eprintid: 11372
rev_number: 9
eprint_status: archive
userid: 3170
dir: disk0/00/01/13/72
datestamp: 2020-02-14 05:56:47
lastmod: 2020-02-14 05:56:47
status_changed: 2020-02-14 05:56:47
type: article
metadata_visibility: show
creators_name: Huang, L
creators_name: Liu, X
creators_name: Pandey, M K
creators_name: Ren, X
creators_name: Chen, H
creators_name: Xue, X
creators_name: Liu, N
creators_name: Huai, D
creators_name: Chen, Y
creators_name: Zhou, X
creators_name: Luo, H
creators_name: Chen, W
creators_name: Lei, Y
creators_name: Liu, K
creators_name: Xiao, Y
creators_name: Varshney, R K
creators_name: Liao, B
creators_name: Jiang, H
icrisatcreators_name: Pandey, M K
icrisatcreators_name: Varshney, R K
affiliation: Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of AgriculturalSciences, (Wuhan)
affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, (Wuhan)
affiliation: Novogene Bioinformatics Technology Co., Ltd, (Beijing)
affiliation: ICRISAT (Patancheru)
country: China
country: India
title: Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut
ispublished: pub
subjects: s1.3
subjects: s2.13
subjects: s355
divisions: CRPS3
crps: CG1
full_text_status: public
keywords: Expression Quantitative Trait Loci (eQTLs), Peanut, Gene Expression Variation, RNA-based Sequencing (RNA-seq), Testa colour
note: 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.
abstract: 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.
date: 2019-09
date_type: published
publication: Plant Biotechnology Journal (TSI)
volume: 18
number: 3
publisher: Wiley Open Access
pagerange: 779-790
id_number: doi:10.1111/pbi.13246
refereed: TRUE
issn: 1467-7644
official_url: https://doi.org/10.1111/pbi.13246
related_url_url: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=10.1111%2Fpbi.13246&btnG=
related_url_type: pub
citation:   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     
document_url: http://oar.icrisat.org/11372/1/pbi.13246.pdf