Molecular markers and marker trait associations

Abstract Chickpea has a narrow genetic base, and consequently many DNA-based markers were unsuccessful in revealing polymorphism. The problem was overcome by the development of simple sequence repeat and single nucleotide polymorphism markers that revealed adequate polymorphism and these became markers of choice in chickpea. In addition, transcription factor gene–derived microsatellite markers, intron targeted primers, expressed sequence tag polymorphisms, diversity arrays technology, and insertion-deletion markers have also been developed for chickpea. Genotyping by sequencing is also gaining popularity. Saturated linkage maps of chickpea with adequate marker density on each linkage group have also been constructed; however, several of the recently developed markers are still to be placed on linkage maps. The markers have subsequently been used to map genes or identify quantitative trait loci (QTLs) for biotic stress resistance, abiotic stress tolerance, and agro-morphological traits. Using reference genomes of chickpea and QTL intervals, candidate genes in QTL regions for several of these characters have been identified. Notably, genes involved in flowering in chickpea have been identified. Same QTL was also found to govern more than one trait, e.g., drought tolerance and plant vigor, salinity tolerance and higher plant vigor, salinity tolerance and higher reproductive success. The markers linked closely to genes/QTLs of interest have also been exploited to introgress wilt and blight resistance, and double podding character into agronomically superior cultivars.