文献类型：期刊文献

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

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

第一作者：Chen, Mengjiao

通信作者：Huang, XH[1];Yang, J[2];Pei, D[3];Zhang, P[4]

机构：[1]Shanghai Normal Univ, Coll Life Sci, Shanghai Key Lab Plant Mol Sci, Shanghai 200234, Peoples R China;[2]Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, Shanghai Key Lab Plant Funct Genom & Resources, Shanghai Chenshan Bot Garden, Shanghai 201602, Peoples R China;[3]Chinese Acad Forestry, Res Inst Forestry, State Key Lab Tree Genet & Breeding, Key Lab Tree Breeding & Cultivat State Forestry &, Beijing 100091, Peoples R China;[4]Taian Acad Agr Sci, Tai An 271000, Shandong, Peoples R China;[5]Chinese Acad Sci, CAS MPG Partner Inst Computat Biol, Shanghai Inst Nutr & Hlth, Natl Genom Data Ctr,Biomed Big Data Ctr,CAS Key L, Shanghai 200031, Peoples R China;[6]Chinese Acad Sci, CAS Ctr Excellence Mol Plant Sci, Inst Plant Physiol & Ecol, Shanghai Inst Biol Sci, Shanghai 200233, Peoples R China

年份：2021

卷号：14

期号：4

起止页码：556-570

外文期刊名：MOLECULAR PLANT

收录：;Scopus(收录号：2-s2.0-85100401976);WOS:【SCI-EXPANDED(收录号:WOS:000637322000010)】；

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.), and the State Key Laboratory of Tree Genetics and Breeding support Program (CA-FYBB2019ZY001 to D.P.).

语种：英文

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

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.YY