LI Ting-yu,LI Yong-li,GAN Zhuo-ran,et al.Research Progress of Genome-Wide Association Studies in Soybean[J].Soybean Science,2020,39(03):479-484.[doi:10.11861/j.issn.1000-9841.2020.03.0479]
全基因组关联分析在大豆中的研究进展
- Title:
- Research Progress of Genome-Wide Association Studies in Soybean
- 文献标志码:
- A
- 摘要:
- 全基因组关联分析(GWAS)是目前发现复杂农艺性状相关遗传基础最有力和最有效的研究方法。随着遗传学的发展，基因分型、统计学方法等许多关键性技术的进步，以连锁不平衡为基础的全基因组关联分析应运而生。近年来GWAS在大豆复杂性状研究和作物育种中得到了广泛的应用。本研究在简要介绍GWAS的原理、流程的基础上，总结其在大豆重要农艺性状研究中取得的最新进展，最后讨论GWAS存在的问题和未来发展趋势，以期为进一步利用GWAS进行大豆遗传育种研究提供理论依据。
- Abstract:
- Genome wide association studies (GWAS) is the most powerful and effective method to find the genetic basis of complex agronomic traits. With the development of genetics, gene typing and statistical methods, genome-wide association analysis based on linkage disequilibrium came into being. In recent years, GWAS has been widely used in the research of soybean complex characters and crop breeding. Based on the brief introduction of GWAS′s principle and process, this paper summarizes its latest progress in the research of important agronomic characters of soybean, and finally discusses the existing problems and future development trend of GWAS, in order to provide theoretical basis for further research of soybean genetic breeding with GWAS.
参考文献/References:
［1］Zhang Y H, Liu M F, He J B, et al. Marker-assisted breeding for transgressive seed protein content in soybean ［Glycine max (L.) Merr.］［J］. Theoretical and Applied Genetics, 2015, 128(6): 1061-1072.［2］Juhi C, Patil G B, Humira S, et al. Expanding omics resources for improvement of soybean seed composition traits［J］. Frontiers in Plant Science, 2015, 6: 1021.［3］Risch N, Merikangas K. The future of genetic studies of complex human diseases［J］. Science, 1996, 273(5281): 1516-1517. ［4］Hansen M, Kraft T,Ganestam S, et al. Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers［J］. Genetical Research, 2001, 77(1): 61-66.［5］Aranzana M J, Kim S, Zhao K Y, et al. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes［J］. PLoS Genetics, 2005, 1(5): e60.［6］Wang M, Yan J, Zhao J, et al. Genome-wide association study (GWAS) of resistance to head smut in maize［J］. Plant Science, 2012, 196: 125-131.［7］Morris G P,Ramu P, Deshpande S P, et al. Population genomic and genome-wide association studies of agroclimatic traits in sorghum［J］. Proceedings of the National Academy of Sciences, 2013, 110(2): 453-458.［8］Alqudah A M, Sharma R, Pasam R K, et al. Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley［J］. PLoS One, 2014, 9(11): 113-120.［9］Wu J H,Feng F J, Lian X M, et al. Genome-wide association study (GWAS) of mesocotyl elongation based on resequencing approach in rice［J］. BMC Plant Biology, 2015, 15(1): 218.［10］Zhou Y, Tang H, Cheng M P, et al. Genome-wide association study for pre-harvest sprouting resistance in a large germplasm collection of Chinese wheat landraces［J］. Frontiers in Plant Science, 2017, 8 (93): 401.［11］Hatzig S V, Frisch M, Breuer F, et al. Genome-wide association mapping unravels the genetic control of seed germination and vigor in Brassica napus［J］. Frontiers in Plant Science, 2015, 6(221): 221.［12］Si W, Saleh A, lvaro C.I, et al. Combined use of genome-wide association data and correlation networks unravels key regulators of primary metabolism in Arabidopsis thaliana［J］. PLoS Genetics, 2016, 12(10): 1-36.［13］Schmutz J, Cannon S B,Chlueter J, et al. Genome sequence of the palaeopolyploid soybean［J］. Nature, 2010, 463(7278): 178-183.［14］Song Q,Hyten D L, Jia G, et al. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean［J］. PLoS One, 2013, 8(1): e54985.［15］Hsiao C F, Chiu Y F, Chiang F T, et al. Genome-wide linkage analysis of lipids in nondiabetic Chinese and Japanese from the SAPPHIRe family study［J］. American Journal of Hypertension, 2006, 19(12): 1270-1277.［16］Gaut B S, Long A D. The lowdown on linkage disequilibrium［J］. The Plant Cell, 2003, 15(7): 1502-1506.［17］王荣焕, 王天宇, 黎裕. 关联分析在作物种质资源分子评价中的应用［J］. 植物遗传资源学报, 2016, 8(3): 366-372. (Wang R H, Wang T Y, Li Y. Application of association analysis in molecular evaluation of crop germplasm resources［J］. Journal of Plant Genetic Resources, 2016, 8(3): 366-372.) ［18］Gaut B S, Long A D. The lowdown on linkage disequilibrium［J］. The Plant Cell, 2003, 15(7): 1502-1506.［19］Zondervan K T, Cardon L R. The complex interplay among factors that influence allelic association［J］. Nature Reviews Genetics, 2004, 5(2): 89-100. ［20］谭贤杰, 吴子恺, 程伟东, 等. 关联分析及其在植物遗传学研究中的应用［J］. 植物学报, 2011, 46(1): 108-118. (Tan X J, Wu Z F, Cheng D W, et al. Association analysis and its application in plant genetics［J］. Chinese Bulletin of Botany, 2011, 46 (1): 108-118.)［21］Myles S, Peiffer J, Brown P J, et al. Association mapping: Critical considerations shift from genotyping to experimental design［J］. Plant Cell, 2009, 21(8): 2194.［22］Flint-Garcia S A, Thuillet A C, Yu J M, et al. Maize association population: A high-resolution platform for quantitative trait locus dissection［J］. Plant Journal, 2005, 44(6): 1054-1064.［23］Kriz A L, Larkins B A. Molecular genetic approaches to maize improvement［M］. Germany: Springer Berlin Heidelberg, 2009: 365-369.［24］Purcell S, Neale B, Todd-Brown K, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses［J］. American Journal of Human Genetics, 2007, 81(3): 559-575.［25］Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: Software for association mapping of complex traits in diverse samples［J］. Bioinformatics, 2007, 23(19): 2633-2635.［26］Lyu H Y, Li H W, Fan R, et al. Genome-wide association study of dynamic developmental plant height in soybean［J］. Canadian Journal of Plant Science, 2017, 97(2): 308-315.［27］Jing Y, Zhao X, Wang J, et al. Identification of loci and candidate genes for plant height in soybean (Glycine max) via genome wide association study［J］. Plant Breeding, 2019, 138(6): 721-732.［28］Chang F G, Guo C, Zhang J et al. Genome-wide association studies for dynamic plant height and number of nodes on the main stem in summer sowing soybeans［J］. Frontiers in Plant Science, 2018, 9: 1184.［29］Shim S, Ha J, Kim M Y, et al. GmBRC1 is a candidate gene for branching in soybean ［Glycine max (L.) Merrill］［J］. Plant Genetics and Molecular Breeding, 2019, 20(1): 135.［30］Li Y H, Li D, Jiao Y Q, et al. Identification of loci controlling adaptation in Chinese soybean landraces via a combination of conventional and bioclimatic GWAS［J］. Plant Biotechnology Journal, 2019, 18(2): 389-401.［31］Pan L Y, He J B, Zhao T J, et al. Efficient QTL detection of flowering date in a soybean RIL population using the novel restricted two-stage multi-locus GWAS procedure［J］. Theoretical and Applied Genetics, 2018, 131(12): 2581-2599.［32］Zhang J P, Song Q J, Cregan P B, et al. Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm［J］. BMC Genomics, 2015, 16(1): 217.［33］Liu Z X, Li H H, Fan X H, et al. Phenotypic characterization and genetic dissection of growth period traits in soybean (Glycine max) using association mapping［J］. PLoS One, 2017, 256: 76-87.［34］Zhao X, Dong H R, Chang H, et al. Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean ［Glycine max (L.) Merrill］ ［J］. BMC Genomics, 2019, 20: 648.［35］Contreras R, Mora F, Mar O, et al. A genome-wide association study for agronomic traits in soybean using SNP markers and SNP-based haplotype analysis［J］. PLoS One, 2017, 12(2): e0171105.［36］Wen Z X, Boyse J F, Song Q J, et al. Genomic consequences of selection and genome-wide association mapping in soybean［J］. BMC Genomics, 2015, 16(1): 671.［37］Hu Z D, Kan G Z, Hu W, et al. Identification of loci and candidate genes responsible for pod dehiscence in soybean via genome-wide association analysis across multiple environments［J］. Frontiers in Plant Science, 2019, 10: 811.［38］Zhang T F, Teng F, Wu T T, et al. A combined linkage and GWAS analysis identifies QTLs linked to soybean seed protein and oil content［J］. International Journal of Molecular Sciences, 2019, 20(23): 5915.［39］Zhang K X, Liu S L, Li W B, et al. Identification of QTNs controlling seed protein content in soybean using multi-locus genome-wide association studies［J］. Frontiers in Plant Science, 2018, 9: 1690.［40］Zhang Y H, He J B, Meng S, et al. Identifying QTL-allele system of seed protein content in Chinese soybean landraces for population differentiation studies and optimal cross predictions［J］. Euphytica, 2018, 214(9): 157.［41］Li D, Zhao X, Han Y, et al. Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions［J］. Genomics, 2018, 111(1): 90-95.［42］Zhao X, Chang H, Feng L, et al. Genome-wide association mapping and candidate gene analysis for saturated fatty acid content in soybean seed［J］. Plant Breeding, 2019, 138: 588-598.［43］Zhang D, Zhang H Y, Hu Z B, et al. Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication［J］. PLoS Genetics, 2019, 15(7): e1008267.［44］Li S G, Xu H F, Yang J Y, et al. Dissecting the genetic architecture of seed protein and oil content in soybean from the Yangtze and Huaihe River Valleys using multi-locus genome-wide association studies［J］. International Journal of Molecular Sciences, 2019, 20(12): 3041.［45］Hwang E Y, Song Q, Jia G, et al. A genome-wide association study of seed protein and oil content in soybean［J］. BMC Genomics, 2014, 15(1): 1.［46］Dhanapal A, Ray J, Singh S, et al. Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean ［Glycine max (L.) Merr.］ genotypes［J］. Theoretical and Applied Genetics, 2015, 128(1): 73-91.［47］Zhang W, Liu X L, Cui Y M, et al. A cation diffusion facilitator, GmCDF1, negatively regulates salt tolerance in soybean［J］. PLoS Genetics, 2019, 15(1): e1007798.［48］Mamidi S, Lee R K, Goos J R, et al. Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max)［J］. PLoS One, 2014, 9(9): e107469.［49］Zhang D, Song H, Cheng H, et al. The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress［J］. PLoS Genetics, 2014, 10(1): e1004061.［50］Wen Z, Tan R, Zhang S, et al. Integrating GWAS and gene expression data for functional characterization of resistance to white mold in soybean［J］. Plant Biotechnology Journal, 2018, 16(11): 1825-1835.［51］Zhang J, Wen Z, Li W, et al. Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars［J］. Molecular Breeding, 2017, 37(5): 60.［52］Santos J, Ferreira E, Passianotto A, et al. Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development［J］. BMC Genomics, 2019, 20(1): 798.［53］Chu S S, Wang J, Zhu Y, et al. An R2R3-type MYB transcription factor, GmMYB29, regulates isoflavone biosynthesis in soybean［J］. PLoS Genetics, 2017, 13(5): e1006770.［54］Contreras R, Mora F, Mar O, et al. A Genome-wide association study for agronomic traits in soybean using SNP markers and SNP-based haplotype analysis［J］. PLoS One, 2017, 12(2): e0171105.［55］Yu J, Holland J B, Mc Mullen M D, et al. Genetic design and statistical power of nested association mapping in maize［J］. Genetics, 2008, 178(1): 539-551.［56］Yang J, Jiang H, Yeh C T, et al. Extreme-phenotype genome-wide association study (XP-GWAS): A method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel［J］. The Plant Journal, 2015, 84(3): 587-596.［57］Huang X, Wei X, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces［J］. Nature Genetics, 2010, 42(11): 961-967.［58］Stacey J W, Joanna M B. Gene-environment interactions in Genome-Wide Association studies: Current approaches and new directions［J］. Journal of Child Psychology and Psychiatry, 2013, 54(10): 1120-1134.［59］Yang Q, Wu H S, Guo C Y, et al. Analyze multivariate phenotypes in genetic association studies by combining univariate as sociation tests［J］. Genetic Epidemiology, 2010, 34(5): 444-454.
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