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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Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376
Barchi L, Lanteri S, Portis E, Acquadro A, Vale G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genom 12:304
Barker GL, Edwards KJ (2009) A genome-wide analysis of single nucleotide polymorphism diversity in the world’s major cereal crops. Plant Biotechnol J 7:318–325
Batley J, Barker G, O’Sullivan H, Edwards K, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91
Bus A, Hecht J, Huettel B, Reinhardt R, Stich B (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genom 13:281
Cloutier S, Niu Z, Datla R, Duguid S (2009) Development and analysis of ESTSSRs for flax (Linum usitatissimum L.). Theor Appl Genet 119:53–63
Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, Homer N, Huentelman MJ (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887–893
da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FI, de Oliveira AC: SSR Locator (2008) Tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics 412696
Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK, Datta S, Singh MN, Bashasab F, Kulwal P, Wanjari KB, Varshney RK, Cook DR, Singh NK (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol 11:17
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379
Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci 107:16196
Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422
Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14:1812–1819
Gaur R, Azam S, Jeena G, Khan AW, Chaudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 19:357–373
Herselman L (2003) Genetic variation among Southern African cultivated peanut (A. hypogaea L.) genotypes as revealed by AFLP analysis. Euphytica 133:319–327
Hilu KW, Stalker HT (1995) Genetic relationships between peanut and wild species of Arachis sect Arachis (Fabaceae): evidence from RAPDs. Plant Syst Evol 198:167–178
Hohenlohe P, Amish S, Catchen J, Allendorf F, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Resour 11:117–122
Holbrook CC, Stalker HT (2003) Peanut breeding and genetic resources. Plant Breed Rev 22:297–356
Holmquist R (1983) Transitions and transversions in evolutionary descent: an approach to understanding. J Mol Evol 19:134–144
Hong Y, Chen X, Liang X, Liu H, Zhou G, Li S, Wen S, Holbrook CC, Guo B (2010) A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC Plant Biol 10:17
Huang X, Feng Q, Qian Q, Quaing Z, Wang L et al (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076
Hyten DL, Choi I-Y, Song Q, Specht JE, Carter TE, Shoemaker RC, Hwang E-Y, Matukumalli LK, Cregan PB (2010) A high density integrated genetic linkage map of soybean and the development of a 1,536 universal soy linkage panel for QTL mapping. Crop Sci 50:960–968
Khera P, Upadhyaya HD, Pandey MK, Roorkiwal M, Sriswathi M, Janila P, Guo Y, McKain M, Nagy ED, Knapp SJ, Leebens-Mack J, Conner JA, Ozias-Akins P, Varshney RK (2013) SNP-based genetic diversity in the reference set of peanut (Arachis spp.) by developing and applying cost-effective KASPar genotyping assays. Plant Genome. doi:10.3835/plantgenome2013.06.0019
Kochert G, Halward T, Branch WD, Simpson CE (1991) RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet 81:565–570
Kochert G, Stalker HT, Gimenes M, Galgaro L, Romero Lopes C, Moore K (1996) RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am J Bot 83:1282–1291
Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, Hasegawa M, Kiyoshima H, Isobe S (2012) Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Mol Breed 30:125–138
Kumar S, You FM, Cloutier S (2012) Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genom 13:684
Kumpatla S, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Li F, Kitashiba H, Inaba K, Nishio T (2009a) A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits. DNA Res 16:311–323
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al (2009b) The Sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Liang X, Chen X, Hong Y, Liu H, Zhou G, Li S, Guo B (2009) Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol 9:35
Moretzsohn MC, Hopkins MS, Mitchell SE, Kresovich S, Valls JF, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4:11
Moretzsohn MC, Barbosa AVG, Alves-Freitas DMT, Teixeira C, Leal-Bertioli SCM, Guimarães PM, Pereira RW, Lopes CR, Cavallari MM, Valls JFM, Bertioli DJ, Gimenes MA (2009) A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9:40
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200
Nagy ED, Guo Y, Tang S, Bowers JE, Okashah RA, Taylor CA, Zhang D, Khanal S, Heesacker AF, Khalilian N, Farmer AD, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Stalker HT, Nielsen N, Ozias-Akins P, Knapp SJ (2012) A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genom 13:469
Naito Y, Suzuki S, Iwata Y, Kuboyama T (2008) Genetic diversity and relationship analysis of peanut germplasm using SSR markers. Breed Sci 58:293–300
Paik-Ro OG, Smith RL, Knauft DA (1992) Restriction fragment length polymorphism evaluation of six peanut species within the Arachis section. Theor Appl Genet 84:201–208
Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK (2012) Advances in Arachis genomics for peanut improvement. Biotechnol Adv 30:639–651
Peng JH, Lapitan NL (2005) Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct Integr Genomics 5:8–96
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135
Pfender WF, Saha MC, Johnson EA, Slabaugh MB (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122:1467–1480
Portis E, Nagy I, Sasvari Z, Stagel A, Barchi L, Lanteri S (2007) The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci 172:640–648
Qin H, Feng S, Chen C, Guo Y, Knapp S, Culbreath A, He G, Wang ML, Zhang X, Holbrook CC, Ozias-Akins P, Guo B (2012) An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations. Theor Appl Genet 124:653–664
Ramirez M, Graham M, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair M, Hernandez G, Vance C, Lara M (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 137:1211–1227
Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genom 13:3
Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726
Seijo G, Lavia GI, Fernandez A, Krapovickas A, Ducasse DA, Bertioli DJ, Moscone EA (2007) Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. Am J Bot 94:1963–1971
Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Robin Buell C, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7:e40563
Subramanian V, Gurtu S, Nageswara Rao RC, Nigam SN (2000) Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay. Genome 43:656–660
Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genome, survey and analysis. Genome Res 10:1967–1981
Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, van der Knaap E, Francis D (2007) Diversity in conserved genes in tomato. BMC Genom 8:465
van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD et al (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247–252
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55
Varshney RK, Grosse I, Hahnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L, Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows nonuniform distribution of genes in the barley genome. Theor Appl Genet 113:239–250
Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, Nigam SN, Moss BJ, Seetha K, Ravi K, He G, Knapp SJ, Hoisington DA (2009) The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet 118:729–739
Yang Z, Yoder AD (1999) Estimation of the transition/transversion rate bias and species sampling. J Mol Evol 48:274–283
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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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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DOI: https://doi.org/10.1007/s11032-015-0343-0