Record Details

The first high density genotyping ‘Axiom_Arachis’ 58K SNPs array for genetic studies and molecular breeding in groundnut

OAR@ICRISAT

View Archive Info
 
 
Field Value
 
Relation http://oar.icrisat.org/10250/
 
Title The first high density genotyping ‘Axiom_Arachis’ 58K SNPs array for genetic studies and molecular breeding in groundnut
 
Creator Pandey, M K
Agarwal, G
Kale, S M
Clevenger, J
Nayak, S N
Sriswathi, M
Chitikineni, A
Chavarro, C
Chen, X
Upadhyaya, H D
Vishwakarma, M K
Leal-Bertioli, S
Liang, X
Bertioli, D J
Guo, B
Jackson, S A
Ozias-Akins, P
Varshney, R K
 
Subject Genetic Engineering
Molecular biology
Groundnut
Genetics and Genomics
 
Description Genome complexity and narrow genetic base are the major
problems that hinder achieving accelerated genetic gains in
groundnut or peanut, a major source of vegetable oil (48%)
and protein (25%). High density genotyping is a must-have
genomic resource in a crop for use in several genetic and
breeding applications. Availability of genome sequence for
both the diploid genome progenitors of cultivated groundnut
has provided an opportunity for discovery of structural variations
in large-scale including single nucleotide polymorphisms
(SNPs), the most abundant DNA sequence variation in the genomes.
In this context, we developed a high-density SNP array
‘Axiom_Arachis’ with 58K SNPs with uniform genome coverage.
We identified initially a total of 163,782 SNPs that included
118,860 SNPs (58,438 SNPs for A-genome and 60,422 SNPs
for B-genome) from 30 tetraploids and 44,922 SNPs (39,937
SNPs for A-genome and 4,985 SNPs for B-genome) from 11
diploids. Finally, a total of 58,233 highly informative SNPs with
genome specificity were used for array development. In addition
to cultivated groundnuts (Arachis hypogaea), this array has
fair representation of other diploids (A. duranensis, A. stenosperma,
A. cardenasii, A. magna and A. batizocoi). Genotyping of the
groundnut ‘Reference Set’ containing 300 genotypes identified
44,424 polymorphic SNPs and genetic diversity analysis
provided in-depth insights into the genetic architecture of this
material. In summary, this high-density SNP array will accelerate
the process of trait dissection and molecular breeding
including genomic selection for achieving higher genetic gains
in groundnut.
 
Date 2017-02
 
Type Conference or Workshop Item
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/10250/1/Abstract_Book_94.pdf
Pandey, M K and Agarwal, G and Kale, S M and Clevenger, J and Nayak, S N and Sriswathi, M and Chitikineni, A and Chavarro, C and Chen, X and Upadhyaya, H D and Vishwakarma, M K and Leal-Bertioli, S and Liang, X and Bertioli, D J and Guo, B and Jackson, S A and Ozias-Akins, P and Varshney, R K (2017) The first high density genotyping ‘Axiom_Arachis’ 58K SNPs array for genetic studies and molecular breeding in groundnut. In: InterDrought-V, February 21-25, 2017, Hyderabad, India.