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Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea

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Title Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea
 
Creator Bajaj, Deepak
Das, Shouvik
Badoni, Saurabh
Kumar, Vinod
Singh, Mohar
Bansal, Kailash C.
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Natural variation in plants
Plant domestication
 
Description Accepted date: 29 June 2015
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66–85%) and broader natural allelic diversity (6–64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.
The authors gratefully acknowledge the financial support for this study provided by a research grant from
the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14). We thank
the Vice Chancellor, CSKHPKV, Palampur, Himachal Pradesh, India for providing off-season nursery
facility for phenotyping of Wild Cicer accessions at its Regional Station, Sangla. SD acknowledges the
DBT for Junior Research Fellowship award.
 
Date 2015-12-31T10:30:17Z
2015-12-31T10:30:17Z
2015
 
Type Article
 
Identifier Scientific Reports, 5: 12468
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/484
http://www.nature.com/articles/srep12468
10.1038/srep12468
 
Language en_US
 
Publisher Nature Publishing Group