A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.).

Publication Overview
TitleA 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.).
AuthorsSingh S, Mahato AK, Jayaswal PK, Singh N, Dheer M, Goel P, Raje RS, Yasin JK, Sreevathsa R, Rai V, Gaikwad K, Singh NK
TypeJournal Article
Journal NameScientific reports
Volume10
Issue1
Year2020
Page(s)4960
CitationSingh S, Mahato AK, Jayaswal PK, Singh N, Dheer M, Goel P, Raje RS, Yasin JK, Sreevathsa R, Rai V, Gaikwad K, Singh NK. A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.).. Scientific reports. 2020 Mar 18; 10(1):4960.

Abstract

Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array 'CcSNPnks' for Affymetrix GeneTitan® platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5'UTR and 10.46% 3'UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, 'CcSNPnks' chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.

Stocks
This publication contains information about 1 stocks:
Stock NameUniquenameType
Pusa_Dwarf/H2001-4-RIL-F8Pusa_Dwarf/H2001-4-RIL-F8population
Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
CcSNPnksCcSNPnksN/A N/A
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This publication contains information about 55,893 features:
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AGCP-1_1106AGCP-1_1106genetic_marker
AGCP-1_1485AGCP-1_1485genetic_marker
AGCP-1_1713AGCP-1_1713genetic_marker
AGCP-1_1775AGCP-1_1775genetic_marker
AGCP-1_1814AGCP-1_1814genetic_marker
AGCP-1_685AGCP-1_685genetic_marker
AGCP-10_1035AGCP-10_1035genetic_marker
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AGCP-10_992AGCP-10_992genetic_marker
AGCP-100_1074AGCP-100_1074genetic_marker
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AGCP-100_2155AGCP-100_2155genetic_marker
AGCP-100_216AGCP-100_216genetic_marker
AGCP-100_2573AGCP-100_2573genetic_marker
AGCP-100_326AGCP-100_326genetic_marker
AGCP-100_3982AGCP-100_3982genetic_marker
AGCP-100_4575AGCP-100_4575genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Pigeon_pea-Yield-Singh-2020
Featuremaps
This publication contains information about 1 maps:
Map Name
Pigeon_pea-Pusa_Dwarf/H2001-4-RIL-F8
Properties
Additional details for this publication include:
Property NameValue
DOI10.1038/s41598-020-61889-0
Elocation10.1038/s41598-020-61889-0
Publication ModelElectronic
ISSN2045-2322
eISSN2045-2322
Publication Date2020 Mar 18
Journal AbbreviationSci Rep
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
Cross References
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DatabaseAccession
PMID: PubMedPMID:32188919