Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.)

Abstract

Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs.Electronic supplementary materialThe online version of this article (10.1007/s11105-018-1088-9) contains supplementary material, which is available to authorized users.

High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.)

“…A total of seven QTLs on five LGs were identified in the current study (Table 4). Previous studies have also observed that the trait of oil content was controlled by multiple QTLs, indicating that oil content is polygenetically inherited (Pandey et al 2014;Shasidhar et al 2017;Wang et al 2018a;Wilson et al 2017). According to the physical position of linked markers in the reference genomes of the two diploids, seven QTLs in the present study were mapped to pseudomolecules A04, A05, and A08 in A. duranensis, and to pseudomolecules B05 and B04 in A. ipaensis.…”

“…According to the physical position of flanking markers, annotated information on the putative genes in the QTL interval was downloaded from PeanutBase (https ://www.peanu tbase .org/home). Differentially expressed genes between high-oil cultivars and low-oil cultivars were obtained from Wang et al (2018a).…”

“…In Sub D, more than half of the genes were predominantly expressed in seeds at different developmental stages. In addition, 36 genes in the QTL intervals have been reported to be differentially expressed between high-oil cultivars and low-oil cultivars (Wang et al 2018a). Of these 36 genes, three oil-related genes and one transcription factor gene were upregulated in high-oil cultivars (Table S3).…”

Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance

“…The population structure and relative kinship were calculated by the genotype of association panel, and then used in five GWAS statistical methods to control false-positive results. Similar to other studies using peanuts [37,38], the 99 accessions of the Chinese mini-mini core collection in this study were classified into two subgroups (Figure 3). Breeding for peanut varieties for resistance to aflatoxin contamination is the most effective approach for reducing hazards by aflatoxin.…”

Dissection of the genetic basis of oil content in Chinese peanut cultivars by association mapping

“…This genetic method has been successfully used to reveal the genetic basis of complex agronomic traits in multiple crops [17][18][19][20]. In peanut, the limited works on association analysis were conducted to evaluate genetic variation in diverse germplasm [21,22].…”