title: Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability.
abstract: To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.
authors.affiliation: Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas 79409.
authors.forename: Ratan
authors.initials: R
authors.lastname: Chopra
authors.affiliation: United States Department of Agriculture, Agriculture Research Service, Cropping Systems Research Laboratory, Lubbock, Texas 79415.
authors.forename: Gloria
authors.initials: G
authors.lastname: Burow
authors.affiliation: Texas A&M AgriLife Research, Stephenville, Texas 76401.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Simpson
authors.affiliation: Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas 79409.|Texas A&M AgriLife Research, Lubbock, Texas 79403.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Chagoya
authors.affiliation: National Center for Genome Resources, Santa Fe, New Mexico 87505.
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.affiliation: Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas 79409 mburow@tamu.edu.|Texas A&M AgriLife Research, Lubbock, Texas 79403.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Burow
mesh_terms: D000483:Alleles; D010367:Arachis / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D059467:Transcriptome
keywords: SNPs; alleles; domestication; evolution; groundnut