Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2016
Publication Date: 12/1/2016
Citation: Chopra, R., Burow, G.B., Chagoya, J., Simpson, C., Mudge, J., Burow, M. 2016. Transcriptome sequencing of diverse peanut (arachis) wild species and the cultivated species reveals a wealth of untapped genetic variability. Genes, Genomes, Genetics. 6:3825-3827. Interpretive Summary: The goal of this manuscript is show the applications of new sequencing technologies in combination with improved bioinformatics methods towards a better understanding of complex genomes such as peanut. A total of 306,820 variation at the nucleotide level (expressed as single nucleotide polymorphism, SNP) were identified across all 22 germplasm of peanut (composed of both diploid and tetraploid genotypes) utilized in the study. Notably, a high degree of genetic variability was observed in diploids, but there was low genetic variation among tetraploid germplasm. The variant nucleotides or SNPs were tested further to determine their utilities as possible markers for use in QTL mapping. A subset of 85 SNPs selected from the dataset was validated in two of the sequenced genotypes and 77.5% of the SNPs were confirmed. This report on variability for gene based SNPs among a diverse panel of 22 peanut germplasm provide a valuable genomic resource for general legume research with a focus on peanut breeding.
Technical Abstract: Next generation sequencing technologies and improved bioinformatics methods have provided opportunities to study sequence variability in complex polyploid transcriptomes. In this study, we used a diverse panel of twenty-two Arachis accessions representing seven Arachis hypogaea market classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species for sequencing transcriptomes and detection of polymorphisms. The realignment of individual reads to the contigs of the cultivar OLin enabled the detection of ca. 306,820 bi-allelic SNPs across all 22 genotypes. Diversity analysis based on these variants indicated grouping of diploids according to genome classifications, and the tetraploid subspecies of Arachis. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest accession belonged to the A genome species. A subset of 85 SNPs selected from the dataset was validated in two of the sequenced genotypes and 77.5% of the SNPs were confirmed. Understanding SNP variants in the Arachis accessions will benefit in developing markers for trait selection.