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

Wang, X and Xu, P and Yin, L and Ren, Y and Li, S and Shi, Y and Alcock, T D and Xiong, Q and Qian, W and Chi, X and Pandey, M K and Varshney, R K and Yuan, M (2018) Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.). Plant Molecular Biology Reporter (TSI). pp. 1-12. ISSN 0735-9640

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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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals
Uncontrolled Keywords: Peanut, Seed oil content, Insertion/deletion (InDel), Genome-wide association study, GWAS, Differentially expressed genes, DEGs, Oil content, Phenotypic Variation, Genotyping
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 27 Jun 2018 08:20
Last Modified: 27 Jun 2018 08:20
URI: http://oar.icrisat.org/id/eprint/10776
Official URL: http://dx.doi.org/10.1007/s11105-018-1088-9
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: This work was supported by the grants from the National High Technology Research and Development Program of China (No.2013AA102602); the Agricultural Scientific And Technological Innovation Project of Shandong Academy of Agricultural Sciences (No.CXGC2016B02); the National Natural Science Foundation of China (No.31471533); the National Ten Thousand Youth Talents Plan of 2014 (No. W02070268); and the China Agriculture Research System (No.CARS-13). The work reported in this article was undertaken as a part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of the CGIAR.
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