Bananas and plantains belong to the family
DNA marker technologies have been widely used in banana genetics and diversity analysis, e.g., in taxonomy, cultivar true-to-type assessment and genetic linkage map development. Currently, proteomic analysis is giving rise to new trends in genetic diversity and plant system biology analyses. These approaches will yield detailed insights into the
With the advent of modern DNA sequencing technologies and powerful bioinformatics tools, the sequencing and assembly of genomes for economically important crops and their relatives is becoming more common . Knowing and understanding the genetic make-up of these crops represents a great opportunity to not only elucidate the function of genes of interest, but also to detect regions in the genome that could present polymorphism associated with agronomic traits . This genetic variability is extremely valuable in plant breeding programmes where the selection of individuals with desirable characteristics is carried out.
Significant progress has being made towards gaining a better understanding of the
A large dataset of genomic information is publicly available through different databases, such as The Banana Genome Hub (http://banana-genome.cirad.fr/home), resources from the Global Musa Genomics Consortium (GMGC; http://musagenomics.org/), and the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/), among many others.
3. DNA markers
Molecular DNA-based markers are powerful tools for gaining insights into individual genetic characteristics, and for determining allele frequency. DNA markers were developed first for humans, then applied in plants, and subsequently for the analysis of the banana genome (Figure 2). This feature allows plant breeders to select only those individuals with desirable characteristics and significantly reduce the selection time. In this chapter, we discuss the development and applications of molecular marker technology to improve some of the commercially available
3.1. Restriction Fragment Length Polymorphism (RFLP)
RFLPs markers are widely used to detect variations in DNA fragment length banding patterns of electrophoresed restriction digests of DNA samples . These variations are mainly due to the presence of a restriction enzyme cleavage site at one site in the genome of one individual, and the absence of the site in another individual. It can also detect changes in fragment size due to insertions or deletions between the restriction fragments. RFLP is a codominant marker, meaning that it is able to distinguish between homozygotes and heterozygotes. RFLP is robust, easily transferred between laboratories, and requires no prior sequence information for its use.
RFLPs have been found to be useful in
RFLPs make locus-specific estimations of conserved synteny possible; however, some of the disadvantages are that it is expensive to develop, requires large amounts of DNA, is not possible to automate, unlike other DNA markers [AFLP, diversity array technology (DArT), or variable number tandem repeats (VNTR)], needs a suitable probe library, may require radioactive labelling, is laborious and time consuming. The relatively high cost and technically demanding nature of this technique make it inappropriate for routine breeding applications . The use of more specific, PCR-based types of markers overcomes most of the disadvantages associated with RFLPs.
3.2. Random Amplified Polymorphic DNA (RAPD)
With the development of the polymerase chain reaction (PCR) technique, amplifying specific regions of an individual genome became possible, and identifying polymorphisms is made more precise by detecting small nucleotide changes compared to RFLPs. Random amplified polymorphic DNA (RAPD) depends on the PCR and is used as a very fast way to obtain information about genetic variation with a relatively low cost . Some other characteristics are the fact that no prior knowledge of the genome sequence is required; low amounts of DNA template are used; and the advantage of technical simplicity. RAPD assays have proven to be powerful and efficient means of assisting introgression and backcross breeding . But reproducibility is sometimes limited, and reliability depends on the skills of the operator, which is a dominant feature of the marker system.
RAPD has been widely used to distinguish diverse
Kaemmer  was first to report the use of RAPDs for fingerprinting of wild species and cultivars of banana (
The use of RAPDs was reported to identify 57 cultivars by using 60 10-mer random primers, where only 49 primers gave consistent results, and the primer OPC-15 (5’-GACGGATCAG-3’) helped to distinguish 55 of the cultivars by producing 24 bands of all tested primers . These markers failed to properly characterize the clones that Gros Michel and Venkel had previously thought belonged to the
3.3. Variable Number Tandem Repeats (VNTR)
VNTR are generated by highly specific PCR amplification and, therefore, should not suffer from the reproducibility problems experienced with RAPD analysis. VNTR are regions of short, tandemly repeated DNA motifs (generally less than or equal to 4 bp), with an overall length in the order of tens of base pairs . VNTR have been reported to be highly abundant and randomly dispersed throughout the genomes of many plant species. Variation in the number of times the motif is repeated is thought to arise through slippage errors during DNA replication.
Furthermore, the isolation of VNTR is becoming increasingly routine with the availability of automated DNA sequencing facilities, along with improved techniques for the construction of genomic libraries enriched for VNTR and improved techniques for the screening of appropriate clones , bacterial artificial chromosome (BAC) end-sequences and, recently, the availability of genome sequencing facilities attributed to the discovery of VNTRs .
The development and utilization of VNTR in
3.4. Inter Simple Sequence Repeats (ISSR)
The ISSR technique developed by  does not require the knowledge of flanking sequences and has wide applications for all organisms, regardless of the availability of information about their genome sequence. They have also proved to be simple, fast, cost effective and versatile sets of markers for repeatable amplification of DNA sequences using single primers. As for the disadvantages, the homology of the bands is uncertain, and because they are dominant markers, they do not allow the calculation of certain parameters, requiring that heterozygous be distinguished from homozygous dominance.
ISSR and RAPD were used in determinate genetic stability of three economically important micropropagated banana (
3.5. Sequence-Related Amplified Polymorphism (SRAP)
The sequence-related amplified polymorphism (SRAP) technique is a simple and efficient marker system that can be adapted for a variety of purposes, including map construction, gene tagging, genomic and cDNA fingerprinting, and map-based cloning. It has several advantages over other molecular marker systems, such as simplicity, reasonable throughput rate, disclosure of numerous codominant markers, ease of isolation of polymorphic bands for sequencing, and most importantly, the targeting of open reading frames (ORFs) .
The SRAP marker has been adopted recently for the assessment of genetic diversity and relationships in
In another study, SRAP and AFLP were used to study 40
Moreover, the study of genetic relationships among some banana cultivars from China analysed by SRAP showed a correlation between the cultivars and their region of origin; the cultivars closely clustered into two major clusters according to their genome composition. Likewise, the genetic data generated by the SRAP marker were reliable in respect to the morphology and agronomic trait classification, indicating the efficiency of SRAP for estimating genetic similarity among banana cultivars and providing a scientific basis for banana genetic and breeding research . More recently, the fluorescently labelled SRAP molecular marker system was used to characterize the genetic variability within 71 accessions of a core collection, including wild species and cultivars of different subgroups , which complements previous work from the same collection .
The fluorescent SRAP marker information shows that
3.6. Amplified Fragment Length Polymorphism (AFLP)
AFLP is a DNA marker based on PCR amplification of selected restricted fragments obtained from the digestion of total genomic DNA or cDNA [55, 56]. It is a robust and reliable molecular technique recently employed in many systematic plant studies. AFLP banding patterns should be treated initially as dominant markers; this makes the information content limited. However, AFLP patterns can be detected as codominant markers in a segregating population when the analysis is applied to large populations .
The nature of an individual, whether a homozygote or heterozygote, could be distinguished using software developed on the basis of band intensity. Moreover, AFLP results in a binary band presence–absence matrix profile. In that case, two factors may affect band detection and analysis: the first is that identical bands may correspond to different fragments (homoplasy); the second is that different fragments appear as a single band (collision). An estimation method was reported for solving the effect of these factors , in which AFLP was demonstrated as a sampling procedure of fragments, with lengths sampled from a distribution. This study focused on estimation of pairwise genetic similarity, defined as average fraction of common fragments. Levels of polymorphism in
The relationship between
On the other hand, the AFLP marker technique was shown to be a good tool for detection of genetic variation in banana organogenesis and somatic embryogenesis-derived plants [67-69]. AFLP techniques have some disadvantages compared to other PCR-based markers, in that they are technically challenging, time consuming and relatively expensive, while requiring a number of DNA processes including digestion, ligation and amplification, as well as a complex staining system. Additionally, a relatively large amount of high-quality DNA is necessary for complete digestion, which is required to reduce the presence of fake polymorphisms. However, microsatellite markers and AFLP analysis is considered to be one of the most suitable tools for marker-assisted breeding in
4. Single Nucleotide Polymorphism (SNP)
Single nucleotide variations in the genome sequence of individuals of a population or species are known as single nucleotide polymorphisms (SNPs). The development of this technique in humans demonstrated improvements in sequencing technology and availability of an increasing number of SNP sequences ; this development has made direct analysis of genetic variation at the DNA sequence level possible in genomes from different organisms . Modern high-throughput DNA sequencing technologies and bioinformatics tools have led to the discovery that SNPs constitute the most abundant molecular markers in the plant genomes, which has revolutionized the pace and precision of plant genetic analysis, and the discovery that SNPs are widely distributed throughout genomes, although their occurrence and distribution varies among species .
4.1. Diversity Arrays Technology (DArT)
DArTs are attractive approaches to detecting large numbers of genome-specific single nucleotide polymorphism (SNP) markers  and EcoTILLING. In principle, DArT is a DNA hybridization-based genotyping technology, which enables low-cost whole-genome profiling of crops without prior sequence information. DArT reduces the complexity of a representative sample (such as pooled DNA representing the diversity of
Sequenced DArT markers have been used with
DArT revealed genetic relationships among
4.2. (Eco) Targeting Induced Local Lesions in Genomes (EcoTILLING)
EcoTILLING is a high-throughput method for the discovery and characterization of SNPs and small insertions/deletions (indels) in genomes [53, 79, 80]. It is an adaptation of the enzymatic mismatch cleavage and fluorescence detection methods originally developed for the targeting induced local lesions in genomes (TILLING) reverse-genetic strategy [79, 81]. The technique was first described for
The EcoTILLING method was used for the discovery and characterization of nucleotide polymorphisms in
Furthermore, differentiation between
More recently, single nucleotide polymorphism (SNP) studies for marker discovery of the use of beta carotene (provitamin A) in plantains , and SNPs found in the partial sequence of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase, a key enzyme related to starch metabolism, in banana and plantains , give important information for new approaches to investigating the wide range of banana germplasm biodiversity and incorporating the information in banana and plantain breeding.
5. Molecular cytogenetic
Using cytogenetics, chromosome studies of humans and several plant species have been going on for more than a century, helping to establish the typical number of chromosomes for each of the species and to assign a chromosome number according to their size and centromere position. Chromosome size and banding pattern helped to identify subchromosomal regions and were associated with some phenotypic characteristics. Chromosome number has also been important for identifying individuals among species. Even though cytogenetic tools have been improved to obtain high-resolution banding patterns for identifying deletions, insertions or translocations , it remains a challenge to elucidate the origins of the chromosomes that are involved in chromosome rearrangements. Molecular cytogenetics is adding a set of powerful tools to those already available for studying genome organization, evolution and recombination. This technology can help to identify small changes at the level of the gene, for which several techniques have been developed.
in situ Hybridization (FISH) to chromosomes
Additionally, a dual colour FISH showed that in all studied accessions, the satellite chromosomes carrying the 18S-25S loci did not carry the 5S loci . On the other hand, the telomeric sequence was detected as pairs of dots at the ends of all the chromosomes analysed, but no intercalary sequences were seen .
Detection of the integration of viral sequences of banana streak badnavirus (BSV) in two metaphase spreads of
Furthermore, a modern chromosome map technology known as high-resolution fluorescent
in situ Hybridization (GISH)
The first study that used GISH in
On the other hand, GISH has been used on meiotic chromosomes in plants. It is quite challenging, and the protocols used are complex and highly variable depending on the species. A method was developed to prepare chromosomes at meiosis metaphase I suitable for GISH in
5.3. Flow cytometry
Flow cytometry (FCM) protocols have been applied for studying the natural variation in
The study of genomic composition of
Research on the genetic stability/instability of
|Quantity of DNA required||High||Low||Low/higha||Low||Low||Moderate||Low|
|Quantity of information||Low||High||High||High||High||High||Low|
|Resolution of genetic differences||High||Moderate||High||Moderate||High||High||High|
|Ease of use and development||Difficult||Easy||Easy||Easy||Easy||Moderateb||Moderate|
|Operational costs||High||Low||Low||Low||Low||Moderate||Moderate /High|
|Major application||Physical mapping||Gene tagging||Genetic diversity||Gene tagging||Genetic diversity||Gene tagging||SNP mapping|
6. Protein polymorphism
Proteomics can be defined as the systematic analysis of proteome, the protein complement of the genome, which deals with information on proteins’ abundance, their variations and modifications, and their interacting partnerships and networks, in order to understand cellular processes in biological systems. Thus, proteomics is important for understanding the molecular mechanisms involved in plant and crop biodiversity, which is a driving force behind speciation, crop domestication and improvement. This is of particular interest in bananas, which are good representatives of a complex allopolyploid and an important fruit crop.
6.1. Proteome analysis
In recent years, several proteomic studies, based on combined use of two-dimensional electrophoresis (2DE) and mass spectrometric methods, have been successfully applied to investigate the effect of osmotic stresses on banana growth and development , cold tolerance , inter-and intra-cultivar protein polymorphisms , the fruit proteome of banana [112, 113], and the proteomic profiling of banana roots in response to
In contrast, comparative quantitative proteomic analysis of plantain (AAB genome) response to cold stress treatments revealed that about 23.3 % of the 3477 total proteins identified were differentially expressed. The largest parts of the expressed proteins were predicted to be involved in the oxidation reduction process (including oxylipin biosynthesis), cellular process, response to stress and primary metabolic process. Interestingly, among the cold-responsive proteins involved in the oxidation reduction process, Cu/Zn SOD (superoxide dismutase), CAT 2 (catalase isozyme 2) and LOX (lipoxygenease) were found to be differentially expressed in the cold-tolerant plantain, in contrast to the cold-susceptible banana . Altogether, the previous works provided clues as to the existence of inter-variety protein polymorphism related to their
Moreover, evidence from the proteome analysis of different triploid banana varieties using 2D electrophoresis revealed the following results: i) principal component analysis (PCA) showed that the principal component PC1 (which explains 39 % of the variance information) was positively correlated with the presence of the B genome; and, ii) the hierarchical clustering revealed that the first level of clustering separates the varieties of genome BBB and ABB composition from both AAB and the two AAA varieties, the second level splits both AAB varieties from the two AAA varieties and the ABB from the BBB varieties, and the third level divides both AAA varieties and both AAB varieties. Although proteome analysis does not always correspond to the presumed genome formulae, perhaps because following polyploidization new gene copies may undergo modifications allowing functional diversification, in general, the observations at the protein level provide good indications for a more complex genome structure and genomic rearrangement in some banana varieties .
The limited genetic knowledge of the banana genome and the nature of the crop as a parthenocarpic fruit and a mostly triploid, sterile plant mean that many aspects of breeding and selection that have been possible in other crops cannot be applied in the banana. Several approaches to breeding and selection have been applied in numerous plant species; however, they could not be used in banana due to the unclear genetic knowledge of its genome and the natural characteristics of the crop, including parthenocarpy, ploidy and sterility. Unconventional biotechnological strategies including DNA and protein-based marker techniques have contributed considerably in providing a vast amount of information that helps in understanding the nature of
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