Journal article
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, Vol.11(3), Art. 180005
2018
Abstract
Axiom Cajanus SNP array revealed genetic architecture and temporal diversity in pigeonpea varieties.
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.
Details
- Title
- Development and application of High‐Density axiom cajanus SNP array with 56K SNPs to understand the genome architecture of released cultivars and founder genotypes
- Authors/Creators
- R.K. Saxena (Author/Creator)A. Rathore (Author/Creator)A. Bohra (Author/Creator)P. Yadav (Author/Creator)R.R. Das (Author/Creator)A.W. Khan (Author/Creator)V.K. Singh (Author/Creator)A. Chitikineni (Author/Creator)I.P. Singh (Author/Creator)C.V.S. Kumar (Author/Creator)K.B. Saxena (Author/Creator)R.K. Varshney (Author/Creator)
- Publication Details
- The Plant Genome, Vol.11(3), Art. 180005
- Publisher
- Wiley Periodicals LLC on behalf of Crop Science Society of America
- Identifiers
- 991005542763707891
- Copyright
- © 2018 Crop Science Society of America
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Genetics & Heredity
- Plant Sciences
- ESI research areas
- Plant & Animal Science