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Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

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Title Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea
 
Creator Basu, Udita
Srivastava, Rishi
Bajaj, Deepak
Thakro, Virevol
Daware, Anurag
Malik, Naveen
Upadhyaya, Hari D.
Parida, Swarup K.
 
Subject chickpea
SNPs
genotyping
 
Description Accepted date: 18 June 2018
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual
assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions.
Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived
(DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs
and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped
on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory
sequence components of genes. The MAD-SNPs were efcient to detect high intra-specifc polymorphic
potential and wide natural allelic diversity level including high-resolution admixed-population
genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This
signifes their efectiveness in introgression breeding and varietal improvement studies targeting
useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait
nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP).
A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN signifcantly associated
with SYP trait was found most-promising in chickpea. The essential information delineated can be of
immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.
The authors gratefully acknowledge the fnancial support by the core grant of National Institute of Plant Genome
Research (NIPGR), New Delhi, India.
 
Date 2018-09-09T10:25:23Z
2018-09-09T10:25:23Z
2018
 
Type Article
 
Identifier Scientific Reports, 8(1): 13240
2045-2322
http://223.31.159.10:8080/jspui/handle/123456789/885
https://www.nature.com/articles/s41598-018-29926-1
10.1038/s41598-018-29926-1
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature Limited