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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #298156

Title: Transcriptome analysis of SNPs in an array of peanut cultivated and wild species accession using illumina sequencing

item CHOPRA, RATAN - Texas Tech University
item Burow, Gloria
item FARMER, ANDREW - National Center For Genome Resources
item MUDGE, JOANN - National Center For Genome Resources
item LINDQUIST, INGRID - National Center For Genome Resources
item SIMPSON, CHARLES - West Texas A & M University
item Xin, Zhanguo
item WILKINS, THEA - Texas Tech University
item BUROW, MARK - Texas Tech University

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 4/15/2013
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Sequences of four previously-sequenced A. hypogaea cultivars representing all four U.S. market types (approx. 40 million reads each) were aligned to a reference of 46,813 contigs, generated by combining of ESTs and Transcriptome Shotgun Assembly of A. hypogaea, and 36,102 contigs were identified. An N50 read length of ca. 500bp was obtained using the Alpheus software. From 4,370 to 6,922 SNPs distinguishing pairwise combination of the cultivars were found. Initial attempts to validate these using Kasp primers has indicated high repeatability as long as the parameters for SNP selection are sufficiently stringent. However, screening against an array of 48 accessions suggested the presence of additional alleles. For this reason, total RNA was isolated from shoot, root, and pod tissue of 18 additional accessions of peanut, including 8 tetraploid cultivars, minicore accessions, or landraces, representing all seven botanical types, plus 8 diploid wild species representing the A, B, and K genomes of section Arachis, plus the tetraploid A. monticola and the TxAG-6 amphidiploid. Sequencing (2x50) was performed on an Illumina HiSeq 2000. A minimum of 13 million reads was obtained per diploid species, and at least 20 million reads were obtained per tetraploid accession. Preliminary analyses of A. cardenasii K38901 using SOAP, ABYSS and Trinity have resulted in longer read lengths than obtained previously, with N50 values for 25kmer ranging from 982 to 1200 bases, with from 29K to 37K contigs for Abyss and SOAP, respectively. Analyses of the additional sequences is underway, and efforts will be made to develop A-, B-, and K-genome specific contigs. We expect that data will eventually be useful in development of rapid marker assays for introgression of alleles from wild species via synthetic amphidiploids. In addition, data should be useful for accurate classification of transcriptome sequences of tetraploids to A or B genomes, which will allow proper genomic assignment of SNPs among cultivated peanut accessions, facilitating assays for homologous SNPs.