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

doi: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

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

UWA School of Agriculture and Environment

Research output: Contribution to journal › Article › peer-review

151 Citations (Scopus)

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 language	English
Article number	40577
Journal	Scientific Reports
Volume	7
DOIs	https://doi.org/10.1038/srep40577
Publication status	Published - 16 Jan 2017

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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. (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, 7, Article 40577. https://doi.org/10.1038/srep40577

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

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.",

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

year = "2017",

month = jan,

day = "16",

doi = "10.1038/srep40577",

language = "English",

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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

TY - JOUR

T1 - Development and Evaluation of a High Density Genotyping 'Axiom-Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

AU - Pandey, Manish K.

AU - Agarwal, Gaurav

AU - Kale, Sandip M.

AU - Clevenger, Josh

AU - Nayak, Spurthi N.

AU - Sriswathi, Manda

AU - Chitikineni, Annapurna

AU - Chavarro, Carolina

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.

PY - 2017/1/16

Y1 - 2017/1/16

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.

AB - 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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U2 - 10.1038/srep40577

DO - 10.1038/srep40577

M3 - Article

C2 - 28091575

AN - SCOPUS:85009452486

SN - 2045-2322

VL - 7

JO - Scientific Reports

JF - Scientific Reports

M1 - 40577

ER -

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

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