LEA and DHN under low relative soil moisture content (RSMC) level. However, the transcriptome analysis revealed that the most affected genes were related to tetrapyrrole binding, photosystem and photosynthetic membrane under drought stress conditions.

The proteomic approach also plays significant roles to understand alterations in the context of physiological and morphological responses to biotic and abiotic stresses in barley. Rollins et al. [183] have investigated the proteins differentially regulated in response to drought, high temperature or a combination of both treatments by using differential gel electrophoresis and mass spectrometry. The study showed that the drought treatment induced strong reductions of biomass and yield, but not causing significant alterations in photosynthetic performance and the proteome. In contrast, the heat treatment and the combination of heat and drought caused the reduction of photosynthetic performance and changes of the leaf proteome. 14 proteins among 99 protein spots were identified as a genotype-specific manner in response to heat treatment. The analysis indicated that the differentially regulated proteins were related to photosynthesis, detoxification, energy metabolism and protein biosynthesis. Barley, also, used to identify the quantitative proteome changes under different drought conditions by Vítámvás et al. [184]. They cultivated plants for 10 days under different drought conditions that the soil water content was held at 65, 35 and 30% of soil water capacity (SWC), respectively. The proteomic alterations of barley crowns grown under different drought conditions were determined utilizing two-dimensional difference gel electrophoresis (2D-DIGE). Analysis of 2D-DIGE revealed that 105 differentially abundant spots were detected between the controls and drought-treated plants. The identified proteins were classified into stress-associated proteins, amino acid metabolism, carbohydrate metabolism, as well as DNA and RNA regulation and processing.


5. Genome editing

Genome editing has recently emerged as a novel transgenic method to improve crop plants has great opportunities over conventional gene targeted techniques. The most important advantage of gene editing is the modification of the targeting specific genes in situ. Genome editing, uses ‘programmable’ nucleases such as zinc finger nucleases (ZFNs), TAL effectors nucleases (TALENs) or clustered regularly inter-spaced short palindromic repeat (CRISPR)-associated endonucleases, may also be used to introduce gene insertions, gene replacements, insertions or deletions at specific genomic locations [185]. These proteins have a recognition domain, is provided by the FokI domain in both ZFNs and TALENs, and Cas9 in CRISPR systems, can be engineered to target specific sequences. Genome editing is based on double-strand break (DSB) induction [186], and subsequent repaired by the cell’s own non-homologous end-joining (NHEJ) or homologous recombination (HR) mechanisms [185]. Genome editing is a key tool for advancing knowledge of gene function as well as allowing targeted mutagenesis with high efficiency in plants, including barley [187, 188].

Wendt et al. [187] reported the assembly of several TALENs for a specific genomic locus in barley. They tested the cleavage activity of individual TALENs in vivo using a yeast-based, single-strand annealing assay, and then the most efficient TALEN have been selected for barley transformation. Cleavage of the non-specific target was not observed, but analysis of the resulting transformants demonstrated that TALEN-induced double strand breaks led to the introduction of short deletions at the target site. Another study with TALENs has been reported by Gurushidze et al. [188] that they used TALENs in pollen-derived, regenerable cells to establish the generation of instantly true-breeding mutant plants. A gfp-specific TALEN pair was expressed via Agrobacterium-mediated transformation in embryogenic pollen with 22% of the TALEN transgenics. During gene replacement, desired DNA could integrate into the genome by homologous recombination that provides great promise to the introduction of mutations at pre-determined positions in the genome. Watanabe et al. [189] used a model system based on double-strand break induction by the mega nuclease I-SceI to target specific position in the genome. They obtained two transformants that were stably inherited as a single Mendelian trait. They suggested that stable gene replacement could be achieved in barley for routine applications by targeted double-strand break induction. The RNA-guided Cas9 system also represents a flexible approach for gene editing in barley and provides a valuable tool to create specific mutations that knock-out or alters target gene function. Lawrenson et al. [190] investigated the use and target specificity of RNA-guided Cas9 genome editing in barley. They demonstrated Cas9-induced mutations in the first generation of 23% for barley line. And also, they observed that stable Cas9-induced mutations were transmitted to T2 plants independently of the T-DNA construct thus establishing the potential for rapid characterisation of gene function in barley.


6. Transposons, epigenetic studies and non-coding RNAs

Transposons, is a segment of DNA moves to new location in a chromosome or to another chromosome or cell, were first identified in maize by McClintock [191]. Several studies have been revealed that transposons affect gene structure, epigenetic regulations and genome dynamics of almost all living organisms [30]. Transposons alter the existing genome structure that can lead to significant changes such as deletions and/or insertions. Percentages and types of transposons can vary among species [192] that prokaryotic genomes contain 1–3% transposons. However, their percentage may reach 85% or more in eukaryotic genomes, especially plants [193]. Due to having larger genome, barley has larger transposon-derived DNA content with up to 85% [194]. Also, it was demonstrated that Copia retrotransposons remained intact and active for much longer time periods in the larger genomes such as barley than the smaller genomes [195].

Our group has been studying barley transposon effects on somaclonal variation, stability of aging barley calli and callus regeneration by using IRAP markers derived from BARE-1 [47, 50] and Nikita [48]. In addition, mature embryo, leaf, root tissues were investigated for BARE-1 and BAGY2 movements by Marakli et al. [49] and Sukkula movement in barley, which is a non-autonomous retrotransposon, have been investigated by our group [51]. We demonstrated that BAGY2 was more stable than BARE-1. Another study on transposon movements of retrotransposons and methylation alteration was performed by Temel and Gozukirmizi [196]. We found that not all callus induction conditions increased the retrotransposon activity. However, increase in cytosine methylation has been observed during callus formation using Sensitive Restriction Fingerprinting. Yilmaz et al. [197] also investigated the stability of aging barley calli and regenerated plantlets from those calli. We used the BAGY2 retrotransposon-specific IRAP technique to determine level of variations of DNA. We found that the culture conditions caused genetic variations, and also copy numbers of internal domains of BAGY2 have increased. Moreover, IRAP technique has been utilized to assess the genotoxicity of some drugs such as epirubicin [52] and amiprophos-methyl [53]. Recently, Yuzbasioglu et al. [198] used IRAP markers to identify variation in single seed derived leaves and roots in rice.

Epigenetic chromatin modification is defined as heritable changes in gene expression which are not occurred by alterations in the nucleotide sequences of DNA. DNA methylation and modifications of covalent histone N-terminal tail are mainly regarded as chromatin modifications that can be changed in plants during the cell cycle [199, 200], plant development [201, 202] or in stress response [203]. The epigenetic mechanisms keep gene or genes active or repressive states [204, 205]. Braszewska-Zalewska and Hasterok [206] investigated the differences of epigenetic modification between root meristematic tissues of barley. Their study indicated that levels of epigenetic modifications varied between RAM tissues. Studies on environmental stresses showed that both DNA methylation and histone modifications are involved in DNA damage response. Also, Braszewska-Zalewska et al. [207] observed that chemical (maleic acid hydrazide; MH) and physical (gamma rays) mutagens strongly affected the level of histone methylation and acetylation. One of the major components of epigenetic variations is the combinations of histones carrying different covalent modifications that Baker et al. [208] have mapped nine modified histones in the barley seedling epigenome using chromatin immune precipitation next‐generation sequencing (ChIP‐seq) technique. They defined 10 chromatin states (five states to genes and five states to inter-genic regions) representing local epigenetic environments in the barley genome. Moreover, it was found that H3K36me3-containing two genic states were related to constitutive gene expression. However, one genic state involving an H3K27me3 was related to differentially expressed genes.

The recent wide applications of whole-genome tilling array and RNA-sequencing (RNA-seq) approaches have revealed that the transcription landscape in eukaryotes is much more complex than had been expected [209]. These approaches have facilitated the identification of thousands of novel ncRNAs (or npcRNAs) in many organisms, such as humans, animals and plants [210214]. ncRNAs are classified as short (<200 nt) and long ncRNAs (lncRNAs; >200 nt). Transcriptional and post-transcriptional regulation of gene expression of short ncRNAs, including siRNAs, miRNAs and piRNAs, has been well recognized and the molecular mechanisms of short ncRNA-mediated regulation have been well understood [215, 216]. On the contrary, the regulatory roles of lncRNAs are only beginning to be recognized and the molecular basis of lncRNA-mediated gene regulation is still poorly understood [217]. Our group has been investigating the association between salinity stress metabolism and barley lncRNAs (unpublished data). Identification of novel lncRNAs is likely to provide new insight into the complicated gene regulatory network involving lncRNAs, provide novel diagnostic opportunities, and pinpoint novel therapeutically targets.


7. Conclusion

Barley is an economically important crop plant, the fourth cereal worldwide in terms of the planting area, utilized almost 60% as animal feed, around 30% for malt production, 7% for seed production and only 3% for human food [11, 12]. In recent years, the malt derived from the germinated barley is the key material for the malting represents the most economically favourable application for beer brewing [13]. There is tremendous genetic research on barley at morphological, biochemical and molecular level for development of superior barley varieties. However, detailed analyses should be performed to investigate for the environmental extrapolation of laboratory developed lines. The relationship between environmental effects and genetic studies, especially field studies will provide knowledge about interaction of environment and genetically developed varieties. We tried to cite as many papers as possible. Yet we apologize to authors whose works are gone unmentioned in this chapter.



We are grateful to the Research Fund of Istanbul University for financial support (Projects FDK-2016-23086)


  1. 1. Gujral HS, Gaur S. Instrumental texture of chapati as affected by barley flour, glycerol monostearate and sodium chloride. International Journal of Food Properties. 2005;8:377-385
  2. 2. Shewry PR. Barley: genetics, biochemistry, molecular biology and biotechnology. Wallingford: C.A.B International; 1992. 085198-725-7.
  3. 3. USDA, NRCS. The PLANTS database. National Plant Data Team, Greensboro, NC 2016; USA. NC27401-4901., 17 November 2016
  4. 4. von Bothmer R. The wild species of hordeum: Relationships and potential use for improvement of cultivated barley. In: SWEWRY PR, editor. Barley: Genetics, Biochemistry, Molecular Biology and Biotechnology. Willingford, Oxon: C.A.B International; 1992. pp. 3-18. Chapter 1
  5. 5. The International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711-716
  6. 6. Salamini F, Özkan H, Brandolini A, Schȁfer-Pregl R, Martin W. Genetics and geography of wild cereal domestication in the near east. Nature Reviews Genetics. 2002;3(6):429-441
  7. 7. Harlan JR. Barley Hordeum vulgare (Gramineae--Triticinae). In: Simmonds NW, editor. Evolution in Crop Plants. London: Longman; 1976. pp. 93-98
  8. 8. Poehlman JM. Adaptation and distribution. In: Rasmusson DC, editor. Barley. Madison, Wisconsin: American Society of Agronomy, Inc., Crop Science Society of America, Inc., Soil Science Society of America, Inc.; 1985. pp. 1-17
  9. 9. Dunwell JM. Barley. In: Evans DA, Sharp R, Ammirato PV, editors. Handbook of Plant Cell Culture. Vol. 4. 1st ed. London: MacMillan and Co.; 1986. pp. 339-369
  10. 10. Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S, Blum A, Nguyen HT. Location genomic regions associated with components of drought resistance in rice: Comparative mapping within and across species. Theoretical and Applied Genetics. 2001;103:19-29
  11. 11. Baik BK, Ullrich SE. Barley for food: Characteristics, improvement, and renewed interest. Journal of Cereal Science. 2008;48:233-242
  12. 12. Dawson IK, Russell J, Powell W, Steffenson B, Thomas WT, Waugh R. Barley: a translational model for adaptation to climate change. New Phytologist. 2015;206:913-31
  13. 13. Bond J, Capehart T, Allen E, Kim G. Boutique brews, barley, and the balance sheet: Changes in malt barley industrial use require an updated forecasting approach. Economic Research Division, United Stated Department of Agriculture. 2015;18-23
  14. 14. Lan W,Wang W, Yu Z, Qin Y, Luan J, Li X. Enhanced germination of barley (Hordeum vulgare L.) using chitooligosaccharide as an elicitor in seed priming to improve malt quality. Biotechnology Letters. 2016;38:1935-1940
  15. 15. Holtekjolen AK, Baevere AB, Rodbotten M, Berg H, Knutsen SH. Antioxidant properties and sensory profiles of breads containing barley flour. Food Chemistry. 2008;110(2):414-421
  16. 16. Baba WN, Rashid I, Shah A, Ahmad M, Gani A, Masoodi FA. Effect of microwave roasting on antioxidant and anti-cancerous activities of barley flour. Journal Saudi Society of Agricultural Sciences. 2014;27:143-154
  17. 17. Ahmad M, Gani A, Shah A, Gani A, Masoodi FA. Germination and microwave processing of barley (Hordeum vulgare L.) changes the structural and physicochemical properties of β-d-glucan & enhances its antioxidant potential. Carbohydrate Polymers. 2016;153:696-702
  18. 18. Nevo E. Origin, evolution, population genetics and resources for breeding of wild barley, Hordeum spontaneum, in the Fertile Crescent. In: Shewry P, editor. Barley: Genetics, Molecular Biology and Biotechnology, C.A.B. International; Wallingford, U.K., 1992. pp. 19-43
  19. 19. Lundqvist U. Scandinavian mutation research in barley – a historical review. Hereditas. 2014;151:123-131
  20. 20. Technical Brochure (1970). Milne Marsters Company.
  21. 21. Bilge E, Oraler G, Gozukirmizi N, Olgun A, Topaktafl M, Experimental mutations in barley (Hordeum vulgare L.). Istanbul Universitesi Fen Fakultesi Mec. 1981;46:29-35
  22. 22. Bilge E, Oraler G, Gozukirmizi N, Olgun A, Topaktafl M, Cytogenetic studies on Hordeum vulgare L. treated with mutagens. Istanbul Universitesi Fen Fakultesi Mec. 1981;46:37-42
  23. 23. Moose SP, Mumm RH. Molecular plant breeding as the foundation for 21 century crop improvement. Plant Physiology. 2008;147:969-977
  24. 24. Rajib R, Abdelmoumen T, Hakeem KR, Mohamed RAG, Tah J. Molecular marker-assisted technologies for crop improvement. In: Roychowdhury R, editor. Crop improvement in the era of climate change. Delhi, India: I.K. International Publication House Pvt. Ltd; 2013. pp. 241-258
  25. 25. Foolad MR, Sharma A. Molecular markers as selection tools in tomato breeding. Acta Horticulturae. 2005;695:225-240
  26. 26. Heun M, SchäFer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F. Site of einkorn wheat domestication identified by DNA fingerprinting. Science. 1997;278:1312-1314
  27. 27. Badr A, Müller K, Schäfer-Pregl R, El Rabey H, Effgen S, Ibrahim H, Pozzi C, Rohde W, Salamini F. On the origin and domestication history of barley (Hordeum vulgare). Molecular Biology and Evolution. 2000;17:499-510
  28. 28. El Rabey HA, Badr A, Schäfer-Pregl R, Martin B, Salamini F. Species separation and incipient speciation in Hordeum (Poaceae) resolved by discontinuous molecular markers. Plant Biology. 2002;4:1-9
  29. 29. El Rabey H, Khan JA, Al-Malki AL, Hussein HK. Synteny (co-linearity) in some cereal crops genomes as revealed by amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSR) and inter simple sequence repeats (ISSR) markers. African Journal of Biotechnology. 2012;11(88):15387-15397
  30. 30. Gozukirmizi N, Temel A, Maraklı S, Yilmaz S. Transposon activity in plant genomes. In: Hakeem KR, Tombuloglu H, Tombuloglu, editors. Plant Omics: Trends and Applications. London/Berlin, Switzerland: Springer; 2016. pp. 83-108
  31. 31. Gupta PK, Rustgi S, Mir RR. Array-based high-throughput DNA markers for crop improvement. Heredity (Edinb) 2008;101:5-18
  32. 32. Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M. Gene expression quantitative trait locus analysis of 16000 barley genes reveals a complex pattern of genome wide transcriptional regulation. Plant Journal. 2008;53:90-101
  33. 33. Springer NM, Ying K, Fu Y, Ji TJ, Yeh C-T, Jia Y, Wu W, Richmond TA, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable P. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PloS Genetics. 2009;5:11
  34. 34. Belo A, Beatty MK, Hondred D, Fengler KA, Li B, Rafalski A. Allelic genome structural variations in maize detected by array comparative genome hybridization. Theoretical and Applied Genetics. 2010;120:355-367
  35. 35. Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino A, Valè G, Cattivelli L. Next generation breeding. Plant Science. 2016;242:3-13
  36. 36. Tao F, Rötter R, Palosuo T, Díaz-Ambrona CGH, Mínguez-Tudela MI, Semenov M, Kersebaum KC, Nendel C, Cammarano D, Hoffmann H, Ewert F, Dambreville A, Martre P, Rodríguez L, Ruiz-Ramos M, Gaiser T, Höhn JG, Salo T, Ferrise R, Bindi M, Schulman AH. Designing future barley ideotypes using a crop model ensemble. European Journal Agronomy. 2016;82:144-162
  37. 37. Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG. Construction of an RFLP map of barley. Theoretical and Applied Genetics, 1991;83(2):250-256
  38. 38. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A. A 1,000-loci transcript map of the barley genome: New anchoring points for integrative grass genomics. Theoretical and Applied Genetics. 2007;114(5):823-839
  39. 39. Okumus A, Uzun F. Genetic and geographic variation of bulbous barley (Hordeum bulbosum L.) assessed by RAPD markers. Russian Journal of Genetics. 2007;43(3):294-298
  40. 40. Agrama HA, Dahleen L, Wentz M, Jin Y, Steffenson B. Molecular mapping of the crown rust resistance gene Rpc1 in barley. Phytopathology. 2004;94(8):858-861
  41. 41. Altinkut A, Kazan K, Gozukirmizi N. AFLP marker linked to water-stress-tolerant bulks in barley (Hordeum vulgare L.). Genetics and Molecular Biology. 2003;26(1):77-82
  42. 42. Janiak A, Szarejko I. Molecular mapping of genes involved in root hair formation in barley. Euphytica. 2007;157(1-2):95-111
  43. 43. Li XL, Yu XM, Wang NN, Feng QZ, Dong ZY, Liu LX, Shen JL, Liu B. Genetic and epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum (Trin.) Link). Plant, Cell, Tissue and Organ Culture. 2007;90(2):153-168
  44. 44. Ablett GA, Karakousis A, Banbury L, Cakir M, Holton TA, Langridge P, Henry RJ. Application of SSR markers in the construction of Australian barley genetic maps. Australian Journal of Agricultural Research. 2003;54:1187-1195
  45. 45. Karakousis A, Gustafson JP, Chalmers KJ, Barr AR, Langridge P. A consensus map of barley integrating SSR, RFLP, and AFLP markers. Australian Journal of Agricultural Research. 2003;54:1173-1185
  46. 46. Tyrka M, Perovic D, Wardynska A, Ordon F. A new diagnostic SSR marker for selection of the Rym4/Rym5 locus in barley breeding. Journal of Applied Genetics. 2008;49(2):127-134
  47. 47. Evrensel C, Yilmaz S, Temel A, Gozukirmizi N. Variations in BARE-1 insertion patterns in barley callus cultures. Genetics Molecular Research. 2011;10:980-987
  48. 48. Bayram E, Yilmaz S, Hamat-Mecbur H, Kartal-Alacam G, Gozukirmizi N. Nikita retrotransposon movements in callus cultures of barley (Hordeumvulgare L). Plant Omics. 2012;5:211-215
  49. 49. Marakli S, Yilmaz S, Gozukirmizi N. BARE1 and BAGY2 retrotransposon movements and expression analyses in developing barley seedlings. Biotechnology, Biotechnology Equipment. 2012;26:3451-3456
  50. 50. Yilmaz S, Gozukirmizi N. Variation of retrotransposon movement in callus culture and regenerated shoots of barley. Biotechnology, Biotechnology Equipment. 2013;27:4227-4230
  51. 51. Kartal-Alacam G, Yilmaz S, Marakli S, Gozukirmizi N. Sukkula retrotransposon insertion polymorphism in barley. Russian Journal of Plant Physiology. 2014;61:828-833
  52. 52. Hamat-Mecbur H, Yilmaz S, Temel A, Sahin K, Gozukirmizi N. Effects of epirubicin on barley seedlings. Toxicology and Industrial Health. 2014;30:52-59
  53. 53. Temel A, Gozukirmizi N. Genotoxicity of metaphase-arresting methods in barley. Turkish Journal of Biology. 2015;39:139-146. DOI: 10.3906/biy-1405-58.
  54. 54. Russell JR, Dawson IK, Flavell A, Steffenson B, Weltzien E, Booth A, Ceccarelli S, Waugh R. Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes. New Phytologistogist. 2011;191: 564-578
  55. 55. Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA,Springer NM, Muehlbauer GJ, Stein N. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biology. 2013;14(6): 58
  56. 56. Albayrak G, Gozukirmizi N. RAPD Analysis of Genetic Variation in Barley. Turkish Journal of Agriculture and Forestry. 1999;23:627-630
  57. 57. Mylonas IG, Georgiadis A, Apostolidis AP, Bladenopoulos K, Koutsika-Sotiriou M. Barley cultivar discrimination and hybrid purity control using RAPD markers. Romanian Biotechnological Letters. 2014;19(3):9421-9428
  58. 58. Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, et al. Development and implementation of high-throughput SNP genotyping in barley. BMCGenomics. 2009;10:582.
  59. 59. Shavrukov Y. Comparison of SNP and CAPS markers application in genetic research in wheat and barley. BMC Plant Biology. 2016;16(1):11
  60. 60. Zhang X, Lu C, Xu R, Zhou M. Development of molecular markers linked to barley heterosis. Euphytica. 2015;203:309-319
  61. 61. Ovesná J, Kučera L, Vaculová K, Milotová J, Snape J, Wenzl P, et al. Analysis of the genetic structure of a barley collection using DNA Diversity Array Technology (DArT). Plant Molecular Biology Reporter. 2013;31:280-288
  62. 62. Lex J, Ahlemeyer J, Friedt W, Ordon F. Genome-wide association studies of agronomic and quality traits in a set of German winter barley (Hordeum vulgare L.) cultivars using Diversity Arrays Technology (DArT). Journal of Applied Genetics. 2014;55:295-305
  63. 63. Zhou H, Liu S, Liu Y, Liu Y, You J, Deng M, Ma J, Chen G, Wei Y, Liu C, Zheng Y.Mapping and validation of major quantitative trait loci for kernel length in wild barley (Hordeum vulgare ssp spontaneum). BMC Genetics. 2016;17(1):130
  64. 64. Jia Q, Tan C, Wang J, Zhang XQ, Zhu J, Luo H, Yang J, Westcott S, Broughton S, Moody D, Li C. Marker development using SLAF-seq and whole-genome shotgun strategy to fine map the semi-dwarf gene ari-e in barley. BMC Genomics. 2016;17(1):911
  65. 65. Ren X, Wang J, Liu L, Sun G, Li C, Luo H, Sun D. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley. Scientific Reports. 2016;6:31741. PMID 27530597
  66. 66. Zhou G, Zhang Q, Tan C, Zhang X, Li C. Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map. BMC Genomics. 2015;16:804
  67. 67. George EF. Plant Tissue Culture Procedure – Background, In: E.F. George, M.A. Hall, G.J. De Klerk (Eds.). Plant Propogation by Tissue Culture. 3rd ed. Dordrecht, the Netherlands: Springer; 2008. pp. 1-28
  68. 68. Cardoza V. Tissue culture: The manipulation of plant development. In: Stewart Jr CN, editor. Plant Biotechnology and Genetics: Principles, Techniques and Applications. 1st ed. Hoboken, New Jersey: John Wiley and Sons; 2008. pp. 112-134
  69. 69. Dahleen LS. Donor-plant environment effects on regeneration from barley embryo-derived callus. Crop Science. 1999;39(3):682-685
  70. 70. Dahleen LS, Bregitzer P. An Improved Media System for High regeneration rates from barley immature embryo-derived callus cultures of commercial cultivars. Crop Science. 2002;42:934-938
  71. 71. Sharma VK, Hansch R, Mendel RR, Schulze J. Mature embryo axis-based high frequency somatic embryogenesis and plant regeneration from multiple cultivars of barley (Hordeum vulgare L.). Journal of Experimental Botany. 2005;56(417):1913-1922
  72. 72. Temel A, Gözükırmızı N. Advances in barley biotechnology: Tissue culture and molecular markers. In: Elfson SB, editor. Barley: Production, Cultivation and Uses. Ottawa: Nova Science Publishers; 2011. pp. 129-159
  73. 73. Breiman A. Plant regeneration from hordeum spontaneum and hordeum bulbosum immature embryo derived calli. Plant Cell Reports. 1985;4(2):70-73
  74. 74. Thomas MR, Scott KJ. Plant regeneration by somatic embryogenesis from callus initiated from immature embryos and immature inflorescences of Hordeum vulgare. Journal of Plant Physiology. 1985;121(2):159-169
  75. 75. Goldstein CS, Kronstad WE. Tissue culture and plant regeneration from immature embryo explants of barley, Hordeum vulgare. Theoretical and Applied Genetics. 1986;71(4):631-636
  76. 76. Jorgensen RB, Jensen CJ, Andersen B, Bothmer R. High capacity of plant regeneration from callus of interspecific hybrids with cultivated barley (Hordeum vulgare L.). Plant Cell, Tissue and Organ Culture. 1986;6(3):199-207
  77. 77. Karp A, Steele SH, Breiman A, Shewry PRS, Parmar S, Jones MGK. Minimal variation in barley plants regenerated from cultured immature embryos. Genome. 1987;29:405-412
  78. 78. Luhrs R, Lorz H. Plant regeneration in vitro from embryogenic cultures of spring- and winter-type barley (Hordeum vulgare L.) varieties. Theoretical and Applied Genetics. 1987;75(1):16-25
  79. 79. Rotem-Abarbanell D, Breiman A. Plant regeneration from immature and mature embryo derived calli of Hordeum marinum. Plant Cell, Tissue and Organ Culture. 1989;16(3):207-216
  80. 80. Rikiishi K, Matsuura T, Maekawa M, Takeda K. Light control of shoot regeneration in callus cultures derived from barley (Hordeum vulgare L.) immature embryos. Breeding Science. 2008;58(2):129-135
  81. 81. Temel A, Kartal G, Gozukirmizi N. Genetic and epigenetic variations in barley calli cultures. Biotechnology and Biotechnological Equipment. 2008;22(4):911-914
  82. 82. Lupotto E. Callus induction and plant regeneration from barley mature embryos. Annals of Botany. 1984;54:523-529
  83. 83. Katoh Y, Hasegawa T, Suzuki T, Fujii T. Plant regeneration from the callus derived from mature embryos of hiproly barley, Hordeum distichum L. Agricultural and Biological Chemistry. 1986;50(3):761-762
  84. 84. Ahloowalia BS. Plant regeneration from embryo-callus culture in barley. Euphytica. 1987;36(2):659-665
  85. 85. Rengel Z. Embryogenic callus induction and plant regeneration from cultured Hordeum vulgare mature embryos. Plant Physiology and Biochemistry. 1987;25:43-48
  86. 86. Ukai Y, Nishimura S. Regeneration of plants from calli derived from seeds and mature embryos in barley. Japanese Journal of Breeding. 1987;37:405-411
  87. 87. Gozukirmizi N, Ari S, Oraler G, Okatan Y, Palavan N. Callus induction, plant regeneration and chromosomal variations in barley. Acta Botanica Neerlandica. 1990;39(4):379-387
  88. 88. Cheng TY, Smith HH. Organogenesis from callus culture of Hordeum vulgare. Planta. 1975;123(3):307-310
  89. 89. Weigel RC, Hughes KW. Long term regeneration by somatic embryogenesis in barley (Hordeum vulgare L.) tissue cultures derived from apical meristem explants. Plant Cell, Tissue and Organ Culture. 1985;5(2):151-162
  90. 90. Ganeshan S, Baga M, Harwey BL, Rossnagel BG, Scoles GJ, Chibbar RN. Production of multiple shoots from thiadiazuron-treated mature embryos and leaf-base/apical meristems of barley (Hordeum vulgare L.). Plant Cell Tissue and Organ Culture. 2003;73:57-64
  91. 91. Huang B, Sunderland N. Temperature-stress pretreatment in barley anther culture. Annals of Botany. 1982;49(1):77-88
  92. 92. Piccirilli M, Arcioni S. Haploid plants regenerated via anther culture in wild barley (Hordeum spontaneum Kock C). Plant Cell Reports. 1991;10(6-7):273-276
  93. 93. Hoekstra S, van Zijderveld MH, Louwerse JD, Heidekamp F, van der Mark F. Anther and microspore culture of Hordeum vulgare L. cv. Igri. Plant Science. 1992;86(1):89-96
  94. 94. Bednarek PT, Orlowska R, Koebner RMD, Zimny J. Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.). BMC Plant Biology. 2007;7:10
  95. 95. Kohler F, Wenzel G. Regeneration of isolated barley microspores in conditioned media and trials to characterize the responsible factor. Journal of Plant Physiology. 1985;121(2):181-191
  96. 96. Kao KN, Saleem M, Abrams S, Pedras M, Horn D, Mallard C. Culture conditions for induction of green plants from barley microspores by anther culture methods. Plant Cell Reports. 1991;9(11):595-601
  97. 97. Obert B, Middlefell-Williams J, Millam S. Genetic transformation of barley microspores using anther bombardment. Biotechnology Letters. 2008;30(5):945-949
  98. 98. Castillo AM, Cistue L. Production of gynogenic haploids of Hordeum vulgare L. Plant Cell Reports. 1993;12(3):139-143
  99. 99. Holme IB, Brinch-Pedersen H, Lange M, Holm PB. Transformation of different barley (Hordeum vulgare L.) cultivars by Agrobacterium tumefaciens infection of in vitro cultured ovules. Plant Cell Reports. 2008;27(12):1833-1840
  100. 100. Kott LS, Kasha KJ. Initiation and morphological development of somatic embryoids from barley cell cultures. Canadian Journal of Botany. 1984;62(6):1245-1249.
  101. 101. Seguin-Swartz G, Kott L, Kasha KJ. Development of haploid cell lines from immature barley, Hordeum vulgare, embryos. Plant Cell Reports. 1984;3(3):95-97
  102. 102. Luhrs R, Lorz H. Initiation of morphogenic cell-suspension and protoplast cultures of barley (Hordeum vulgare L.). Planta. 1988;175(1):71-81
  103. 103. Muller B, Schulze J, Wegner U. Establishment of barley cell suspension cultures of mesocotyl origin suitable for isolation of dividing protoplasts. Biochemie und Physiologie der Pflanzen. 1989;185(1-2):123-130
  104. 104. Luhrs R, Nielsen K. Microspore cultures as donor tissue for the initiation of embryogenic cell suspensions in barley. Plant Cell, Tissue and Organ Culture. 1992;31(2):169-178
  105. 105. Lazzeri PA, Brettschneider R, Luhrs R, Lorz H. Stable transformation of barley via PEG-induced direct DNA uptake into protoplasts. Theoretical and Applied Genetics. 1991;81(4):437-444
  106. 106. Sahrawat AK, Chand S. High frequency plant regeneration from coleoptile tissue of barley (Hordeum vulgare L.). Plant Science. 2004;167(1):27-34
  107. 107. Li HP, Huang T, Wang CX, Liao YC. An efficient regeneration system of barley cultivars from leaf base segments. Biologia Plantarum. 2009;53(4):733-736
  108. 108. Vitanova Z, Vitanov V, Trifonova A, Savova D, Atanasov A. Effect of 2, 4-D precultivation on regeneration capacity of cultivated barley. Plant Cell Reports. 1995;14:437-441
  109. 109. Chang Y, Zitzewitz J, Hayes PM, Chen THH. High frequency plant regeneration form immature embryos of elite barley cultivars (Horedum vulgare L cv. Morex). Plant Cell Reports. 2003;21:733-738
  110. 110. Bregitzer P. Plant regeneration and callus type in barley: Effect of genotype and culture medium. Crop Science. 1992;32:1108-1112
  111. 111. Castillo AM, Egana B, Sanz JM, Cistue L. Somatic embryogenesis and plant regeneration from barley cultivars grown in Spain. Plant Cell Repots. 1998;17:902-906
  112. 112. Sener O, Can E, Arslan M, Çeliş N. Effects of genotype and picloram concentrations on callus induction and plant regeneration from immature inflorescence of spring barley cultivars (Hordeum vulgare L.). Biotechnology & Biotechnological Equipment. 2008;22:915-920
  113. 113. He T, Jia JF. High frequency plant regeneration from mature embryo explants of highland barley (Hordeum vulgare L. var. nudum Hk. f.) under endosperm-supported culture. Plant Cell Tissue and Organ Culture. 2008;95(2):251-254
  114. 114. Bregitzer P, Campbell RD. Genetic markers associated with green and albino plant regeneration from embryogenic barley callus. Crop Science. 2001;41:173-179
  115. 115. Gaponenko AK, Petrova TF, Iskakov AR, Sozinov AA. Cytogenetics of in vitro cultured somatic cells and regenerated plants of barley (Hordeum vulgare L.). Theoretical and Applied Genetics. 1998;75(6):905-911
  116. 116. Choi HW, Lemaux PG, Cho MJ. High frequency of cytogenetic aberration in transgenic oat (Avena sativa L.) plants. Plant Science. 2000;160(4):761-772
  117. 117. Choi HW, Lemaux PG, Cho MJ. Increased chromosomal variation in transgenic versus nontransgenic barley (Hordeum vulgare L.) plants. Crop Science. 2000;40:524-533
  118. 118. Bregitzer P, Dahleen LS, Neate S, Schwarz P, Mancharan M. A single backcross effectively eliminates agronomic and quality alterations caused by somaclonal variation in transgenic barley. Crop Science. 2008;48(2):471-479
  119. 119. Jiang W, Cho MJ, Lemaux PG. Improved callus quality and prolonged regenerability in model and recalcitrant barley (Hordeum vulgare L.) cultivars. Plant Biotechnology. 1998;15:63-69
  120. 120. Espinasse A, Lay C. Shoot regeneration of callus derived from globular to torpedo embryos from 59 sunflower genotypes. Crop Science. 1989;29:201-205
  121. 121. Bregitzer P, Campbell RD, Wu Y. Plant regeneration from barley callus: effects of 2, 4-dichlorophenoxyacetic acid and ohenylacetic acid. Plant Cell, Tissue and Organ Culture. 1995;43:229-235
  122. 122. Chauhan M, Kothari SL. Optimization of nutrient levels in the medium increase the effeciency of callus induction and plant regeneration in recalcitrant Indian barley (Hordeum vulgare L.) in vitro. In Vitro Cellular and Developmental Biology-Plant. 2004;40:520-527
  123. 123. Šerhantová V, Ehrenbergerová J, Ohnoutková L. Callus induction and regeneration efficiency of spring barley cultivars registered in the Czech Republic. Plant, Soil and Environment. 2004;50:456-462
  124. 124. Nasircilara G, Kenan T, Callan F. Callus induction and plant regeneration from mature embryos of different wheat genotypes. Pakistan Journal of Botany. 2006;38(2):637-645
  125. 125. Ward KA, Jordan MC. Callus formation and plant regeneration from immature and mature embryos of rye (Secale cereale L.). In vitro Cellular and Developmental Biology – Plant. 2001;37:361-268
  126. 126. Fahmy AH, El-Shihy O. Improvement of plant regeneration from long term callus cultures of two Egyptian wheat cultivars. Arab Journal of Biotechnology. 2006;8(1):177-188
  127. 127. Ozawa K, Komamine A. Establishment of a system of high-frequency embryogenesis from long-term cell suspension cultures of rice (Oryza sativa L.). Theoretical Applied Genetic. 1989;77:205-211
  128. 128. Denchev PO, Conger BV. Plant regeneration from callus cultures of switchgrass. Crop Science. 1994; 34:1623-1627.
  129. 129. Przetakiewicz A, Orczyk W, Nadolska-Orczyk A. The effect of auxin on plant regeneration of wheat, barley and triticale. Plant Cell, Tissue Organ Culture. 2003;73:245-256
  130. 130. Murray F, Brettell R, Matthews P, Bishop D, Jacobsen J. Comparison of Agrobacterium-mediated transformation of four barley cultivars using the GFP and Gus reporter genes. Plant Cell Reports. 2004;22:397-402
  131. 131. Travella S, Ross SM, Harden J, Everett C, Snape JW, Harwood WA. A comparison of transgenic barley lines produced by particle bombardment and Agrobacterium-mediated techniques. Plant Cell Reports. 2005;23:780-789
  132. 132. Hanzel JJ, Miller JP, Brinkman MA, Fendos E. Genotype and media effects on callus formation and regeneration in barley. Crop Science. 1985;25:27-31
  133. 133. von Arnold S, Sabala I, Bozhkov P, Dyachok J, Filonova L. Development pathways of somatic embryogenesis. Plant Cell Tissue Organ Culture. 2002;69:233-249
  134. 134. Marthe C, Kumlehn J, Hensel G. Barley (Hordeum vulgare L.) transformation using immature embryos. Methods in Molecular Biology. 2015;1223:71-83
  135. 135. Hisano H, Matsuura T, Mori IC, Yamane M, Sato K. Endogenous hormone levels affect the regeneration ability of callus derived from different organs in barley. Plant Physiology and Biochemistry. 2016;99:66-72
  136. 136. Powell W, Dunwell JM. In vitro genetics of barley (Hordeum vulgare L.) 1. Response of immature embryos to 2, 4-dichlorophenozyacetic acid. Heredity. 1987;59:293-299 DOI:10.1038/hdy.1987.126.
  137. 137. Baillie AMR, Rossnagel BG, Kartha KK. Evaluation of 10 Canadian barley (Hordeum vulgare L.) cultivars for tissue culture response. Canadian Journal of Plant Science. 1993;73:171-174
  138. 138. Tiidema A, Truve E. Efficient regeneration of fertile barley plants from callus cultures of several Nordic cultivars. Hereditas. 2004;140:171-176
  139. 139. Gozukirmizi N, Arı S, Gürel F, Gümüsel F, Çirakoglu B. Fingerprinting barley genome using PCR with arbitrary primers in barley regenerated from tissue culture. Proceedings of the Asia Pacific Conference on Agricultural Biotechnology; 20-24 August 1992; Science and Technology Press, Beijing, China; 1992. pp.143-146
  140. 140. Rostami H, Giri A, Nejad ASM, Moslem A. Optimization of multiple shoot induction and plant regeneration in Indian barley (Hordeum vulgare) cultivars using mature embryos. Saudi Journal of Biology Sciences. 2013;20(3):251-255
  141. 141. Wojnarowiez G, Jacquard C, Devaux P, Sangwan RS, Clément C. Influence of copper sulfate on anther culture in barley (Hordeum vulgare L.). Plant Science. 2002;162:843-847
  142. 142. Tingay S, McElroy D, Kala R, Fieg S, Wang M, Thornton S, Brettell R. Agrobacterium tumefaciens-mediated barley transformation. Plant Journal. 1997;11:1369-1376
  143. 143. Matthews PR, Wang MB, Waterhouse PM, Thornton S, Fieg SJ, Gubler F Jacobsen JV. Marker gene elimination from transgenic barley, using co-transformation with adjacent ‘twin T-DNAs’ on a standard Agrobacterium transformation vector. Molecular Breeding. 2001;7(3):195-202
  144. 144. Trifonova A, Madsen S, Olesen A. Agrobacterium-mediated transgene delivery and integration into barley under a range of in vitro culture conditions. Plant Science. 2001;161(5):871-880
  145. 145. Ashok KS, Becker D, Lorz H. Agrobacterium tumefaciens-mediated genetic transformation of barley (Hordeum vulgare L.). Plant Science. 2007;172:281-290
  146. 146. Kumlehn J, Serazetdinova L, Hensel G, Becker D, Loerz H. Genetic transformation of barley (Hordeum vulgare L.) via infection of androgenetic pollen cultures with Agrobacterium tumefaciens. Plant Biotechnology Journal. 2006;4(2):251-261
  147. 147. Gurel F, Gozukirmizi N. Optimization of gene transfer into barley (Hordeum vulgare L.) mature embryos by tissue electroporation. Plant Cell Reports. 2000;19:787-791
  148. 148. Bartlett JG, Alves SC, Smedley M, Snape LW, Harwood WA. High-throughput Agrobacterium-mediated barley transformation. Plant Methods. 2008;4:22
  149. 149. Hensel G, Valkov V, Middlefell-Williams J, Kumlehn J. Efficient generation of transgenic barley: The way forward to modulate plant–microbe interactions. Journal of Plant Physiology. 2008;165:71-82
  150. 150. Harwood WA, Ross SM, Bulley SM, Travella S, Busch B, Harden J, Snape JW. Use of the firefly luciferase gene in a barley (Hordeum vulgare) transformation system. Plant Cell Reports. 2002;21:320-326
  151. 151. Hisano H, Sato K. Genomic regions responsible for amenability to Agrobacterium-mediated transformation in barley. Scientific Reports. 2016;6:37505
  152. 152. Gozukirmizi N, Temel A. Advances in barley biotechnology: Tissue culture and molecular markers. In: Elfson SB, editor. Barley: Production, Cultivation and Uses. Ottawa: Nova Science Publishers; 2011. pp. 129-159
  153. 153. Yeo FKS, Hensel G, Vozábová T, Martin-Sanz A, Marcel TC, Kumlehn J, Niks RE. Golden SusPtrit: a genetically well transformable barley line for studies on the resistance to rust fungi. Theoretical and Applied Genetics. 2014;127:325
  154. 154. Nagy B, Majer P, Mihály R, Pauk J, Horváth GV. Stress tolerance of transgenic barley accumulating the alfalfa aldose reductase in the cytoplasm and the chloroplast. Phytochemistry. 2016;129:14-23
  155. 155. Han N, Na C, Chai Y, Chen J, Zhang Z, Bai B, Bian H, Zhang Y, Zhu M. Over-expression of (1,3;1,4)-β-d-glucanase isoenzymes EII gene results in decreased (1,3;1,4)-β-d-glucan content and increased starch level in barley grains. Journal of the Science of Food and Agriculture. 2017;97:122-127. DOI: 10.1002/jsfa.7695.
  156. 156. Wan Y, Lemaux PG. Generation of large number of independently transformed fertile barley plants. Plant Physiology. 1994;104:37-48
  157. 157. Ritala A, Aspegren K, Kurten U, Salmenkallio-Martilla M, Mannonen L, Hannus R, Kaupennin R, Terri H, Enari T. Fertile transgenic barley by particle bombardment of immature embryos. Plant Molecular Biology. 1994;24:317-325
  158. 158. Cho M, Jiang B, Lemaux G. Transformation of recalcitrant barley cultivars through improvement of regenerability and decreased albinism. Plant Sciences. 1998;138:229-244
  159. 159. Yadav T, Kachhwaha S, Kothari SL. Efficient in vitro plant regeneration and generation of transgenic plants in barley (Hordeum vulgare L.) using particle bombardment. Journal of Plant Biochemistry and Biotechnology. 2013;22(2):202-213
  160. 160. Zhang Z, Xing A, Staswick P, Clemente T. The use of glufosinate as a selective agent in Agrobacterium-mediated transformation of soybean. Plant Cell Tissue and Organ Culture. 1999;56:37-46
  161. 161. Holme IB, Brinch-Pedersen H, Lange M, Holm PB. Transformation of barley (Hordeum vulgare L.) by Agrobacterium tumefaciens infection of in vitro cultured ovules. Plant Cell Reports. 2006;25:1325-1335
  162. 162. Kovalchuk N, Jia W, Eini O, Morran S, Pyvovarenko T, Fletcher S, Bazanova N, Harris J, Beck-Oldach K, Shavrukov Y, Langridge P, Lopato S. Optimization of TaDREB3 gene expression intransgenic barley using cold-inducible promoters. Plant Biotechnology Journal. 2013;11:659-670
  163. 163. Gürel F, Uçarli C, Tufan F, Kalaskar DM. Enhancing T-DNA transfer efficiency in barley (Hordeum vulgare L.) cells using extracellular cellulose and lectin. Applied Biochemistry and Biotechnology. 2015;176:1203-1216
  164. 164. Uçarli C, Tufan F, Gürel AF. Expression and genomic integration of transgenes after Agrobacterium-mediated transformation of mature barley embryos. Genetics and Molecular Research. 2015;14:1096-1105
  165. 165. Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, Urso S, Valè G, Cattivelli L. Emerging Knowledge from genome sequencing of crop species. Molecular Biotechno-logy. 2011;50:250-266
  166. 166. Mayer KFX, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, et al. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell. 2011;23:1249
  167. 167. Mayer KFX, Waugh R, Langridge P, Close TJ, Wise RP, Graner A, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711
  168. 168. Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, deJong P, Wu CC, Graner A, Langridge P, Stein N. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics. 2011;12:247
  169. 169. Yu X, Yang J, Li XR, Liu XX, Sun CB, Wu FJ, He Y. Global analysis of cis-natural antisense transcripts and their heatresponsive nat-siRNAs in Brassica rapa. BMC Plant Biology. 2013;13:208
  170. 170. Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, et al. An improved consensus linkage map of barley based on flow sorted chromosomes and single nucleotide polymorphism markers. Plant Genome. 2011;4:238-49
  171. 171. Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, Chao S, Russell J, Waugh R, Hayes PM, Muehlbauer GJ. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One. 2014;9(4):e94688
  172. 172. Takahagi K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K, Mochida K, Saisho D. Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse biogeographical accessions in barley. Scientific Reports. 2013;6:33199
  173. 173. Urano K, Kurihara Y, Seki M, Shinozaki K. ‘Omics’ analyses of regulatory networks in plant abiotic stress responses. Current Opinion of Plant Biology. 2010;13:132-138
  174. 174. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-Seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research. 2008;18(9):1509-1517
  175. 175. Deyholos MK. Making the most of drought and salinity transcriptomics. Plant Cell Environment. 2010;33: 648-654
  176. 176. Alter S, Bader KC, Spannagl M, Wang Y, Bauer E, Schön CC, Mayer KF. DroughtDB: An expert-curated compilation of plant drought stress genes and their homologs in nine species. Database (Oxford). 2015;2015: bav046. DOI: 10.1093/database/bav046.
  177. 177. Quan X, Zeng J, Ye L, Chen G, Han Z, Shah JM, Zhang G. Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen. BMC Plant Biology. 2016;16:30
  178. 178. Tang Y, Zeng X, Wang Y, Bai L, Xu Q, Wei Z, Yuan H, Nyima T. Transcriptomics analysis of hulless barley during grain development with a focus on starch biosynthesis. Function and Integrative Genomics. 2017;17(1):107-117
  179. 179. Tombuloglu G, Tombuloglu H, Sakcali MS, Unver T. High-throughput transcriptome analysis of barley (Hordeum vulgare) exposed to excessive boron. Gene. 2015;557(1):71-81
  180. 180. Cao F, Chen F, Sun H, Zhang G, Chen ZH, Wu F. Genome-wide transcriptome and functional analysis of two contrasting genotypes reveals key genes for cadmium tolerance in barley. BMC Genomics. 2014;15:611
  181. 181. Bahieldin A, Atef A, Sabir JS, Gadalla NO, Edris S, Alzohairy AM, Radhwan NA, Baeshen MN, Ramadan AM, Eissa HF, Hassan SM, Baeshen NA, Abuzinadah O, Al-Kordy MA, El-Domyati FM, Jansen RK. RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress. Compets Rendus Biologies. 2015;338(5):285-297
  182. 182. Zeng X, Bai L, Wei Z, Hongjun Y, Wang Y, Xu Q, Tang Y, Nyima T. Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley. BMC Genomics. 2016;17:386
  183. 183. Rollins JA, Habte E, Templer SE, Colby T, Schmidt J, von Korff M. Leaf proteome alterations in the context of physiological and morphological responses to drought and heat stress in barley (Hordeum vulgare L.). Journal of Experimental Botany. 2013;64(11):3201-3212
  184. 184. Vítámvás P, Urban MO, Škodáček Z, Kosová K, Pitelková I, Vítámvás J, Renaut J, Prášil IT. Quantitative analysis of proteome extracted from barley crowns grown under different drought conditions. Frontiers in Plant Science. 2015;6:479
  185. 185. Sprink T, Metje J, Hartung F. Plant genome editing by novel tools: TALEN and other sequence specific nucleases. Current Opinion in Biotechnology. 2015;32:47-53
  186. 186. Bogdanove AJ, Voytas DF. 2011. TAL Effectors: Customizable proteins for DNA targeting. Science. 2011;333(6051):1843-1846
  187. 187. Wendt T, Holm PB, Starker CG, Christian M, Voytas DF, Brinch-Pedersen H, Holme IB. TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants. Plant Molecular Biology. 2013;83(3):279-285
  188. 188. Gurushidze M, Hensel G, Hiekel S, Schedel S, Valkov V, Kumlehn J. True-breeding targeted gene knock-out in barley using designer TALE-nuclease in haploid cells. PLoS ONE. 2014;9(3):e92046
  189. 189. Watanabe K, Breier U, Hensel G, Kumlehn J, Schubert I, Reiss B. Stable gene replacement in barley by targeted double-strand break induction. Journal of Experimental Botany. 2016;67(5):1433-1445
  190. 190. Lawrenson T, Shorinola O, Stacey N, Li C, Ostergaard L, Patron N, Uauy C, Harwood W. Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Biology. 2015;16:258
  191. 191. McClintock B. The significance of responses of the genome to challenge. Science. 1984;226:792-801
  192. 192. Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annual Review Genetics. 2007;41:331-368
  193. 193. Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nature Review Genetics. 2009;10:691-703
  194. 194. Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N. A detailed look at 7 million years of genome evolution in a 439-kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. Plant Journal. 2015;41:184-194
  195. 195. Wicker T, Keller B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Research. 2007;17:1072-1081
  196. 196. Temel A, Gozukirmizi N. Analysis of retrotransposition and DNA methylation in barley callus culture. Acta Biologica Hungarica. 2013;64:86-95
  197. 197. Yilmaz S, Marakli S, Gozukirmizi N. BAGY2 retrotransposon analyses in barley calli cultures and regenerated plantlets. Biochemistry Genetics. 2014;52:233-244
  198. 198. Yuzbasioglu G, Yilmaz S, Marakli S, Gozukirmizi N. Analysis of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons in rice. Biotechnology & Biotechnological Equipment. 2016;30:213-218
  199. 199. Jasencakova Z, Meister A, Schubert I. Chromatin organization and its relation to replication and histone acetylation during the cell cycle in barley. Chromosoma. 2001;110:83-92
  200. 200. Jasencakova Z, Soppe WJ, Meister A, Gernand D, Turner BM, Schubert I. Histone modifications in Arabidopsis—high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant Journal. 2003;33:471-480
  201. 201. Santamaría ME, Hasbún R, Valera MJ, Meijón M, Valledor L, Rodríguez JL, Toorop PE, Cañal MJ, Rodríguez R. Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. Journal of Plant Physiology. 2009;166:1360-1369
  202. 202. Meijón M, Feito I, Valledor L, Rodríguez R, Cañal MJ. Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea. BMC Plant Biology. 2010;10:10
  203. 203. Luo M, Liu X, Singh P, Cui Y, Zimmerli L, Wu K. Chromatin modifications and remodeling in plant abiotic stress responses. Biochimistry and Biophysics Acta. 2012;1819:129-136
  204. 204. Finnegan EJ, Genger RK, Peacock WJ, Dennis ES. DNA methylation in plants. Annual Review of Plant Physiology and Plant Molecular Biology. 1998;49(1):223-247
  205. 205. Cheung P, Lau P. Epigenetic regulation by histone methylation and histone variants. Molecular Endocrinology. 2005;19(3):563-573
  206. 206. Braszewska-Zalewska A, Hasterok R. Epigenetic modifications of nuclei differ between root meristematic tissues of Hordeum vulgare. Plant Signal Behavior. 2013;8(10): e26711
  207. 207. Braszewska-Zalewska A, Tylikowska M, Kwasniewska J, Szymanowska-Pulka J. Epigenetic chromatin modifications in barley after mutagenic treatment. Journal of Applied Genetics. 2014; 55(4):449-456
  208. 208. Baker K, Dhillon T, Colas I, Cook N, Milne I, Milne L, Bayer M, Flavell AJ. Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance. Plant Journal. 2015;84(1):111-24
  209. 209. Jacquier A. The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nature Review Genetics. 2009;10:833-844
  210. 210. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Research. 2006;16:11-9
  211. 211. Consortium EP, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799-816
  212. 212. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009;458:223-7
  213. 213. Matera AG, Terns RM, Terns MP. Non-coding RNAs: Lessons from the small nuclear and small nucleolar RNAs. Nature Reviews Molecular Cell Biology. 2007;8:209-220
  214. 214. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136:629-641
  215. 215. Ghildiyal M, Zamore PD. Small silencing RNAs: An expanding universe. Nature Review Genetics. 2009;10:94-108
  216. 216. Chitwood DH, Timmermans MC. Small RNAs are on the move. Nature. 2010;467:415-419
  217. 217. Qian-Hao Z, Ming-Bo W. Molecular functions of long non-coding RNAs in plants. Genes. 2012;3(1):176-190

Written By

Nermin Gozukirmizi and Elif Karlik

Submitted: 18 November 2016 Reviewed: 07 March 2017 Published: 19 July 2017