Development and Evaluation of a High Density Genotyping 'Axiom-Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

Manish K. Pandey, Gaurav Agarwal, Sandip M. Kale, Josh Clevenger, Spurthi N. Nayak, Manda Sriswathi, Annapurna Chitikineni, Carolina Chavarro, Xiaoping Chen, Hari D. Upadhyaya, Manish K. Vishwakarma, Soraya Leal-Bertioli, Xuanqiang Liang, David J. Bertioli, Baozhu Guo, Scott A. Jackson, Peggy Ozias-Akins, Rajeev K. Varshney

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Abstract

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array Axiom-Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for 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. The availability of the high-density SNP array Axiom-Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.

Original languageEnglish
Article number40577
JournalScientific Reports
Volume7
DOIs
Publication statusPublished - 16 Jan 2017

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Breeding
Single Nucleotide Polymorphism
Diploidy
DNA Shuffling
Genome
RNA Sequence Analysis
Arachis
Genotype
Phenotype
DNA
Genes

Cite this

Pandey, Manish K. ; Agarwal, Gaurav ; Kale, Sandip M. ; Clevenger, Josh ; Nayak, Spurthi N. ; Sriswathi, Manda ; Chitikineni, Annapurna ; Chavarro, Carolina ; Chen, Xiaoping ; Upadhyaya, Hari D. ; Vishwakarma, Manish K. ; Leal-Bertioli, Soraya ; Liang, Xuanqiang ; Bertioli, David J. ; Guo, Baozhu ; Jackson, Scott A. ; Ozias-Akins, Peggy ; Varshney, Rajeev K. / Development and Evaluation of a High Density Genotyping 'Axiom-Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut. In: Scientific Reports. 2017 ; Vol. 7.
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abstract = "Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array Axiom-Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for 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. The availability of the high-density SNP array Axiom-Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.",
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Pandey, MK, Agarwal, G, Kale, SM, Clevenger, J, Nayak, SN, Sriswathi, M, Chitikineni, A, Chavarro, C, Chen, X, Upadhyaya, HD, Vishwakarma, MK, Leal-Bertioli, S, Liang, X, Bertioli, DJ, Guo, B, Jackson, SA, Ozias-Akins, P & Varshney, RK 2017, 'Development and Evaluation of a High Density Genotyping 'Axiom-Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut' Scientific Reports, vol. 7, 40577. https://doi.org/10.1038/srep40577

Development and Evaluation of a High Density Genotyping 'Axiom-Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut. / Pandey, Manish K.; Agarwal, Gaurav; Kale, Sandip M.; Clevenger, Josh; Nayak, Spurthi N.; Sriswathi, Manda; Chitikineni, Annapurna; Chavarro, Carolina; Chen, Xiaoping; Upadhyaya, Hari D.; Vishwakarma, Manish K.; Leal-Bertioli, Soraya; Liang, Xuanqiang; Bertioli, David J.; Guo, Baozhu; Jackson, Scott A.; Ozias-Akins, Peggy; Varshney, Rajeev K.

In: Scientific Reports, Vol. 7, 40577, 16.01.2017.

Research output: Contribution to journalArticle

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AU - Clevenger, Josh

AU - Nayak, Spurthi N.

AU - Sriswathi, Manda

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AU - Chen, Xiaoping

AU - Upadhyaya, Hari D.

AU - Vishwakarma, Manish K.

AU - Leal-Bertioli, Soraya

AU - Liang, Xuanqiang

AU - Bertioli, David J.

AU - Guo, Baozhu

AU - Jackson, Scott A.

AU - Ozias-Akins, Peggy

AU - Varshney, Rajeev K.

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N2 - Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array Axiom-Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for 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. The availability of the high-density SNP array Axiom-Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.

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