Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

Abstract

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.

Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

“…Henceforth, novelty and population-specific characteristics of the identified six major and robust QTLs governing PH trait was apparent in chickpea. A number of QTL mapping studies involving high resolution intra- and inter-specific genetic linkage maps as references/anchors have been undertaken for rapid molecular mapping as well as fine mapping/map-based cloning of major genes/QTLs governing multiple stress tolerance- and yield-component traits to expedite marker-assisted genetic enhancement in chickpea26282935363759. Interestingly, with the use of an ultra-high density genetic linkage map as a reference in the present investigation, the major PH QTLs significantly scaled-down into the marker intervals of 0.058–0.688 cM (average <0.5 cM) in chickpea.…”

“…These available genomic resources have accelerated the process of NGS (next-generation sequencing)-based whole genome and transcriptome sequencing of numerous cultivated ( desi and kabuli ) and wild accessions as well as NGS-/array-based large-scale discovery and high-throughput genotyping of informative microsatellite and SNP (single nucleotide polymorphism) markers in natural and mapping populations of chickpea101112131415161718. Consequently, these efforts have significantly driven the process of constructing high-density intra- and inter-specific genetic linkage maps and genetic/association mapping to identify QTLs (quantitative trait loci)/genes governing useful agronomic traits in chickpea121920212223242526272829303132333435. One such most promising outcome includes the use of GBS (genotyping-by-sequencing) assay in discovery/genotyping of genome-wide SNPs in natural germplasm lines and mapping populations for understanding domestication and LD (linkage disequilibrium) pattern and constructing ultra-high density genetic linkage maps.…”

Identification of candidate genes for dissecting complex branch number trait in chickpea

“…This emphasizes the potential utility of GBS assay in quick large-scale discovery and high-throughput genotyping of reliable and high-quality genome-wide SNPs simultaneously in chickpea. The GBS assay has been successfully deployed in high-resolution genetic and association mapping to identify potential genes/QTLs governing important agronomic traits in chickpea [23,26,31,41,42]. Therefore, GBS-based genome-wide SNPs differentiating cultivated desi and kabuli accessions identified in our study have significance for their immense utilization in genomics-assisted breeding applications of chickpea.…”

“…An extended LD decay in a self-pollinating crop plant like chickpea due to its narrow genetic base (low intra-specific polymorphism) along with extensive contribution of four sequential bottlenecks during domestication is quite anticipated [26,31]. Henceforth, GWAS integrated with candidate gene-based association analysis will be of much relevance for efficient genetic dissection of diverse complex quantitative traits in chickpea [26,[42][43][44]. In this context, a combinatorial strategy of GWAS and candidate gene-based association analysis has been utilized in the present study to delineate numerous high-resolution potential genomic loci regulating quantitative trait of branch number at a genome-wide scale in chickpea.…”

“…Strong association of one regulatory SNP in a BA1/LAX1 (BARREN STALK1/LIKE AUXIN1) known cloned gene (P ≤ 10 −9 with R 2 : 12%) and another synonymous SNP in a candidate lipase gene (P ≤ 10 −9 with R 2 : 11%) with BN was evident in chickpea. The functionally relevant non-synonymous and regulatory SNP loci-containing known/candidate genes associated with branch number trait identified by combining both GWAS and candidate gene-based association mapping could essentially be utilized for ascertaining the rapid marker-trait linkages and efficient detection of potential genes/QTLs governing branch number trait in chickpea [20,[24][25][26][27]31,42]. The determination of (A) population structure (with optimal population number K = 2 indicated by two different colors: red and blue), (B) unrooted phylogenetic tree construction and (C) principal component analysis (PCA) employing 4957 genome-wide GBS-and candidate gene-derived SNPs classified 60 desi and kabuli Cicer accessions into two major populations (POP I and POP II).…”