Whole Genome Resequencing in Soybean Breeding: Research Progress

doi:10.11923/j.issn.2095-4050.cjas19020011

Abstract

Abstract:

Soybean is one of the most important oil crops in the world. With the rapid development and the wide application of gene sequencing technology, soybean breeding research has been deeply affected. This paper briefly described the main methods of gene sequencing and the whole genome resequencing application in soybean breeding and genetic transformation research, summarized the whole genome resequencing to study the molecular mechanisms of soybean breeding and disease development from the perspective of functions and structures of functional genes through discovering mutation sites, revealing evolutionary relationships, and mining functional genes. The study could provide certain reference for the research and application of the gene sequencing technology in the future.

Key words: Soybean Breeding, Whole Genome Resequencing, High-throughput Sequencing

CLC Number:

S565.1

Zhao Haihong, Guo Tai, Wang Zhixin, Zheng Wei, Li Candong, Xu Jiefei, Zhang Zhenyu, Zhao Xingqi, Wang Shiqiang. Whole Genome Resequencing in Soybean Breeding: Research Progress[J]. Journal of Agriculture, 2020, 10(12): 38-41.

References 41

[1]	殷瑞锋, 徐雪高, 张振. 2017年大豆市场形势分析与2018年展望[J]. 农业展望, 2017(12):4-7.
[2]	成升魁, 徐增让, 谢高地, 等. 中国粮食安全百年变化历程[J]. 农学学报, 2018,8(1):186-192.
[3]	李顺萍. 世界大豆生产布局及中国大豆对外依存度分析[J]. 世界农业, 2018(11):108-112.
[4]	原梓涵, 邵娜. 中美贸易摩擦对大豆市场的影响及前景分析[J]. 农业展望, 2018,10,89-93.
[5]	Schmutz J, Cannon S B, Schlueter J, et al. Genome sequence of the palaeopolyploid soybean[J]. Nature, 2010,463:178-183. doi: 10.1038/nature08670 URL pmid: 20075913
[6]	张彦威, 李伟, 张礼凤, 等. 基于重测序的大豆新品种齐黄34 的全基因组变异挖掘[J]. 中国油料作物学报, 2016,38(2):150-158. doi: 10.7505/j.issn.1007-9084.2016.02.003 URL
[7]	Park J, Lee Y, Kang B, Wi. Co-transformation using a negative selectable marker gene for the production of selectable marker gene-free transgenic plants[J]. Theoretical and Applied Genetics, 2004,109:1562-1567. doi: 10.1007/s00122-004-1790-x URL
[8]	Vidal J R, Kikkert J R, Wallace PGReisch B I. High-efficiency biolistic co-transformation and regeneration of 'Chardonnay' (Vitis vinifera L.) containing npt-II and antimicrobial peptide genes[J]. Plant Cell Reports, 2003,22(4):252-260. doi: 10.1007/s00299-003-0682-x URL
[9]	马潞林, 宋一萌, 葛力源. 基因测序技术的发展与临床应用概述[J]. 重庆医科大学学报, 2018,43(4):477-479.
[10]	Maxam A M, Gilbert W. A New Method for Sequencing DNA[J]. Proc Natl Acad Sci USA, 1977,74(2):560-564. doi: 10.1073/pnas.74.2.560 URL pmid: 265521
[11]	陶申童. 基于重测序的杨树基因组重组事件的研究[D]. 南京:南京林业大学, 2017.
[12]	Mardis E R. The impact of next-generation sequencing technology on genetics[J]. Trends in Genetics, 2008,24(3):133-141. doi: 10.1016/j.tig.2007.12.006 URL
[13]	Shendure J, Porreca G J, Reppas N B, et al. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome[J]. Science, 2005,309(5741):1728-1732. doi: 10.1126/science.1117389 URL pmid: 16081699
[14]	Pop M, Salzberg S L. Bioinformatics challenges of new sequencing technology[J]. Trend in Genetics, 2008,24(3):133-141. doi: 10.1016/j.tig.2007.12.007 URL
[15]	Steinmann K E, Hart C E, Thompson J F, et al. Helicos Single-molecule Sequencing of Bacterial Genomes[J]. Methods Mol Biol., 2011,733:3-24. doi: 10.1007/978-1-61779-089-8_1 URL pmid: 21431759
[16]	Ying Y L, Cao C, Long Y T. Single MoleculeAnalysis by Bio-logical Nanopore Sensors[J]. Analyst, 2014,139(16):3826-3835. doi: 10.1039/c4an00706a URL
[17]	Miten J, Hugh E. Olsen, Benedict Paten, et al. The Oxford Nanopore Min ION: delivery of nanopore sequencing to the genomics community[J]. Genome Biology, 2016,17(1):239. doi: 10.1186/s13059-016-1103-0 URL pmid: 27887629
[18]	Tyson J R, O'Neil N J, Jain M, et al. Min ION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome[J]. Genome Research, 2018,28:266-274. doi: 10.1101/gr.221184.117 URL pmid: 29273626
[19]	Giordano F, Aigrain L, Quail M A., et al. De novo yeast genome assemblies from Min ION, Pac Bio and Mi Seq platforms[J]. Scienific Reports, 2017,7(1):3935.
[20]	Haque F, Li J, Wu H C, et al. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA[J]. Nano Today, 2013,8(1):56-74. doi: 10.1016/j.nantod.2012.12.008 URL
[21]	冉洪. 厚壁毛竹种质性状的重测序研究[D]. 北京:中国林业科学研究院, 2016.
[22]	GOFF, Stephen A, RICKE, et al. A draft séquence of the rice genome (Oryza sativa L. ssp. japonica):The rice.genome[J]. Science, 2002,296(5565):92-100. doi: 10.1126/science.1068275 URL pmid: 11935018
[23]	Huang S, Li R, Zhang Z, et al. The genome of the cucumber, Cucumis sativus L[J]. Nature genetics, 2009,41(12):1275-81. doi: 10.1038/ng.475 URL pmid: 19881527
[24]	Schnable P S, Ware D, Fulton R S, et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics[J]. Science, 2009,326(5956):1112-5. doi: 10.1126/science.1178534 URL pmid: 19965430
[25]	Paterson A H, Bowers J E, Bruggmann R, et al. The Sorghum bicolor genome and the diversification of grasses[J]. Nature, 2009,457(7229):551-6. doi: 10.1038/nature07723 URL pmid: 19189423
[26]	陈璇, 郭蓉, 王璐, 等. 基于全基因组重测序的野生型大麻和栽培型大麻的多态性SNP分析[J]. 分子植物育种, 2018,16(3):893-897.
[27]	Barabaschi D, Tondelli A, Desiderio F, et al. Next generation breeding[J]. Plant Science, 2016,242:3-13. doi: 10.1016/j.plantsci.2015.07.010 URL pmid: 26566820
[28]	胡鸣, 姚圣黎, 程晓晖, 等. 基于高深度重测序的春性、半冬性和冬性甘蓝型油菜基因组遗传变异分析[J]. 中国油料作物学报, 2018,40(4):469-478.
[29]	任民, 程立锐, 刘旦, 等. 基于RAD 重测序技术开发烟草品种 SNP 位点[J]. 中国烟草科学, 2018,39(3):10-17.
[30]	Wang W S, Ramil M, Hu Z Q, et al. Genomic variation in 3010 diverse accessions of Asian cultivated rice[J]. Nature, 2018,557:43-49. doi: 10.1038/s41586-018-0063-9 URL pmid: 29695866
[31]	赵庆英, 张瑞娟, 王瑞良, 等. 基于名优谷子品种晋谷 21 全基因组重测序的分子标记开发[J]. 作物学报, 2018,44(5):686-696.
[32]	Lam H M, Xu X, et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection[J]. Nat Genet, 2010,42:1053-1059. doi: 10.1038/ng.715 URL pmid: 21076406
[33]	李泽锋. 一个中国南方野生大豆基因组深度测序及其分析[D]. 杭州:浙江大学, 2012.
[34]	Zhou L, Wang S B, Jian J, et al. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method[J]. Scientific Reports, 2015,5:9350. doi: 10.1038/srep09350 URL pmid: 25797785
[35]	Wu X, Zhou G, Chen Y, et al. Soybean cyst nematode resistance emerged via artificial selection of duplicated serine hydroxymethyltransferase genes[J]. Frontiers in Plant Science, 2016,7(17):998.
[36]	周航. 利用Gm ARR10 基因创制大豆新种质[D]. 贵阳:贵州大学, 2017.
[37]	葛逢勇. 抗大豆孢囊线虫4号生理小种的P1437654突变体的筛选与全基因组测序[D]. 北京:中国农业科学院, 2018.
[38]	张峰阁. 大豆结荚习性控制基因的遗传定位[D]. 北京:中国科学院大学, 2018.
[39]	Zhong-feng Li, Yong Guo, Lin Ou, et al. Identifcation of the dwarf gene GmDW1 in soybean (Glycine max L.) by combining mapping-by-sequencing and linkage analysis[J]. Theoretical and Applied Genetics, 2018,131:1001-1016. doi: 10.1007/s00122-017-3044-8 URL pmid: 29550969
[40]	Zeng H Q, Wang G P, Zhang Y Q, et al. Genome-wide identification of phosphate- deficiency- responsive genes in soybean roots by high-throughput sequencing[J]. Plant Soil, 2016,398:207-227. doi: 10.1007/s11104-015-2657-4 URL
[41]	朱晓岚. 黑豆抗胞囊线虫基因序列多样性及功能分析[D]. 沈阳:沈阳农业大学, 2017.