Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L.
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Single-nucleotide polymorphisms, which can be identified in the thousands or millions from comparisons of transcriptome or genome sequences, are ideally suited for making high-resolution genetic maps, investigating population evolutionary history, and discovering marker–trait linkages. Despite significant results from their use in human genetics, progress in identification and use in plants, and particularly polyploid plants, has lagged. As part of a long-term project to identify and use SNPs suitable for these purposes in cultivated peanut, which is tetraploid, we generated transcriptome sequences of four peanut cultivars, namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter, which represent the four major market classes of peanut grown in the world, and which are important economically to the US southwest peanut growing region. CopyDNA libraries of each genotype were used to generate 2 × 54 paired-end reads using an Illumina GAIIx sequencer. Raw reads were mapped to a custom reference consisting of Tifrunner 454 sequences plus peanut ESTs in GenBank, compromising 43,108 contigs; 263,840 SNP and indel variants were identified among four genotypes compared to the reference. A subset of 6 variants was assayed across 24 genotypes representing four market types using KASP chemistry to assess the criteria for SNP selection. Results demonstrated that transcriptome sequencing can identify SNPs usable as selectable DNA-based markers in complex polyploid species such as peanut. Criteria for effective use of SNPs as markers are discussed in this context.
KeywordsPeanut Groundnut Arachis Transcriptome SNP KASP
Expressed sequence tag
RNA integrity number
Transcriptome shotgun assembly
Restriction fragment length polymorphism
Amplified fragment length polymorphism
Simple sequence repeat
The authors wish to thank Jennifer Chagoya at Texas A&M AgriLife Research, and Halee Hughes and Nancy Layland at the USDA-ARS, Lubbock for technical support. This work was funded by grants from the Texas Peanut Producers Board award CY2008-Burow-TTU-Development to MDB and CES, and 2009-TTU-Burow-Genotyping to MDB, National Peanut Board grant #332/TX-99/1139 to MDB, and #332/TX-99/1213 to MDB and CES, Peanut Foundation grant 04-810-08 to MDB, Ogallala Aquifer Initiative award IPM12.06 to MDB, and United States Department of Agriculture/National Institute of Food and Agriculture Hatch Act award TEX08835 to MDB.
Conflict of interest
The authors declare that they have no conflict of interest. All experiments were performed in accordance with current biomedical research ethical standards in the US.
- Allen AM, Barker GL, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D’Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 9:1086–1099CrossRefPubMedGoogle Scholar
- Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Burow MD (2014) Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-seq data. PLoS ONE 9(12):e115055Google Scholar
- Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582CrossRefPubMedCentralPubMedGoogle Scholar
- Doyle JJ (2012) Polyploidy in Legumes. In: Soltis PS, Soltis DE (eds) Polyploidy and genome evolution. Springer, BerlinGoogle Scholar
- FAO, Food and Agriculture Organization of the United Nations (2012) FAOSTAT. Groundnuts (in Shell). http://faostat.fao.org/site/339/default.aspx. Accessed 28 Jan 2015
- Gautami B, Fonceka D, Pandey MK, Moretzsohn MC, Sujay V, Qin H, Hong Y, Faye I, Chen X, BhanuPrakash A, Shah TM, Gowda MVC, Nigam SN, Liang X, Hoisington DA, Guo B, Bertioli DJ, Rami J-F, Varshney RK (2012) An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS ONE 7:e41213CrossRefPubMedCentralPubMedGoogle Scholar
- Horn M, Eikenberry E, Romero-Lanuza J, Sutton J (2001) High stability peanut oil. US. Patent 6,214,405 AGoogle Scholar
- Khera P, Upadhyaya HD, Pandey MK, Roorkiwal M, Sriswathi M, Janila P, Guo Y, McKain MR, Nagy ED, Knapp SJ, Leebens-Mack J, Conner JA, Ozias-Akins P, Varshney RK (2013) Single nucleotide polymorphism–based genetic diversity in the reference set of peanut (spp.) by developing and applying cost-effective kompetitive allele specific polymerase chain reaction genotyping assays. Plant Genome 6:1–11CrossRefGoogle Scholar
- Knauft D, Ozias-Akins P (1995) Recent methods for germplasm enhancement and breeding. In: Pattee HE, Stalker HT (eds) Advances in peanut science. APRES, Stillwater, pp 54–94Google Scholar
- Knauft DA, Gorbet DW, Norden AJ, Norden CK (1997) Peanut oil from enhanced peanut products. US patent no 5,922,390 A. Accessed 27 Jan 2015Google Scholar
- Lopez Y, Nadaf HL, Smith OD, Connell JP, Reddy AS, Fritz AK (2000) Isolation and characterization of the Δ12-fatty acid desaturase in peanut (Arachis hypogaea L.) and search for polymorphisms for the high oleate trait in spanish market-type lines. Theor Appl Genet 101:1131–1138CrossRefGoogle Scholar
- Miller NA, Kingsmore SF, Farmer A, Langley RJ, Mudge J, Crow JA, Gonzalez AJ, Schilkey FD, Kim RJ, van Velkinburgh J, May GD, Black CF, Myers MK, Utsey JP, Frost NS, Sugarbaker DJ, Bueno R, Gullans SR, Baxter SM, Day SW, Retzel EF (2008) Management of high-throughput DNA sequencing projects: Alpheus. J Comput Sci Syst Biol 1:132CrossRefPubMedCentralPubMedGoogle Scholar
- 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 Genomics 13:469CrossRefPubMedCentralPubMedGoogle Scholar
- Pimratch S, Jogloy S, Toomsan B, Jaisil P, Sikhinarum J, Kesmala T, Patanothai P (2004) Evaluation of seven peanut genotypes for nitrogen fixation and agronomic traits Songklanakarin. J Sci Technol 26:295–304Google Scholar
- Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12:80CrossRefPubMedCentralPubMedGoogle Scholar
- Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami J-F, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume. Genomes DNA Res 20:173–184CrossRefGoogle Scholar
- Xiao-Ping R, Hui-Fang J (2010) Comparison of genetic diversity between peanut mini core collections from China and ICRISAT by SSR Markers. Acta Agronomica Sinica 36:1084Google Scholar
- Zhao Y, Prakash C, He G (2012) Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database. BMC Res Notes C7–362(5):1–7Google Scholar
- Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H (2014) Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics 15:351CrossRefPubMedCentralPubMedGoogle Scholar