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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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Relation http://oar.icrisat.org/10861/
http://dx.doi.org/10.1038/s41598-018-29926-1
10.1038/s41598-018-29926-1
 
Title Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea
 
Creator Basu, U
Srivastava, R
Bajaj, D
Thakro, V
Daware, A
Malik, N
Upadhyaya, H D
Parida, S K
 
Subject Plant Breeding
Crop Yield
Plant Genetic Resources
Chickpea
Genetics and Genomics
 
Description 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 efficient to detect high intra-specific 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 signifies their effectiveness 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 significantly 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.
 
Publisher Nature Publishing Group
 
Date 2018-09-05
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/10861/1/Genome-wide%20generation.pdf
Basu, U and Srivastava, R and Bajaj, D and Thakro, V and Daware, A and Malik, N and Upadhyaya, H D and Parida, S K (2018) Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea. Scientific Reports (TSI), 8 (13240). pp. 1-11. ISSN 2045-2322