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Genome-wide polymorphism detection in peanut using next-generation restriction-site-associated DNA (RAD) sequencing

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Abstract

Peanut (Arachis hypogaea) is an important oilseed crop. Low genetic variability and limited genetic resources are major hurdles in the improvement of peanut. In this study, we used next-generation sequencing of restriction-site-associated DNA (RAD) fragments for genome-wide discovery of SNPs and SSRs in 11 diverse peanut genotypes. Reduced representation RAD libraries of 11 peanut genotypes were sequenced on Illumina HiSeq 2000 platform. A total of 102 million reads, approximately 10 Gb of sequence data, were collected. High-quality RAD sequence reads of genotype Tiffrunner and accession A. ipaensis were clustered to make a non-redundant set of representative sequences and to serve as a reference sequence for tetraploid peanuts and diploid peanuts, respectively. By using deep multiple alignment, a total of 15,678 SNPs in diploid peanuts and 3248 SNPs in cultivated peanuts were identified. These SNPs were also successfully used to reveal the genetic relationship between the peanut genotypes. In addition, 21,615 putative SSRs were also identified in the RAD sequences with an average of one SSR per 3.4 Kb. The most frequent SSR motifs identified in peanut genome were dinucleotide (67.6 %) followed by trinucleotide (14.6 %) and tetranucleotide (12.5 %) repeats. The high-throughput RAD sequencing allowed rapid genome-wide discovery of molecular markers in peanut. The large number of SNPs and SSRs identified in this study will be useful for constructing high-density genetic linkage maps, QTL analysis, marker-assisted selection and comparative studies in peanut.

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Acknowledgments

Authors thank David Bertoli, Corley Holbrook, Steve Knapp and Weijian Zhuang for providing seed or genomic DNA of peanut genotypes used in the study. SKG also thanks the Department of Biotechnology, Govt. of India, New Delhi, for providing DBT-CREST Award. Work was supported by a grant from the American Peanut Foundation to RVP.

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Authors and Affiliations

  1. Department of Plant Pathology, University of California, Davis, CA, USA

    Sudhir Kumar Gupta, Jongmin Baek, Noelia Carrasquilla-Garcia & R. Varma Penmetsa

  2. Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India

    Sudhir Kumar Gupta

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  1. Sudhir Kumar Gupta
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  2. Jongmin Baek
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  3. Noelia Carrasquilla-Garcia
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Correspondence to Sudhir Kumar Gupta or R. Varma Penmetsa.

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Gupta, S.K., Baek, J., Carrasquilla-Garcia, N. et al. Genome-wide polymorphism detection in peanut using next-generation restriction-site-associated DNA (RAD) sequencing. Mol Breeding 35, 145 (2015). https://doi.org/10.1007/s11032-015-0343-0

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