Genomic Approaches in Wheat Breeding for Sustainable Production under Changing Climate

Abstract

Wheat is the most important cereal crop, a great source of dietary protein. It is grown worldwide for its consumption in the form of different products. Wheat production faces a lot of biotic and abiotic stresses that hinder growth and yield. Changing climate is a worse scenario to be adopted for sustainable production. Food demand is rapidly increasing by a drastic increase in the world population. Conventional breeding techniques are time-consuming and ineffective in attaining high yield goals under changing climates. Next-generation sequencing revolutionized wheat breeding through molecular approaches for effective selection. The use of genomic approaches in wheat breeding is the need of time for sustainable production. Several genomic approaches, such as use of genome-wide markers for gene mapping, genomic selection and recurrent selection through QTL and meta-QTL analysis, markers-assisted selection in haploid breeding, heterosis breeding through genomic tools, and biotechnological tools, are currently used as modern techniques for developing climate-resilient wheat cultivars. This chapter illustrated the challenges of changing climate, molecular techniques in wheat breeding to develop climate-resilient genotypes, sustainable wheat production to cope with food demand, and future breeding strategies.

1. Introduction

The one-third population of the world mainly relies on wheat (Triticum aestivum L.) for their daily diet and it is becoming more important with a great increase in the world’s population [1, 2, 3]. Wheat is grown in an area of about 220 million hectares worldwide [4], with an average annual production of 729 million tons [5]. Wheat is also used as an industrial material and renewable feed resource [6]. Wheat demand is increasing due to increased population thought the world [5]; thus, it is influencing market prices [7], competition, and growing demand [8]. The considerable challenge in sustainable wheat production is to increase the yield with demand in continuously changing environmental conditions. It has been suggested that wheat yield should be increased by 1.7% per annum globally for the next 30 years [9]. Still, its production rate is 0.9% per annum [10], insufficient to meet global hunger and even in main wheat-producing countries, this percentage is gradually decreasing. The goal of sustainable wheat production is only possible to achieve by growing wheat in the best environmental condition since the world is facing the massive challenge of climate change; therefore, this could not be possible [11]. Yield and yield stability are highly affected by climate change [12].

Although agronomic practices and conventional breeding contributed to sustainable wheat production, now it is time to boost wheat production with the latest introduced technologies. So, breeders are looking for highly efficient methods to increase yield in a limited time [13]. Newly developed technologies, such as phenomics [14], marker-assisted selection (MAS) [15], genomic breeding [16], and biotechnological (cis-genic and transgenic) techniques [17], are promising technologies to fight hunger in the future.

Marker-assisted breeding is based on gene linkage and recombination events in meiosis [18]. Different molecular markers are being used to detect the variations in wheat germplasm [19] and resistant genes are being identified in various lines and used in marker-assisted breeding [20, 21]. Genomic selection (GS) is an advanced form of MAS [13]. Initially, a panel of genotypes, training population, is selected in GS, then genotyping is performed with genome-wide markers and lastly, phenotyping is done for the trait of interest. Genome-estimated breeding values (GEBVs) are calculated with the help of a training population for all genotypes included in the panel, newly developed lines, and the validation population [22]. GS is more effective based on computing more variations with the help of GEBVs without phenotyping [23]. Modified methods in GS significantly increase genetic gain and accuracy. Several recent genomic approaches have been illustrated in Figure 1.

Figure 1.

Schematic diagram for recent genomic approaches in wheat breeding.

This chapter focuses on genomic approaches in wheat breeding to combat hunger in changing climate. Genomic breeding in wheat is an efficient way to increase wheat production in changing climate and global warming scenarios. Using molecular markers in QTL-mapping and its combination with genome with association study (GWAS) could significantly improve yield to achieve sustainable wheat production goals.

2. Gene mapping through genome-wide markers

Initially, restriction fragment polymorphism (RFLP) markers were introduced to identify cultivars [24] and gene mapping, but the frequency of markers was not impressive due to the extremely low level of polymorphism for the D genome of bread wheat [25]. International Triticeae Mapping Initiative (ITMI) was very efficient because of generating high-density linkage groups [26]. With the advancement in technology, PCR-based markers were developed. There were two broad categories [27], simple sequence repeat (SSR) [28] and randomly amplified polymorphic DNA (RAPD), considered far better than RFLP markers. These markers proved to be time-saving and cost-effective, especially SSR markers were extensively used in wheat due to reproducibility. RAPD markers were used to make sequence characterized amplified regions (SCAR) or sequence-tagged sites (STS) markers [29] that were more reliable in wheat, for example, Lr24 and Lr2 QTL for Russian wheat aphid [30].

The first discovery of simple sequence repeats (SSR) markers, also known as microsatellites [28], opened a new era of wheat breeding due to their extensive use because they are highly reproducible, genome-specific, highly polymorphic, and relatively abundant [31]. The yield and yield-related traits in wheat were exploited with more resolution on their respective loci in the genome [32]. SSR markers also had limitations due to high cost, random distribution in the genome, finite motifs, and difficulty obtaining exact information [33]. Single nucleotide polymorphism (SNP) markers analyze variations at a single nucleotide level; therefore, they are not very effective in marker-assisted selection of wheat [34, 35, 36, 37].

3. Genome based breeding strategies in wheat

The reciprocal recurrent genomic selection in wheat is important to increase wheat yield [38]. Genomic selection of desired traits speeds up the breeding program with the accurate selection of traits of interest with the help of QTL and GWAS [39, 40]. When additive effects of focused QTL are not determined, they can be estimated by genome-wide prediction. The Ridge regression model has been proposed to be used in the genomic selection of desired traits with more accuracy and unbiased decisions [41, 42]. F∞ metric is implemented to determine additive effects and additive-by-additive epistasis [43]. The superior plants are selected for the next generation with the help of the estimation of additive effects in recurrent genomic selection [22]. The QTL study with the ridge regression model revealed that nonadditive effects were related to grain yield [44]; therefore, they are suggested to be included in the genome prediction model to increase wheat yield. Persistency in predicting models is mainly dependent upon the adequate size of parental population and linkage disequilibrium, size of training population, use of the statistical model to estimate markers effects in recurrent genomic selection, and density of markers [45, 46, 47].

Estimating haploid breeding and genomic breeding values are two important strategies for assessing long-term genetic gain and maintenance in recurrent genomic breeding [48]. Based on these values, optimal population value selection is performed to make blocks of genotypes exhibiting maximum haploid or genomic breeding values. Genotypes with maximum haploid value would fall in the block with minimal segregation. In contrast, minimal value haploid value will lead to minimal population value selection with a haplotype block with maximum segregation for the desired trait [48]. Genomic recurrent selection and its modified form reciprocal recurrent selection increase the efficacy of wheat breeding programs [49] to develop high-yielding, climate-resilient genotypes. Gene pyramiding is a novel concept in modern breeding to accumulate desired genes in a single genotype to develop an ideotype [50]. Implications of this breeding strategy via genomic breeding can be a way forward to achieve a landmark in wheat breeding programs for sustainable production in changing climate.

4. Marker-assisted selection

Genetic linkage between loci of the same chromosome and their recombination events during meiosis are the main basis of MAS [18]. The transfer of two loci together or separately in the next generation is dependent on how closely these loci are located on the chromosome [51]. There will be more chances to be inherited together if they are located closely on the same chromosome. Molecular markers are used to identify a specific region on the chromosome for a gene of interest [52]. Different alleles are detected in several lines, known as a polymorphism for a trait of interest in different lines. Molecular markers detect the presence of linked alleles on the base of genetic linkage [27]. Marker-assisted selection could prove a very effective technique for developing climate-resilient wheat cultivars in changing climates.

Single sequence repeat (SSR) markers were used to detect the cell membrane stability of wheat cultivated under drought stress. SSR markers were significantly linked with cell membrane stability, but the association was weak. SSR markers were suggested to detect increased frequency in progenies with drought tolerance [53] and used Xwmc273.3 marker was used to detect QTL associated with higher grain yield of wheat under drought conditions. Different wheat cultivars in irrigated and rainfed regions were selected with the help of QTL mapping and phenotypic selection based on higher yield in water stress conditions [54]. Marker-assisted backcross breeding was employed to detect and transfer three drought-tolerant QTLs in high-yielding cultivars. QTLs were detected in drought-tolerant cultivar HI5100 and HD2733 was used as a recurrent cultivar. They identified 29 lines having drought tolerant QTLs; further background selection resulted in five varieties for evaluation in the national breeding program [55]. QTL expression in common wheat for cold tolerance was detected in the region of CBF and Cor/Lea gene families located at 5AL [56]. Soriano et al. [40] performed a QTL meta-analysis to identify QTLs for biotic and abiotic stress tolerance in durum wheat. They identified 315 of 85 MQTL, while 71 corresponded to biotic stress and 127 to abiotic stresses.

5. Heterosis breeding through genome based strategies

Only <1% of the wheat cultivated area is under the cultivation of hybrid wheat due to the highly self-pollinated wheat and other technical problems. Meanwhile, genomic breeding has helped resolve the technical issues of hybrid wheat production. Male sterility is not well-understood in wheat because it is highly self-pollinated, and hybrid seed production is very cost-effective. Male sterility is of great importance in the hybridization of wheat. Male sterility II (ms2) has been identified in wheat for 40 years, but its corresponding genes were unknown. It was determined through mapped-based cloning experiments in 2017 that the promoter region of ms2 has TRIM element, activates Ms2 allele in anther, which induces male sterility in wheat [57, 58].

Furthermore, it was also investigated by map-based cloning studies that male sterility 1 (ms1) also prevailed in wheat [59, 60]. Functional analysis of MS1 has revealed a newly introduced protein in the wheat and Poaceae family. It is localized in mitochondria and plastids, associated with the phospholipid-binding activity to induce male sterility. The split gene system also inserts male sterility in wheat by expressing the phytotoxic gene barnase, controlled by two alleles and its activation induces male sterility. This system maintains male sterile female plants while, after crossing, sterile hybrids are produced because it does not need male storer lines and entirely relies on the genetically modified female plants [61].

The utilization of genomics to predict heterotic patterns is another strategy for hybridizing wheat. These patterns are used mainly to characterize parents and the hybrids population on a large scale. Heterotic patterns were used to assess 1604 wheat hybrids for disease resistance and morphological parameters. It was demonstrated that 69 hybrids performed better than the best commercial line by 7.2–10.7% in production [62]. Zhao et al. [63] described a three-way genome-based strategy to predict heterotic wheat patterns in 1604 hybrids and 135 parents. In another experiment, 135 parents and their 1604 hybrids were assessed through genomic prediction of heterotic patterns and a complete performance of hybrids was evaluated to suggest high yielding heterotic patterns.

Heterotic patterns were used to assess a well-defined population and their effectiveness, limitations, and representation were estimated to measure their success. Identifying and exploiting major genes is essential and helpful in hybridization, such as genes responsible for dwarf wheat and very important for selecting the parental population to make hybrids. Further, these genes greatly influence pollen mass and anther extrusion in wheat [64]. Hybrids D1b and B1b with reduced height showed poor anther extrusion due to the expression of genes related to dwarfness [65, 66]. While developing high-yielding cultivars with lodging resistance must be considered for sustainable goals. Using another gene Rht24 for male sterility in hybridization could be very effective because it has no effects on male floral parts and anther extrusion [67]. These studies predicted heterotic patterns via a quantitative genetic framework and laid the basis for the hybridization of wheat, having fine-tuned major genes of plant stature and floral traits [68]. The development of hybrid cultivars at a commercial scale could be feasible through genome-based prediction of these genes.

6. Developing climate-resilient cultivars through biotechnology

In the last 15 years, recombinant DNA technology, genetic manipulation technologies, and culturing methodologies have enabled the efficient transformation and development of transgenics in a wide variety of crop plants [69]. Moreover, transgenesis can be a supplementary technique for single-gene or transgenic plants development [70]. Despite traditional breeding, this method introduces only the cloned gene(s) of agronomic significance without the hazard of transferring any additional undesired genes from the donor [71]. In transgenesis, the backcrossing is unnecessary because the recipient plant/crop genotype is least affected [72]. Furthermore, this genetic transformation method opens the door to a vast array of genetic material, sourced from viruses and bacteria to fungus, insects to animals and human beings to unrelated plants, and even from chemical synthesis [73, 74, 75, 76]. Plant transgenics have been developed and tested for various crops [77], fruits, and trees with surprising speed and success. However, the breeders focus on the gradual enhancement of commercial cultivars by introducing cloned genes of important agronomic values. The gene-transfer methods and strategies have been used to create important agronomic features in numerous crop varieties.

The enormous size and structural complexity of the polyploid wheat genome initially hindered the genomic study. By the passage of time, the development of new genomic technologies has enabled the breeders to map the bread wheat and its ancestors. However, the introduction of modern genomic technologies like next-generation sequencing has resulted in draught genomes for bread wheat and its progenitors [78], paving the door for developing novel crop enhancement strategies. Diverse germplasms are evaluated in pre-breeding for several physiological, agronomical, and biochemical traits [79], then crossing [80] and high throughput phenotyping [81] are required, while marker-based next-generation sequencing [80], genomic prediction [82], and validation of climate-resilient lines [83] can be very helpful in developing high yielding cultivars in changing environment. The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats) technology makes breeding time conservative and helps to find and transfer the same gene of interest in the host wheat genotype [84]. These RNA-guided nucleases are used for genome editing and isolated from the microbial adaptive immune system [85]. A wheat line has been developed that has reduced gluten in the grain by using Cas9 protein with 20 nucleotides in its sequence [86]. A gene Mildew locus O (MLo) was inserted in the wheat genome to introduce resistance against powdery mildew, and this was the first successful attempt of CISPER/Cas9 technology in wheat [87]. Transcription activator-like effector nucleases, an earlier technology, were used with the combination of CRISPER/Cas9 to achieve this goal.

Since the development of CRISPR-Cas technology, wheat genes of agronomical and fundamental scientific interest have been targeted, such as -gliadin genes to reduce gluten grain content [88], TaGW2 to increase grain weight [89], TaZIP4-B2 to understand meiotic homologous crossover [90], TaQsd1 to minimize preharvest sprouting [91], TaMTL and CENH3 for haploid plant induction [92]. The Wheat CRISPR tool, which is freely accessible at https://crispr.bioinfo.nrc.ca/WheatCrispr/, identifies efficient sgRNAs that are anticipated high on-target and low off-target activity scores (enabling researchers to explore all potential sgRNAs inside a target gene or sequence of interest). The Wheat CRISPR tool considers hexaploidy in bread wheat, allowing the researcher to target either a single gene copy or all three homeologs by checking a box.

The recent approaches for modern wheat breeding in the era of genomic studies have been summarized in Table 1.

Breeding techniques	Output	References
Marker-assisted selection (600k SNP marker)	Targeted genotyping and genetic improvement	[15]
Marker-assisted breeding (SNPs)	Evaluation of multiple elite traits	[93]
Marker-assisted back-crossing	Drought tolerance in bread wheat	[55]
Marker-assisted back-crossing	Introgression of drought-tolerant QTLs	[94]
Marker-assisted back-cross selection	Improvement in rust resistance through a selection of Yr59	[95]
Marker-assisted back-crossing	Transfer of recessive skr cross-ability trait	[96]
Marker-assisted back-crossing	Adaptation of a variety of Unnat PBW 343 in diverse environments	[97]
Marker-assisted back-crossing	Enhanced rust resistance; Two genes (Lr19/Sr25 and Lr24/Sr24) for leaf rust resistance; One gene (Yr15) for stripe rust resistance	[98]
Marker-assisted back-crossing	Development of near-isogenic lines for grain softness	[99]
Marker-assisted back-crossing	Development of advanced lines for grain softness	[100]
Marker-assisted recurrent selection	Improved crown rot resistance	[101]
Marker-assisted recurrent selection	Enhanced genetic gains	[49]
Reciprocal recurrent selection	Hybridization	[38]
S1 recurrent selection, early generation genomic selection, marker-assisted back-crossing, and gene pyramiding	Introgression of Ms3 gene for genetic male sterility in hybrid wheat	[102]
Double haploid breeding	Development of thermos-sensitive genic male sterile lines	[103]
Biotechnology (Horizontal gene transfer)	Fhb7 from fungus expression in wheat for Fusarium head blight resistance	[75]
CRISPR-Cas9-based multiplexed gene editing	heritable mutations in the TaGW2, TaLpx-1, and TaMLO genes	[104]
Development of the GlutEnSeq (Gluten gene Enrichment and Sequencing)	Homozygous deletions for the α-gliadins on 6A and the γ-gliadins on 1B in two γ-irradiated lines of cultivar; Homozygous deletions of the γ-gliadins on 1B and heterozygous deletions for the α-gliadins on 6A in four Fielder CRISPR/Cas9 gliadin gene-edited lines	[105]
CRISPR/Cas9 system delivered via Agrobacterium tumefaciens	Obtained thirteen mutant lines by targeting seven sites of three genes (Pinb, waxy, and DA1)	[106]

Table 1.

Recent approaches for modern wheat breeding in the era of genomic studies.

7. Conclusion and future perspective

Wheat is one of the most important food crops and a basic source of calories globally. The rising population necessitates an increase in wheat production for food security. On the other hand, its production faces great challenges under changing climate and global warming. Wheat production is still lower than its demand and conventional methods proved inefficient to cope with this gap. Modern plant breeding techniques need time to be adopted for sustainable wheat production. Genomic breeding and biotechnological tools are more precise and time-conserving techniques with maximum efficiency to increase wheat production. The discovery of molecular markers-initiated, marker-assisted breeding while QTL and meta-QTL analysis improved the technique’s efficacy. Genomic breeding is considered an advanced form of MAS and the genome-wide study provides quick backcrossing and recurrent selection in wheat breeding. Genomic heterotic patterns have been used in molecular hybridization, while different statistical models have also been made to make selection and hybridization more and more precise. Combining genomic knowledge with biotechnological tools makes it quick to breed wheat with sustainable goals in a limited time in changing climate. In the future, the adoption of genomic breeding and biotechnological techniques to develop climate-resilient wheat cultivars at commercial scales will only be the way to achieve sustainable wheat production.

Acknowledgments

We acknowledge all colleagues in the respective departments who guided and helped in the collection of material and outlines.

We do not have any funding source for this book chapter

Conflict of interest

The authors declare no conflict of interest.

Acronyms and abbreviations

MAS	(Marker-assisted selection)
GS	(Genomic selection)
QTL	(Quantitative trait loci)
GEBVs	(Genome-estimated breeding values)
GWAS	(genome-wide association study)
RFLP	(Restriction fragment length polymorphism)
ITMI	(International triticeae mapping initiative)
SSR	(Simple sequence repeat)
RAPD	(Random amplified polymorphic DNA)
SCAR	(Sequence characterized amplified regions)
STS	(Sequence tagged sites)
CRISPER	(Clustered regularly interspaced short palindromic repeats)