Breeding of Vegetable, Spice and Tuber crops (2+1)

Statistical tools in crop improvement

• A study of DNA polymorphism has become an active area of research in all important crops and several model plant species like Arabidopsis thaliana and Brachypodium distachyon.
• This involves development and use of molecular markers, which have proved useful not only for marker-assisted selection during plant breeding, but also for understanding crop domestication and plant evolution.
• To resolve the pattern of DNA polymorphism in any crop, the ultimate approach would be to sequence/resequence the entire genome (or a part of it) in a large number of accessions.
• This was, however, unimaginable during the 1980s and still remains cost ineffective, therefore DNA-based molecular markers (for example, Restriction Fragment Length Polymorphisms(RFLP), Random Amplified Polymorphic DNAs(RAPD), Simple Sequence Repeats (SSRs) and Amplified Fragment Length Polymorphisms (AFLPs)) have largely been employed for the study of DNA polymorphism (Collard et al., 2005).
• Most of these molecular markers are based on the use of restriction digestion of genomic DNA, followed by hybridization of electrophoresed DNA, and/or visualization of the products of PCR carried out using suitably designed PCR primers.
• More recently, however, single nucleotide polymorphisms (SNPs), whose discovery was largely based on sequence information, became the markers of choice due to their abundance and uniform distribution throughout a genome.
• Once discovered, SNP genotyping can be done using any of the dozens of available methods. For SSR/SNP genotyping, some efforts in the past were made to provide for the desired high throughput and cost effectiveness through the use of PCR tetrad machines (handling 384 PCR reactions at a time), multiplexing, multiple loading of the gels and the use of automatic sequencers.
• However, this appeared inadequate and there has been an increasing demand to develop ultra-high-throughput low-cost assays for a variety of novel marker systems including SNPs.
• These new methods will allow ultra-high-throughput genotyping of either one or few individuals for hundreds of thousands of markers, or that of thousands of individuals for one or few markers.
• High-density oligonucleotide arrays, which are now becoming available in several crops, provide a means for achieving this goal of low-cost ultra-high-throughput genotyping.
• These arrays may also be custom made according to specific needs and, therefore, also allowed for the development of novel marker systems like single feature polymorphisms (SFPs) (including gene-specific hybridization polymorphisms and gene expression markers), diversity array technology (DArT) and restriction site-associated DNA (RAD) markers, which have now become the markers of choice.
• Technologies have also been developed, which make use of tag arrays for detection of the products of genotyping reactions.
• These novel array- or chip-based markers are useful for a variety of purposes including genome-wide association studies, population studies, bulk segregant analysis, quantitative trait loci (QTL) interval mapping, whole genome profiling and background screening and so on (Steinmetz et al., 2002; Winzeler et al., 2003; Wenzl et al., 2004, 2007a; Hazen et al., 2005; Kim et al., 2006).
• A brief account of the development and use of these high-throughput array-based molecular markers in plants is presented in this study.