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

Alice Kujur,Vinod Kumar,C L L Gowda,Shivali Sharma,Swarup K Parida,Hari D Upadhyaya,Akhilesh K Tyagi,Tanima Shree,Saurabh Badoni,Shouvik Das,Deepak Bajaj,Shailesh Tripathi,Maneesha S Saxena,Sube Singh

doi:10.1038/srep09468

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.

Highlights

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea
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
Keeping all above in view, we discovered 26785 and 16573 genome-wide SNPs showing differentiation between parental genotypes [ICC 12299 and ICC 8261] by their genotyping in a 275 F7 RIL mapping population (ICC 12299 3 ICC 8261) using reference desi and kabuli genome-based GBS assay, respectively

Summary

Introduction

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea. The highbarcoded multiplexing capacity (pooling up to 384-barcoded accessions in a single sequencing lane) at methylation-sensitive RE (restriction endonuclease)-sites (like APeKI) have enhanced the efficiency of GBS assay in fast discovery and genotyping of genome-wide SNPs in larger mapping populations This in turn made the GBS assay much more advantageous over other available high-throughput traditional genotyping assays for constructing ultra-high density genetic linkage maps and genome-wide high-resolution (major and minor effects QTLs) gene/QTL mapping in small diploid as well as large genome crop species, including rice, wheat, barley, sorghum, Medicago and soybean[24,41,42,43,44,45,46,47,48,49,50]. Very limited reports are available with regard to the use of GBS approach in discovery and genotyping of genome-wide SNPs in intra- and inter-specific mapping populations for constructing ultra-high resolution genetic linkage maps and fine mapping of QTLs regulating important agronomic traits in chickpea vis-a-vis other crop plants[22,45,50,51]

Methods

Results

Conclusion