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

Publication Overview
TitleUltra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea
AuthorsKujur A, Upadhyaya HD, Shree T, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK
TypeJournal Article
Journal NameScientific Reports
Volume5
Year2015
Page(s)9468
CitationKujur A, Upadhyaya HD, Shree T, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea. Scientific Reports. 2015; 5:9468.

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.
Features
This publication contains information about 2,212 features:
Feature NameUniquenameType
Ca_Kabuli_SNP1901Ca_Kabuli_SNP1901genetic_marker
Ca_Kabuli_SNP1902Ca_Kabuli_SNP1902genetic_marker
Ca_Kabuli_SNP1903Ca_Kabuli_SNP1903genetic_marker
Ca_Kabuli_SNP1904Ca_Kabuli_SNP1904genetic_marker
Ca_Kabuli_SNP1905Ca_Kabuli_SNP1905genetic_marker
Ca_Kabuli_SNP1906Ca_Kabuli_SNP1906genetic_marker
Ca_Kabuli_SNP1907Ca_Kabuli_SNP1907genetic_marker
Ca_Kabuli_SNP1908Ca_Kabuli_SNP1908genetic_marker
Ca_Kabuli_SNP1909Ca_Kabuli_SNP1909genetic_marker
Ca_Kabuli_SNP1910Ca_Kabuli_SNP1910genetic_marker
Ca_Kabuli_SNP1911Ca_Kabuli_SNP1911genetic_marker
Ca_Kabuli_SNP1912Ca_Kabuli_SNP1912genetic_marker
Ca_Kabuli_SNP1913Ca_Kabuli_SNP1913genetic_marker
Ca_Kabuli_SNP1914Ca_Kabuli_SNP1914genetic_marker
Ca_Kabuli_SNP1915Ca_Kabuli_SNP1915genetic_marker
Ca_Kabuli_SNP1916Ca_Kabuli_SNP1916genetic_marker
Ca_Kabuli_SNP1917Ca_Kabuli_SNP1917genetic_marker
Ca_Kabuli_SNP1918Ca_Kabuli_SNP1918genetic_marker
Ca_Kabuli_SNP1919Ca_Kabuli_SNP1919genetic_marker
Ca_Kabuli_SNP1920Ca_Kabuli_SNP1920genetic_marker
Ca_Kabuli_SNP1921Ca_Kabuli_SNP1921genetic_marker
Ca_Kabuli_SNP1922Ca_Kabuli_SNP1922genetic_marker
Ca_Kabuli_SNP1923Ca_Kabuli_SNP1923genetic_marker
Ca_Kabuli_SNP1924Ca_Kabuli_SNP1924genetic_marker
Ca_Kabuli_SNP1925Ca_Kabuli_SNP1925genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Chickpea-ICC12299_x_ICC8261-RIL-Kabuli
Projects
This publication contains information about 1 projects:
Project NameDescription
Chickpea-Seed_pod_yield-Kujur-2015
Properties
Additional details for this publication include:
Property NameValue
URLhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25942004/