文献类型：期刊文献

中文题名：Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq

作者：Mengjiao Chen[1,7] Weijuan Fan[2,7] Feiyang Ji[3,7] Hua Hua[1] Jie Liu[1] Mengxiao Yan[2] Qingguo Ma[3] Jiongjiong Fan[1] Qin Wang[1] Shufeng Zhang[1] Guiling Liu[4] Zhe Sun[4] Changgeng Tian[4] Fengling Zhao[4] Jianli Zheng[4] Qi Zhang[1] Jiaxin Chen[1] Jie Qiu[1] Xin Wei[1] Ziru Chen[5] Peng Zhang[6] Dong Pei[3] Jun Yang[2] Xuehui Huang[1]

第一作者：Mengjiao Chen

机构：[1]Shanghai Key Laboratory of Plant Molecular Sciences,College of Life Sciences,Shanghai Normal University,Shanghai 200234,China;[2]Shanghai Key Laboratory of Plant Functional Genomics and Resources,Shanghai Chenshan Plant Science Research Center,Chinese Academy of Sciences,Shanghai Chenshan Botanical Garden,Shanghai 201602,China;[3]State Key Laboratory of Tree Genetics and Breeding,Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration,Research Institute of Forestry,Chinese Academy of Forestry,Beijing 100091,China;[4]Tai'an Academy of Agricultural Sciences,Tai'an 271000,Shandong,China;[5]National Genomics Data Center,Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,CAS-MPG Partner Institute for Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China;[6]CAS Center for Excellence of Molecular Plant Sciences,Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai 200233,China;[7]These authors contributed equally to this article.

年份：2021

卷号：14

期号：4

起止页码：556-570

中文期刊名：分子植物：英文版

收录：CSTPCD;;Scopus;CSCD:【CSCD2021_2022】；PubMed;

基金：We are grateful to Prof.Lars M.Steinmetz for the Tn5 plasmid.This work was funded by the Ministry of Science and Technology of China(2016YFD0100902 to X.H.,2018YFD1000701 and 2019YFD1000703 to J.Y.);the National Natural Science Foundation of China(31825015 to X.H.);the Program of Shanghai Academic Research Leader(18XD1402900 to X.H.);the Innovation Program of the Shanghai Municipal Education Commission(2017-01-07-00-02-E00039 to X.H.);the Shanghai Municipal Afforestation&City Appearance and Environmental Sanitation Administration(G182402,G192413,G192414,and G202402 to J.Y.);the Youth Innovation Promotion Association CAS(to J.Y.);the State Key Laboratory of Tree Genetics and Breeding support Program(CAFYBB2019ZY001 to D.P.).

语种：英文

中文关键词：genotyping;genetic mapping;outcrossing;polyploid

分类号：S51

摘要：Many important crops(e.g.,tuber,root,and tree crops)are cross-pollinating.For these crops,no inbred lines are available for genetic study and breeding because they are self-incompatible,clonally propagated,or have a long generation time,making the identification of agronomically important genes difficult,particularly in crops with a complex autopolyploid genome.In this study,we developed a method,OutcrossSeq,for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population,and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations.We applied OutcrossSeq to a tuberous root crop(sweet potato,autopolyploid),a tree crop(walnut tree,highly heterozygous diploid),and hybrid crops(double-cross populations)to generate high-density genotype maps for the outcrossing populations,which enable precise identification of genomic loci underlying important agronomic traits.Candidate causative genes at these loci were detected based on functional clues.Taken together,our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species,including polyploids,in a cost-efficient way.The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.