|CHOPRA, RATAN - Texas Tech University|
|FARMER, ANDREW - National Center For Genome Resources|
|MUDGE, JOANN - National Center For Genome Resources|
|SIMPSON, CHARLES - Texas A&M Agrilife|
|WILKINS, THEA - Texas Tech University|
|BARING, MICHAEL - Texas A&M Agrilife|
|PUPPALA, NAVEEN - New Mexico State University|
|BUROW, MARK - Texas A&M Agrilife|
Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2014
Publication Date: 2/7/2015
Citation: Chopra, R., Burow, G.B., Farmer, A., Mudge, J., Simpson, C.E., Wilkins, T.A., Baring, M.R., Puppala, N., Chamberlin, K.D., Burow, M.D. 2015. Next-generation transcriptome sequencing, SNP discovery, and SNP validation in four market classes of peanut, Arachis hypogaea L. Molecular Genetics and Genomics. 290(3):1169-1180.
Technical Abstract: Single nucleotide polymorphisms are ideally suited for making high-resolution genetic maps, investigating population evolutionary history, and discovering marker–trait linkages. With advances in sequencing technologies, it is possible to identify thousands or millions of SNPs from transcriptomes or genomes. To identify SNPs suitable for these purposes in cultivated peanut, we generated transcriptome sequences of four peanut cultivars, namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter, which are economically important to the U.S. Southwest peanut growing region, and which represent the four major market classes of peanut grown in the world. CopyDNA libraries of each genotype were used to generate 2x54 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 43,081 contigs, and 302,181 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. Selecting SNPs based on polymorphism alone can create ambiguity in tetraploids, unless there is high read support or the selected gene is present as a single copy.