Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut

Huang, L and Liu, X and Pandey, M K and Ren, X and Chen, H and Xue, X and Liu, N and Huai, D and Chen, Y and Zhou, X and Luo, H and Chen, W and Lei, Y and Liu, K and Xiao, Y and Varshney, R K and Liao, B and Jiang, H (2019) Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut. Plant Biotechnology Journal (TSI), 18 (3). pp. 779-790. ISSN 1467-7644

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The transcriptome connects genome to the gene function and ultimate phenome in biology. Sofar, transcriptomic approach was not used in peanut for performing trait mapping in bi-parentalpopulations. In this research, we sequenced the whole transcriptome in immature seeds in apeanut recombinant inbred line (RIL) population and explored thoroughly the landscape oftranscriptomic variations and its genetic basis. The comprehensive analysis identified total49 691 genes in RIL population, of which 92 genes followed a paramutation-like expressionpattern. Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and15 837 distant eQTLs contributing to the whole-genome transcriptomic variation in peanut.There were 94 eQTL hot spot regions detected across the genome with the dominance of distanteQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putativecandidate gene and developed a linked marker InDel02 underlying a major QTL responsible forpurple testa colour in peanut. Our result provided a first understanding of genetic basis of whole-genome transcriptomic variation in peanut and illustrates the potential of the transcriptome-aidapproach in dissecting important traits in non-model plants.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Expression Quantitative Trait Loci (eQTLs), Peanut, Gene Expression Variation, RNA-based Sequencing (RNA-seq), Testa colour
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Others > Legume Crops
Depositing User: Mr Arun S
Date Deposited: 14 Feb 2020 05:56
Last Modified: 14 Feb 2020 05:56
Official URL:
Acknowledgement: This work was financially supported by National Peanut IndustryTechnology System Construction (CARS-13), National NaturalScience Foundation of China (31761143005), the Plant Germ-plasm Resources Sharing Platform (NICGR2019-036) and theNational Program for Crop Germplasm Protection of China(2019NWB033). This work has been undertaken as part of theCGIAR Research Program on Grain Legumes and Dryland Cereals(GLDC). ICRISAT is a member of CGIAR Consortium. The fundershad no role in study design, data collection and analysis, decisionto publish, or preparation of the manuscript.
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