Dataset Information

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.).

ABSTRACT: Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

SUBMITTER: Zou K

PROVIDER: S-EPMC7822046 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (<i>Arachis hypogaea</i> L.).

Zou Kunyan K Kim Ki-Seung KS Kim Kipoong K Kang Dongwoo D Park Yu-Hyeon YH Sun Hokeun H Ha Bo-Keun BK Ha Jungmin J Jun Tae-Hwan TH

Genes 20201222 1

Peanut (<i>Arachis hypogaea</i> L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data ...[more]

PMID: 33375051

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Project description:BackgroundThe cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut.ResultsA recombinant inbred line (RIL) population was advanced from a cross between a cultivar 'Huayu36' and a germplasm line '6-13' with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16-31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits.ConclusionsThis study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.

Project description:BACKGROUND: Pre-harvest infection of peanuts by Aspergillus flavus and subsequent aflatoxin contamination is one of the food safety factors that most severely impair peanut productivity and human and animal health, especially in arid and semi-arid tropical areas. Some peanut cultivars with natural pre-harvest resistance to aflatoxin contamination have been identified through field screening. However, little is known about the resistance mechanism, which has slowed the incorporation of resistance into cultivars with commercially acceptable genetic background. Therefore, it is necessary to identify resistance-associated proteins, and then to recognize candidate resistance genes potentially underlying the resistance mechanism. RESULTS: The objective of this study was to identify resistance-associated proteins in response to A. flavus infection under drought stress using two-dimensional electrophoresis with mass spectrometry. To identify proteins involved in the resistance to pre-harvest aflatoxin contamination, we compared the differential expression profiles of seed proteins between a resistant cultivar (YJ-1) and a susceptible cultivar (Yueyou 7) under well-watered condition, drought stress, and A. flavus infection with drought stress. A total of 29 spots showed differential expression between resistant and susceptible cultivars in response to A. flavus attack under drought stress. Among these spots, 12 protein spots that consistently exhibited an altered expression were screened by Image Master 5.0 software and successfully identified by MALDI-TOF MS. Five protein spots, including Oso7g0179400, PII protein, CDK1, Oxalate oxidase, SAP domain-containing protein, were uniquely expressed in the resistant cultivar. Six protein spots including low molecular weight heat shock protein precursor, RIO kinase, L-ascorbate peroxidase, iso-Ara h3, 50 S ribosomal protein L22 and putative 30 S ribosomal S9 were significantly up-regulated in the resistant cultivar challenged by A. flavus under drought stress. A significant decrease or down regulation of trypsin inhibitor caused by A. flavus in the resistant cultivar was also observed. In addition, variations in protein expression patterns for resistant and susceptible cultivars were further validated by real time RT-PCR analysis. CONCLUSION: In summary, this study provides new insights into understanding of the molecular mechanism of resistance to pre-harvest aflatoxin contamination in peanut, and will help to develop peanut varieties with resistance to pre-harvested aflatoxin contamination.

Dataset Information

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.).

Publications

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (<i>Arachis hypogaea</i> L.).

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