Abstract
High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8–25.8% with LOD: 7.0–13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1–171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea.
Highlights
A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea
High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 3 ICC 12968) and 92 diverse desi and kabuli genotypes
Keeping all above in view, the present study was undertaken to validate and genotype genome-wide physically mapped 1632 SNP and 500 SSR markers showing in silico polymorphism between ICC 4958 and ICC 12968 in a 190 F4 mapping population (ICC 4958 3 ICC 12968) using Illumina GoldenGate assay, gel-based assay and fluorescent dye-labeled automated fragment analyzer
Summary
Correspondence and requests for materials should be addressed to S.K.P. The available draft assemblies of genome and transcript sequences of diverse desi and kabuli chickpea have enabled to select numerous chromosome-wise well distributed and informative in silico polymorphic SSR and SNP markers for genomicsassisted breeding applications in chickpea[7,47,48,49,50] In this perspective, large-scale validation and high-throughput genotyping of genomewide polymorphic SSR and SNP markers and their use in construction of diverse mapping population-derived high-resolution intra-specific genetic linkage maps are feasible in chickpea. Large-scale validation and high-throughput genotyping of genomewide polymorphic SSR and SNP markers and their use in construction of diverse mapping population-derived high-resolution intra-specific genetic linkage maps are feasible in chickpea It would accelerate the identification, fine mapping and map-based isolation of genes/QTLs associated with traits of agricultural importance, and thereby, genetic enhancement of chickpea through marker-assisted selection. The relevant high-resolution QTL mapping information was integrated with comprehensive marker-based comparative genome mapping and differential expression profiling to delineate a candidate gene at one of the robust seed weight-governing major QTL region in chickpea
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