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.

Presence of resveratrol in wild Arachis species adds new value to this overlooked genetic resource

“…Besides genetic variability, variation in resveratrol production could also be explained by differences in the plant ages and conditions in which the experiments were carried out, since many physiological and environmental factors can influence the synthesis of secondary metabolites 44 – 46 , such as resveratrol. These factors can probably explain the differences on resveratrol content found for IAC Caiapó here and in a previous study that also analyzed leaves after UV exposure 18 .…”

Variant Amino Acid Residues Alter the Enzyme Activity of Peanut Type 2 Diacylglycerol Acyltransferases

“…There are many differences among peanut types with regard to traits such as oil content, seed color, size, and shape, as well as plant morphology. However, previous studies have come to different conclusions regarding the degree of variability at the level of genes, transcript levels, and single nucleotide polymorphisms in wild diploids compared to cultivated allotetraploid peanut species ( Chopra et al, 2016 ). The survey of AhDGAT2 sequences summarized in Supplementary Table S1 and Figure S1 suggests that both cultivated and wild peanut species collectively contain multiple isoforms of AhDGAT2, but all share highly conserved primary sequences and thus would likely contribute very little to any observed genetic variability.…”

Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

“…This approach is referred to as GATK in the following text. Raw transcriptome reads were used from 10 tetraploid accessions ( Supplementary Table S1 ), which were sequenced previously on an Illumina Ga IIx or HiSeq 2500 by Chopra et al [ 23 , 24 ]. A synthetic tetraploid genome reference was generated by concatenating A. duranensis V14167 and A. ipaënsis GKPSSc 30076 diploid genome sequences (pre-release sequences builds) from PeanutBase [ 10 , 25 ].…”