Development and Application of High-Density Axiom Cajanus SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes

Saxena, R K and Rathore, A and Bohra, A and Yadav, P and Das, R R and Khan, A W and Singh, V K and Chitikineni, A and Singh, I P and Sameer Kumar, C V and Varshney, R K (2018) Development and Application of High-Density Axiom Cajanus SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes. The Plant Genome (TSI), 11 (3). pp. 1-10. ISSN 1940-3372

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Abstract

As one of the major outputs of next-generation sequencing (NGS), a large number of genome-wide single-nucleotide polymorphisms (SNPs) have been developed in pigeonpea [Cajanus cajan (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom Cajanus SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole-genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion–deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array. The Axiom Cajanus SNP array developed was used for genotyping 103 pigeonpea lines encompassing 63 cultivars released between 1960 and 2014 and 40 breeding, germplasm, and founder lines. Genotyping data thus generated on 103 pigeonpea lines provided 51,201 polymorphic SNPs and InDels. Genetic diversity analysis provided in-depth insights into the genetic architecture and trends in temporal diversity in pigeonpea cultivars. Therefore, the continuous use of the high-density Axiom Cajanus SNP array developed will accelerate high-resolution trait mapping, marker-assisted breeding, and genomic selection efforts in pigeonpea.

Item Type: Article
Divisions: Research Program : Asia
Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Genome Architecture, Cultivars on Future Breeding, germplasm accessions, pigeonpea, Axiom Cajanus SNP Array, Genome Architecture, pigeonpea, Genotyping
Subjects: Others > Plant Breeding
Mandate crops > Pigeonpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 10 Dec 2018 05:21
Last Modified: 31 Jan 2019 07:13
URI: http://oar.icrisat.org/id/eprint/11001
Official URL: http://dx.doi.org/10.3835/plantgenome2018.01.0005
Projects: UNSPECIFIED
Funders: Science and Engineering Research Board (SERB), Government of India, United States Agency for International Development (USAID), Bill & Melinda Gates Foundation
Acknowledgement: The authors wish to thank the Science and Engineering Research Board (SERB), Government of India; United States Agency for International Development (USAID) and Bill & Melinda Gates Foundation for funding this study. The work was undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals.
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