大豆百粒重QTL定位及多样性评价

doi:10.3864/j.issn.0578-1752.2016.09.002

Abstract

Abstract: 【Objective】 Seed weight is a major target of breeding as it is not only a component of seed yield but it also affects quality, so, different uses have different requirements for it. This study is to identify QTL associated with 100-seed weight, obtain the linkage markers and explore its diversity. Eventually provide a scientific basis of genetic improvement of seed weight.【Method】Recombinant inbred lines (RIL) derived from a cross of Jidou12×Heidou were used to detect the QTL associated with 100-seed weight, the composite interval mapping (CIM) method in WinQTL Cartographer software was used for the QTL analysis based on the seed weight observed in two years. A putative QTL was claimed using a genome-wise type I error of P＜0.05 determined by 300 permutations. In addition, a total of 205 soybean landraces and improved cultivars were used to identify phenotype through 3 years, and genotyped by SSR marker that linked with seed weight. Allelic frequency variation is more than 5% (corresponding to the number of resource materials is more than 10) as the efficient allelic variation.【Result】In RIL, the distribution frequency of seed weight was basically in normal, and the narrow-sense heritability was 88.72%. Five QTL for 100-seed weight were identified. These QTL scattered on Chr.02 (D1b), Chr.06 (C2), Chr.08 (A2) and Chr.17 (D2), respectively and could explain 7.68%-12.83% of the phenotype variation. The additive effect of the QTL varied from 0.65 g to 0.84 g. Two QTL were detected in two years. The qSW-6-1 flanked by SSR markers Satt457 and Sat_062 on Chr.06 explaining 12.02% of the phenotype variation, linked marker was Satt281, and the additive effect was -0.81 g. The qSW-17-1 flanked by SSR markers Satt301 to Satt310 on Chr.17 explaining 12.83% of the variation, and the additive effect was -0.84 g. Based on the germplasm, the allele number of the eight SSR loci, associated with five QTL identified via RIL, varied from 2 to 8, and the genetic diversity index varied from 0.34 to 0.82. Six alleles, Satt281-227 bp, Barcsoyssr_2_304-245 bp, Satt301-199 bp, Sat_406-214 bp, Satt119-136 bp and Satt341-218 bp, were correlated with large seed weight. Satt281-227 bp was the novel alleles in RIL and nature population, mainly distributed in the domestic improved cultivars that with big seed weight. Among the 205 accessions, only three accessions (Lü75, Zhongpindaheidou, Zhongye2) contained more than four alleles associated with large seed weight. 【Conclusion】 In this study, five QTL associated with 100-seed weight were identified by linkage analysis in RIL which crossed by improved cultivars Jidou12 and landraces Heidou. One allele of these was additive effect among RIL and nature population. The diversity distribution was made clear among the 205 accessions. The results can be applied to the parental selection and marker-assisted breeding in the process of seed weight improvement.

Key words: soybean, 100-seed weight, QTL, germplasm, genetic diversity

CHEN Qiang, YAN Long, FENG Yan, DENG Ying-ying, HOU Wen-huan, LIU Qing, LIU Bing-qiang, YANG Chun-yan, ZHANG Meng-chen. Identify QTL Associated with Soybean 100-Seed Weight Using Recombinant Inbred Lines and Determine QTL Diversity Within Nature Population[J].Scientia Agricultura Sinica, 2016, 49(9): 1646-1656.

References

[1] 杜维广, 盖钧镒.大豆超高产育种研究进展的讨论. 土壤与作物, 2014, 3(3): 81-92.

DU W G, GAI J Y. Discussion of the progress on super-high-yielding breeding in soybean. Soil and Crop, 2014, 3(3): 81-92. (in Chinese)

[2] 齐照明, 孙亚男, 陈立君, 郭强, 刘春燕, 胡国华, 陈庆山. 基于Meta分析的大豆百粒重的QTLs定位. 中国农业科学, 2009, 42(11): 3795-3803.

QI Z M, SUN Y N, CHEN L J, GUO Q, LIU C Y, HU G H, CHEN Q S. Meta-analysis of 100-seed weight QTLs in soybean. Scientia Agricultura Sinica, 2009, 42(11): 3795-3803. (in Chinese)

[3] MIAN M A R, BAILEY M A, TAMULONIS J P, SHIPE E R, CARTER T E, PARROTT W A, ASHLEY D A, HUSSEY R S, BOERMA H R. Molecular markers associated with seed weight in two soybean populations. Theoretical and Applied Genetics, 1996, 93: 1011-1016.

[4] CREGAN P B, JARVIK T, BUSH A L, SHOEMAKER R C, LARK K G, KAHLER A L, KAYA N, VANTOAI T T, LOHNES D G, CHUNG J, SPECHT J E. An integrated genetic linkage map of the soybean genome. Crop Science, 1999, 39(5): 1464-1490.

[5] 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(1): 122-128.

[6] HWANG T Y, SAYAMA T, TAKAHASHI M, TAKADA Y, NAKAMOTO Y, FUNATSUKI H, HISANO H, SASAMOTO S, SATO S, TABATA S, KONO I, HOSHI M, HANAWA M, YANO C, XIA Z, HARADA K, KITAMURA K, ISHIMOTO M. High-density integrated linkage map based on SSR markers in soybean. DNA Research, 2009, 16: 213-225.

[7] HYTEN D L, CHOI I Y, SONG Q, SPECHT J E, CARTER T E, SHOEMAKER R C, HWANG E Y, MATUKUMALLI L K, CREGAN P B. A high densityintegrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping. Crop Science, 2010, 50: 960-968.

[8] MANSUR L M, ORF J H, CHASE K, JARVIK T, CREGAN P B, LARK K G. Genetic mapping of agronomic traits using recombi-nant inbred lines of soybean. Crop Science, 1996, 36: 1327-1336.

[9] CSANÁDI G, VOLLMANN J, STIFT G, LELLEY T. Seed quality QTLs identified in a molecular map of early maturing soybean. Theoretical and Applied Genetics, 2001, 103: 912-919.

[10] 宛煜嵩. 大豆遗传图谱的构建及若干农艺性状的QTL定位分析[D]. 北京: 中国农业科学院, 2002.

Wan Y S.Construction of soybean genetie map and QTL Analysis of some agronomic traits[D]. Beijing: Chinese Academy of Agrieultural Sciences, 2002. (in Chinese)

[11] 孙亚男, 仕相林, 蒋洪蔚, 孙殿军, 辛大伟, 刘春燕, 胡国华, 陈庆山. 大豆百粒重QTL的上位效应和基因型×环境互作效应. 中国油料作物学报, 2012, 34(6): 598-603.

Sun Y N, Shi X L, Jiang H W, Sun D J, Xin D W, Liu C Y, Hu G H, Chen Q S. Epistatic effects and qE interaction effects of QTLs for 100-seed weight in soybean. Chinese Journal of Oil Crop Sciences, 2012, 34(6): 598-603. (in Chinese)

[12] Kato S, Sayama T, Fujii K, Yumoto S, Kono Y, Hwang T Y, Kikuchi A, Takada Y, Tanaka Y, Shiraiwa T, Ishimoto M. A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds. Theoretical and Applied Genetics, 2014, 127(6): 1365-1374.

[13] Yan L, Li Y H, Yang C Y, Ren S X, Chang R Z, Zhang M C, Qiu L J. Identification and validation of an over-dominant QTL controlling soybean seed weight using populations derived from Glycine max×Glycine soja. Plant Breeding, 2014, 133: 632-637.

[14] Liu Y L, Li Y H, Reif J C, Mette M F, Liu Z X, Liu B, Zhang S S, Yan L, Chang R Z, Qiu L J. Identification of quantitative trait loci underlying plant height and seed weight in soybean. Plant Genome, 2013, 6(3): 841-856.

[15] Wang W B, Li X L, Chen S X, Song S Y, Gai J Y, Zhao T J. Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean (Glycine soja Sieb. & Zucc.). Euphytica, 2015, 208(1): 1-11.

[16] 刘晓芬. 大豆栽培品种群体粒形性状及百粒重的关联分析[D]. 南京: 南京农业大学, 2010.

Liu X F. Association analysis for seed shape traits and 100-seed weight in soybean (Glycine max L. Merr.)[D]. Nanjing: Nanjing Agricultural University, 2010. (in Chinese)

[17] 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)

[18] 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: II.优异等位变异的发掘. 作物学报, 2008, 34(8): 1339-1349.

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: II. Exploration of elite alleles. Acta Agronomica Sinica, 2008, 34(8): 1339-1349. (in Chinese)

[19] Zhou Z K, Jiang Y, Wang Z, Gou Z H, Lyu J, Li W Y, Yu Y J, Shu L P, Zhao Y J, Ma Y M, Fang C, Shen Y T, Liu T F, Li C C, Li Q, Wu M, Wang M, Wu Y S, Dong Y, Wan W T, Wang X, Ding Z L, Gao Y D, Xiang H, Zhu B G, Lee S H, Wang W, Tian Z X. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotechnology, 2015, 33(4): 408-414.

[20] Zhang J P, Song Q J, Cregan P B, Jiang G L. Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean(Glycine max). Theoretical and Applied Genetic, 2016, 129: 117-130.

[21] 吕世霖, 程舜华. 大豆籽粒性状生态分布与育种. 大豆科学, 1984, 3(3): 201-207.

Lü S L, Cheng S H. The ecological distribution of seed characteristics of soybean and in relation to breeding. Soybean Science, 1984, 3(3): 201-207. (in Chinese)

[22] 陈强. 大豆籽粒相关性状QTL定位分析[D]. 秦皇岛: 河北科技师范学院, 2014.

Chen Q.QTL mapping for seed related traits in soybean (Glycine max L.Merr.)[D]. Qinhuangdao: Hebei Normal University of Science & Technology, 2014. (in Chinese)

[23] 雷雅坤, 闫龙, 杨春燕, 宋晓昆, 张孟臣, 黄占景. 大豆公共遗传图谱C1连锁群SSR标记空白区段的填补. 华北农学报, 2012, 27(6): 5-10.

Lei Y K, Yan L, Yang C Y, Song X K, Zhang M C, Huang Z J. Complete the blank section with SSR markers on linkage group C1 of public genetic map in soybean. Acta Agriculturae Boreali- Sinica, 2012, 27(6): 5-10. (in Chinese)

[24] Kaufinan B, Richards S, Diefig D A. DNA isolation method for high polysaecharide Lesquuerella species. Industrial Crops and Products, 1999, 9(2): 111-114.

[25] Wang L X, Guan R X, Liu Z X, Chang R Z, Qiu L J. Genetic diversity of Chinese cultivated soybean revealed by SSR markers. Crop Science, 2006, 46(3): 1032-1038.

[26] Li Y H, Li W, Zhang C, Yang L, Chang R Z, Gaut B S, Qiu L J. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytologist, 2010, 188(1): 242-253.

[27] Nyquist W E, Baker R J. Estimation of heritability and prediction of selection response in plant populations. Critical Reviews in Plant Sciences, 1991, 10: 235-322.

[28] LuW G, Wen Z X, Li H C, Yuan D H, Li J Y, Zhang H, Huang Z W, Cui S Y, Du W J. Identification of the quantitative trait loci (QTL) underlying water soluble prote incontent in soybean. Theoretical and Applied Genetics,2013, 126(2): 425-433.

[29] Wang S C, Basten C J, Zeng Z B. Windows QTL Cartographer V2.5. Department of Statistics. North Carolina: North Carolina State University, 2007.

[30] Yang J, Hu C C, Hu H, Yu R D, Xia Z, Ye X Z, Zhu J. QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 2008, 24(5): 721-723.

[31] McCouch S , Chen X, Panaud O, Temnykh S, Xu Y, Cho Y G, Huang N, Ishii T, Blair M. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Molecular Biology, 1997, 35: 89-99.

[32] 杨春燕, 闫龙, 张孟臣. 河北省大豆地方品种遗传基础. 植物遗传资源学报, 2009, 10(4): 560-565.

Yang C Y, Yan L, Zhang M C. Genetic basic of landrace soybean in Hebei. Journal of Plant Genetic Resources,2009, 10(4): 560-565. ( in Chinese)

[33] 孙中永, 程爽, 王继变, 黄吉祥, 陈飞, 倪西源, 赵坚义. 油菜含油量性状QTL关联分析及有利等位基因在品种中的构成分析. 中国农业科学, 2015, 45(19): 3921-3931.

Sun Z Y, Cheng S, Wang J B, Huang J X, Chen F, Ni X Y, Zhao J Y. Validation of QTL for oil content in a population of worldwide rapeseed cultivars by association analysis. Scientia Agricultura Sinica, 2015, 45(19): 3921-3931. (in Chinese)

[34] 汪霞. 大豆遗传图谱构建和百粒重等七个农艺性状的QTL定位[D]. 南京: 南京农业大学, 2010.

Wang X. Construction of linkage genetic map and detection of QTL for seven agropomic traits including 100-seed weight in soybean (Glycine max L. Merr.)[D]. Nanjing: Nanjing Agricultural University, 2010. (in Chinese)

[35] Pathan S M, Vuong T, Clark K, Lee J D, Shannon J G, Roberts C A, Ellersieck, M R. Burton J W, Cregan P B, Hyten D L, Nguyen H T, Sleper D A. Genetic mapping and confirmation of quantitative trait loci for seed protein and oil contents and seed weight in soybean. Crop Science, 2013(53): 765-774.

[36] Han Y P, Li D M, Zhu D, Li H Y, Li X P, Teng W L, Li W B. QTL analysis of soybean seed weight across multi-genetic backgrounds and environments. Theoretical and Applied Genetics, 2012, 125: 671-683.

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