栽培大豆农艺性状的关联分析及优异等位变异挖掘

doi:10.3864/j.issn.0578-1752.2014.20.002

Abstract

Abstract: 【Objective】Mining stable quantitative trait loci (QTL), their novel alleles and the corresponding accessions for agronomic traits in soybean can provide important foundation for subsequent studies, such as molecular marker assisted selection and molecular breeding by design. 【Method】There were 135 simple-sequence repeat (SSR) markers uniformly distributed on the soybean genome which were used to scan 257 soybean cultivars obtained by stratified random sampling from six geographic ecotypes in China so that molecular marker information was gotten. Plant height, number of branches, number of nodes on main stem, stem diameter and number of pods per plant for each cultivar were measured at Jiangpu Experimental Station of Nanjing Agricultural University in 2009 and 2010 so that their phenotypic observations were obtained. The above phenotypic observations for each trait, along with the above molecular marker information, in the 257 soybean cultivars were used to carry out association analysis using generalized linear model (GLM), enriched compression mixed linear model (ECMLM) and epistatic association mapping (EAM) approaches. 【Result】Coefficients of variation for the above traits ranged from 24.62% to 52.34%, and significant differences at the 0.01 level among cultivars and for cultivar-by-environment interaction were observed, indicating abundant genetic variation in the mapping population. Forty-seven, eleven and fifty-eight commonly main-effect QTL across two years were detected by the above three approaches, respectively. Four (thirty-four) commonly main-effect QTL were identified across the above three (two) methods. One epistatic QTL and 32 QTL-by-environment interactions were identified by epistatic association mapping. Eighteen QTL identified in this study were consistent with (or linked to) those in previous studies. Some novel alleles for each agronomic trait and their corresponding accessions were mined. For example, satt669-145bp, satt102-154bp, satt382-395 bp and satt534-161bp were novel alleles for number of nodes on main stem, number of branches, stem diameter and plant height, respectively; and the corresponding accessions were Baihuadou, Hefeiliangtangjiaoshuangqingdou, Youhulu and Puxiadadou. 【Conclusion】One hundred and seven stable main-effect QTL for the above traits were detected across years or across methods.

Key words: soybean, agronomic trait, simple-sequence repeat, association mapping, quantitative trait locus, novel allele

YANG Sheng-xian, NIU Yuan, LI Meng, WEI Shi-ping, LIU Xiao-fen, Lü Hai-yan, ZHANG Yuan-ming. Association Mapping of Agronomic Traits in Soybean (Glycine max L. Merr.) and Mining of Novel Alleles[J].Scientia Agricultura Sinica, 2014, 47(20): 3941-3952.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2014.20.002

https://www.chinaagrisci.com/EN/Y2014/V47/I20/3941

References

[1] 于凤瑶, 辛秀君, 张代军, 周顺启, 邱红梅. 群体分布与大豆农艺性状关系的研究. 草业科学, 2010, 27(10): 114-120.

Yu F Y, Xin X J, Zhang D J, Zhou S Q, Qiu H M. Relati-onship between group distribution and agronomic traits in Clycine max. Pratacultural Science, 2010, 27(10): 114-120. (in Chinese)

[2] 吴晓雷, 王永军, 贺超英, 陈受宜, 盖钧镒, 王学臣. 大豆重要农艺性状的QTL分析. 遗传学报, 2001, 28(10): 947-955.

Wu X L, Wang Y J, He C Y, Chen S Y, Gai J Y, Wang X C. QTLs mapping of some agronomic traits of soybean. Journal of Genetics and Genomics, 2001, 28(10): 947-955. (in Chinese)

[3] Mansur L M, Orf J H, Chase K, Jarvik T, Creganand P B, Lark K G. Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Science, 1996, 36: l327-1336.

[4] Hnetkovsky N, Chang S J C, Double T W, Gibson P T, Lightfoot D A. Genetic mapping of loci underlying field response to soybean sudden death syndrome (SDS). Crop Science, 1996, 36: 393-400.

[5] 刘春燕, 齐照明, 韩冬伟, 单大鹏, 蒋洪蔚, 陈庆山, 胡国华. 大豆产量相关性状的多年多点QTL分析. 东北农业大学学报, 2010, 11: 1-9.

Liu C Y, Qi Z M, Han D W, Shan D P, Jiang H W, Chen Q S, Hu G H. QTL analysis of yield components on soybean under different environment. Journal of Northeast Agricultural University, 2010, 11: 1-9. (in Chinese)

[6] 王春娥, 盖钧镒, 傅三雄, 喻德跃, 陈受宜. 大豆豆腐和豆乳得率的遗传分析与QTL定位. 中国农业科学, 2008, 45(5): 1274-1282.

Wang C E, Gai J Y, Fu S X, Yu D Y, Chen S Y. Inheritance and QTL mapping of tofu and soymilk output in soybean. Scientia Agricultura Sinica, 2008, 45(5): 1274-1282. (in Chinese)

[7] 文自翔, 赵团结, 郑永战, 刘顺湖, 王春娥, 王芳, 盖钧镒. 中国栽培和野生大豆农艺品质性状与SSR标记的关联分析: Ⅰ群体结构及关联标记. 作物学报, 2008, 34(7): 1169-1178.

Wen Z X, Zhao T J, Zheng Y Z, Liu S H, Wang C E, Wang F, Gai J Y. Association analysis of agronomic and quality traits with SSR markers in Glycine max and Glycine soja in China: Ⅰ Population structure and associated markers. Acta Agronomica Sinica, 2008, 34(7): 1169-1178. (in Chinese)

[8] Jun T H, Van K, Kim M Y, Lee S H. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica, 2008, 162: 179-191.

[9] Shi A, Chen P, Zhang B, Hou A. Genetic diversity and association analysis of protein and oil content in foodgrade soybeans from Asia and the United States. Plant Breeding, 2010, 129: 250-256.

[10] Li Y H, Smulders M J M, Chang R Z, Qiu L J. Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis. Conservation Genetics, 2011, 12: 1145-1157.

[11] Niu Y, Xu Y, Liu X F, Yang S X, Wei S P, Xie F T, Zhang Y M. Association mapping for seed size and shape traits in soybean cultivars. Molecular Breeding, 2013, 31(4): 785-794.

[12] 范虎, 文自翔, 王春娥, 王芳, 邢光南, 赵团结, 盖钧镒. 中国野生大豆群体农艺加工性状与SSR关联分析和特异材料的遗传构成. 作物学报, 2013, 39(5): 775-788.

Fan H, Wen Z X, Wang C E, Wang F, Xing G N, Zhao T J, Gai J Y. Association analysis between agronomic-processing traits and SSR markers and genetic dissection of specific accessions in Chinese wild soybean population. Acta Agronomica Sinica, 2013, 39(5): 775-788. (in Chinese)

[13] 伍宝朵, 陈海峰, 郭丹丹, 沙爱华, 单志慧, 张晓娟, 杨中路, 邱德珍, 陈水莲, 朱晓玲, 张婵娟, 周蓉, 周新安. 大豆种质资源叶型和荚粒性状的关系及与SSR标记的关联分析. 作物学报, 2012, 38(7): 1196-1204.

Wu B D, Chen H F, Guo D D, Sha A H, Shan Z H, Zhang X J, Yang Z L, Qiu D Z, Chen S L, Zhu X L, Zhang C J, Zhou R, Zhou X A. Relationship of leaflet shape, pod traits and association with SSR markers in soybean germplasm. Acta Agronomica Sinica, 2012, 38(7): 1196-1204. (in Chinese)

[14] 简爽, 文自翔, 李海朝, 袁道华, 李金英, 张辉, 叶永忠, 卢为国. 运用关联分析定位栽培大豆蛋白11S、7S组分的相关基因位点. 作物学报, 2012, 38(5): 820-828.

Jian S, Wen Z X, Li H C, Yuan D H, Li J Y, Zhang H, Ye Y Z, Lu W G. Identification of QTLs for glycinin (11S) and β-Conglycinin (7S) fractions of seed storage protein in soybean by association mapping. Acta Agronomica Sinica, 2012, 38(5): 820-828. (in Chinese)

[15] 魏世平, 刘晓芬, 杨胜先, 吕海燕, 牛远, 章元明. 中国栽培大豆群体结构不同分类方法的比较. 南京农业大学学报, 2011, 34(2): 13-17.

Wei S P, Liu X F, Yang S X, Lü H Y, Niu Y, Zhang Y M. Comparison of various clustering methods for population structure in Chinese cultivated soybean (Glycine max (L.) Merr.). Journal of Nanjing Agricultural University, 2011, 34(2):13-17. (in Chinese)

[16] Saghai-Maroof M A, Soliman K M, Jorgensen R A, Allard R W. Ribisomal DNA space-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the USA, 1984, 81: 8014-8018.

[17] 邱丽娟, 常汝镇. 大豆种质资源描述规范和数据标准. 北京: 中国农业出版社, 2006.

Qiu L J, Chang R Z. Descriptors and Data Stan-dard for Soybean(Glycine spp.). Beijing: Chinese Agriculture Press, 2006. (in Chinese)

[18] Bradbury P J, Zhang Z W, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. TASSEL：Software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23: 2633-2635.

[19] 李梦. 水稻分蘖功能作图和压缩混合线性模型方法优化的研究[D]. 南京: 南京农业大学, 2012.

Li M. Functional mapping of rice tillering and optimization of compression mixed linear model approach[D]. Nanjing: Nanjing Agricultural University, 2012. (in Chinese)

[20] Lü H Y, Liu X F, Wei S P, Zhang Y M. Epistatic association mapping in homozygous crop cultivars. PLoS ONE, 2011, 6(3): 1-10.

[21] Song Q J, Marek L F, Shoemaker R C, Lark K G, Concibido V C, Delannay X, Specht J E, Cregan P B. A new integrated genetic linkage map of the soybean. Theoretical and Applied Genetics, 2004, 109: 122-128.

[22] Voorrips R E. MapChart: Software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 2002, 93: 77-78.

[23] Sun D S, Li W B, Zhang Z C, Chen Q S, Ning H L, Qiu LJ, Sun G L. Quantitative trait loci analysis for the developmental behavior of Soybean (Glycine max L. Merr.). Theoretical and Applied Genetics, 2006, 112: 665-673.

[24] Chen Q, Zhang Z, Liu C, Xin D, Qiu H, Shan D, Shan C, Hu G. QTL analysis of major agronomic traits in soybean. Agricultural Sciences in China, 2007, 6(4): 399-405.

[25] Kabelka E A, Diers B W, Fehr W R, LeRoy A R, Baianu I C, You T, Neece D J, Nelson R L. Putative alleles for increased yield from soybean plant introductions. Crop Science, 2004, 44(3): 784-791.

[26] Wang D, Graef G, Procopiuk A, Diers B. Identification of putative QTL that underlie yield in interspecific soybean backcross populations. Theoretical and Applied Genetics, 2004, 108(3): 458-467.

[27] Kim K S, Diers B W, Hyten D L, Rouf Mian M A, Shannon J G, Nelson R L. Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations. Theoretical and Applied Genetics, 2012, 125: 1353-1369.

[28] Li D, Pfeiffer T, Cornelius P. Soybean QTL for yield and yield components associated with glycine soja alleles. Crop Science, 2008, 48: 571-581.

[29] Zhang D, Cheng H, Wang H, Zhang H, Liu C, Yu D. Identification of genomic regions determining flower and pod numbers development in soybean (Glycine max L.). Journal of Genetics and Genomics, 2010, 37(8): 545-556.

[30] 高静瑶, 刘春燕, 蒋洪蔚, 胡国华, 陈庆山. 多环境下大豆单株荚数性状的QTL分析. 中国油料作物学报, 2012, 34(1): 1-7.

Gao J Y, Liu C Y, Jiang H W, Hu G H, Chen Q S. QTL analysis of pod number per plant in soybean under multiple locations. Chinese Journal of Oil Crop Sciences, 2012, 34(1): 1-7. (in Chinese)

[31] 蒋春志, 裴翠娟, 荆慧贤, 张孟臣, 王涛, 邸锐, 刘兵疆, 闫龙. 大豆品质及农艺性状的QTL分析. 华北农学报, 2011, 26(5): 127-130.

Jiang C Z, Pei C J, Jing H X, Zhang M C, Wang T, Di R, Liu B J, Yan L. QTL analysis of soybean quality and yield related characters. Acta Agriculturae Boreali-Sinica, 2011, 26(5): 127-130. (in Chinese)

[32] 陈庆山, 张忠臣, 刘春燕, 辛大伟, 单大鹏, 邱红梅, 单彩云. 大豆主要农艺性状的QTL分析. 中国农业科学, 2007, 40(1): 41-47.

Chen Q S, Zhang Z C, Liu C Y, Xin D W, Shan D P, Qiu H M, Shan C Y. QTL analysis of major agronomic traits in soybean. Scientia Agricultura Sinica, 2007, 40(1): 41-47. (in Chinese)

[33] Fan D M, Yang Z, Ma Z Z, Zeng Q L, Du X Y, Jiang H W, Liu C Y, Han D W, Luan H H, Pei Y F, Chen Q S, Hu G H. QTL analysis of lodging-related morphological traits of soybean under two eco-environments. Agricultural Science＆Technology, 2012, 13(12): 2518-2525.

[34] Liang H Z, Yu Y L, Yang H Q, Zhang H Y, Dong W, Li C Y, Gong P T, Liu X Y, Fang X J. Epistatic effects and QTL × environment interaction effects of QTLs for yield and agronomic traits in soybean. Acta Agronomica Sinica, 2014, 40(1): 37-44.

[35] 王英, 程立锐, 冷建田, 吴存祥, 侯文胜, 韩天富. 开花后不同光周期条件下大豆农艺性状和品质性状的QTL分析. 作物学报, 2010, 36(7): 1092-1099.

Wang Y, Cheng L R, Leng J T, Wu C X, Hou W S, Han T F. QTL mapping of agronomic and quality traits in soybean under different post-flowering photoperiods. Acta Agronomica Sinica, 2010, 36(7): 1092-1099. (in Chinese)

[36] 周蓉, 王贤智, 陈海峰, 张晓娟, 单志慧, 吴学军, 蔡淑平, 邱德珍, 周新安, 吴江生. 大豆倒伏性及其相关性状的QTL分析. 作物学报, 2009, 35(1): 57-65.

Zhou R, Wang X Z, Chen H F, Zhang X J, Shan Z H, Wu X J, Cai S P, Qiu D Z, Zhou X A , Wu J S. QTL analysis of lodging and related traits in soybean. Acta Agronomica Sinica, 2009, 35(1): 57-65. (in Chinese)

[37] Yu J M, Pressoir G, Briggs W H, Bi I V, Yamasaki M, Doebley J F, McMullen M D, Gaut B S, Holland J B, Nielsen D, Holland J B, Kresovich S, Buckler E S. A unified mixed-model method for association mapping accounting for multiple levels of relatedness, Nature Genetics, 2005, 38: 203-208.

[38] Zhao K, Aranzana M J, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M. An Arabidopsis example of association mapping in structured samples. PLoS Genetics, 2007, 3(1): 0071-0082.

[39] Wang J, McClean P E, Lee R, Goos R J, Helms T. Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theoretical and Applied Genetics, 2008, 116(6): 777-787.

[40] Achleitner A, Tinker N A, Zechner E, Buerstmayr H. Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits. Theoretical and Applied Genetics, 2008, 117: 1041-1053.

[41] Zhang Z, Ersoz E, Lai C Q, Todhunter R J, Tiwari H K, Gore M A, Bradbury P J,Yu J M, Arnett D K, Ordovas J M, Buckler E S. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics, 2010, 42: 355-360.

[42] Yu J, Bernardo R. Changes in genetic variance during advanced cycle breeding in maize. Crop Science, 2003, 44: 405-410.

[43] Laurie C C, Chasalow S D, LeDeaux J R, McCarroll R, Bush D, Hauge B, Lai C, Clark D, Rocheford T R, Dudley J W. The genetic architecture of response to long-term arti?cial selection for oil concentration in the maize kernel. Genetics, 2004, 168: 2141-2155.

Related Articles 15

[1]	DONG YongXin,WEI QiWei,HONG Hao,HUANG Ying,ZHAO YanXiao,FENG MingFeng,DOU DaoLong,XU Yi,TAO XiaoRong. Establishment of ALSV-Induced Gene Silencing in Chinese Soybean Cultivars [J]. Scientia Agricultura Sinica, 2022, 55(9): 1710-1722.
[2]	LI YiLing,PENG XiHong,CHEN Ping,DU Qing,REN JunBo,YANG XueLi,LEI Lu,YONG TaiWen,YANG WenYu. Effects of Reducing Nitrogen Application on Leaf Stay-Green, Photosynthetic Characteristics and System Yield in Maize-Soybean Relay Strip Intercropping [J]. Scientia Agricultura Sinica, 2022, 55(9): 1749-1762.
[3]	GUO ShiBo,ZHANG FangLiang,ZHANG ZhenTao,ZHOU LiTao,ZHAO Jin,YANG XiaoGuang. The Possible Effects of Global Warming on Cropping Systems in China XIV. Distribution of High-Stable-Yield Zones and Agro-Meteorological Disasters of Soybean in Northeast China [J]. Scientia Agricultura Sinica, 2022, 55(9): 1763-1780.
[4]	MA XiaoYan,YANG Yu,HUANG DongLin,WANG ZhaoHui,GAO YaJun,LI YongGang,LÜ Hui. Annual Nutrients Balance and Economic Return Analysis of Wheat with Fertilizers Reduction and Different Rotations [J]. Scientia Agricultura Sinica, 2022, 55(8): 1589-1603.
[5]	JIANG FenFen, SUN Lei, LIU FangDong, WANG WuBin, XING GuangNan, ZHANG JiaoPing, ZHANG FengKai, LI Ning, LI Yan, HE JianBo, GAI JunYi. Geographic Differentiation and Evolution of Photo-Thermal Comprehensive Responses of Growth-Periods in Global Soybeans [J]. Scientia Agricultura Sinica, 2022, 55(3): 451-466.
[6]	YAN Qiang,XUE Dong,HU YaQun,ZHOU YanYan,WEI YaWen,YUAN XingXing,CHEN Xin. Identification of the Root-Specific Soybean GmPR1-9 Promoter and Application in Phytophthora Root-Rot Resistance [J]. Scientia Agricultura Sinica, 2022, 55(20): 3885-3896.
[7]	LIU ShuSen,SUN Hua,SHI Jie,GUO Ning,MA HongXia,ZHANG HaiJian. Grading Criterion of Maize Root Rot Based on Aboveground Symptoms and the Relationship Between Severity and Agronomic Traits [J]. Scientia Agricultura Sinica, 2022, 55(20): 3939-3947.
[8]	XiaoChuan LI,ChaoHai WANG,Ping ZHOU,Wei MA,Rui WU,ZhiHao SONG,Yan MEI. Deciphering of the Genetic Diversity After Field Late Blight Resistance Evaluation of Potato Breeds [J]. Scientia Agricultura Sinica, 2022, 55(18): 3484-3500.
[9]	WANG QiaoJuan,HE Hong,LI Liang,ZHANG Chao,CAI HuanJie. Research on Soybean Irrigation Schedule Based on AquaCrop Model [J]. Scientia Agricultura Sinica, 2022, 55(17): 3365-3379.
[10]	YUAN Cheng,ZHANG MingCong,WANG MengXue,HUANG BingLin,XIN MingQiang,YIN XiaoGang,HU GuoHua,ZHANG YuXian. Effects of Intertillage Time and Depth on Photosynthetic Characteristics and Yield Formation of Soybean [J]. Scientia Agricultura Sinica, 2022, 55(15): 2911-2926.
[11]	ZHAO DingLing,WANG MengXuan,SUN TianJie,SU WeiHua,ZHAO ZhiHua,XIAO FuMing,ZHAO QingSong,YAN Long,ZHANG Jie,WANG DongMei. Cloning of the Soybean Single Zinc Finger Protein Gene GmSZFP and Its Functional Analysis in SMV-Host Interactions [J]. Scientia Agricultura Sinica, 2022, 55(14): 2685-2695.
[12]	REN JunBo,YANG XueLi,CHEN Ping,DU Qing,PENG XiHong,ZHENG BenChuan,YONG TaiWen,YANG WenYu. Effects of Interspecific Distances on Soil Physicochemical Properties and Root Spatial Distribution of Maize-Soybean Relay Strip Intercropping System [J]. Scientia Agricultura Sinica, 2022, 55(10): 1903-1916.
[13]	HanXi LIU,Hao LÜ,GuangYu GUO,DongXu LIU,Yan SHI,ZhiJun SUN,ZeXin ZHANG,YanJiao ZHANG,YingNan WEN,JieQi WANG,ChunYan LIU,QingShan CHEN,DaWei XIN,JinHui WANG. Effect of rhcN Gene Mutation on Nodulation Ability of Soybean Rhizobium HH103 [J]. Scientia Agricultura Sinica, 2021, 54(6): 1104-1111.
[14]	JiaJia LI,HuiLong HONG,MingYue WAN,Li CHU,JingHui ZHAO,MingHua WANG,ZhiPeng XU,Yin ZHANG,ZhiPing HUANG,WenMing ZHANG,XiaoBo WANG,LiJuan QIU. Construction and Application of Detection Model for the Chemical Composition Content of Soybean Stem Based on Near Infrared Spectroscopy [J]. Scientia Agricultura Sinica, 2021, 54(5): 887-900.
[15]	Qian CAI,ZhanXiang SUN,JiaMing ZHENG,WenBin WANG,Wei BAI,LiangShan FENG,Ning YANG,WuYan XIANG,Zhe ZHANG,Chen FENG. Dry Matter Accumulation, Allocation, Yield and Productivity of Maize- Soybean Intercropping Systems in the Semi-Arid Region of Western Liaoning Province [J]. Scientia Agricultura Sinica, 2021, 54(5): 909-920.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

Association Mapping of Agronomic Traits in Soybean (Glycine max L. Merr.) and Mining of Novel Alleles

RichHTML

PDF