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

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Relation http://oar.icrisat.org/10912/
http://dx.doi.org/10.3835/plantgenome2018.01.0005
10.3835/plantgenome2018.01.0005
 
Title Development and Application of High-Density Axiom SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes
 
Creator Saxena, R K
Rathore, A
Bohra, A
Yadav, P
Das, R R
Khan, A W
Singh, V K
Chitikineni, A
Singh, I P
Sameer Kumar, C V
Saxena, K B
Varshney, R K
 
Subject Pigeonpea
Genetics and Genomics
 
Description 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.
 
Publisher Crop Science Society of America
 
Date 2018-11
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/10912/1/Development%20and%20Application%20of%20High-Density.pdf
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 Saxena, K B and Varshney, R K (2018) Development and Application of High-Density Axiom 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