Identification of Single Nucleotide Polymorphisms (SNPs) in Arachis (Peanut) Wild Species and Cultivated Accessions by Solexa Transcriptome Sequencing and Utilization of SNPs for Linkage Mapping in an Arachis A Genome Diploid F2 Population

We report the utilization of de novo assembly for tetraploid and diploid peanut to achieve optimal quality transcriptome references using three different assemblers – Trinity, TransAByss and SOAPdenovo-trans. Results of de novo assembly were used to carry out SNP identification in a panel of twenty two accessions of the Arachis genus, including cultivars representing Arachis hypogaea subsp. hypogaea - var. hypogaea, var. hirsuta, and Arachis hypogaea subsp. fastigiata - var. fastigiata, var. vulgaris, var. peruviana, and var. aequtoriana, and wild species representing the A-, B-, and K- genomes, a wild tetraploid – Arachis monticola, and a synthetic amphidiploid - TxAG-6. SNPs identified in the panel provided an insight into the extent of transcript polymorphism present in the genus. Expression analysis performed on three allopolyploids with their ancestral diploid genome donors indicated that B-genome transcripts of the tetraploids were expressed in a pattern more closely related to the B- genome diploids. Validation of SNP calls was performed using allele-specific chemistry on a LightCycler 480. Polymorphic SNPs between A. duranensis x A. cardenasii from the above dataset were used to develop a genetic map on LightCycler 480 and on a high-throughput genotyping platform the Fluidigm Biomark HD. A total of 31 QTLs using composite interval mapping were identified for ten plant architectural traits such as leaf measurements, main stem height, presence of main stem flowers, and seed weight. In summary, this study generated a transcriptome resource for twenty-two peanut accessions and provided an insight into transcript variability in peanut accessions. Also, the genetic map and QTL studies provide a base to assist future utilization of the transcript-based SNPs in peanut.