欢迎访问作物学报,今天是

作物学报 ›› 2013, Vol. 39 ›› Issue (02): 258-268.doi: 10.3724/SP.J.1006.2013.00258

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用Bayes分层广义线性模型剖析大豆籽粒性状的遗传基础

闫宁,谢尚潜,耿青春,徐宇,李广军,刘兵,汪霞,李其刚,章元明*   

  1. 南京农业大学 / 作物遗传与种质创新国家重点实验室,江苏南京210095
  • 收稿日期:2012-05-31 修回日期:2012-11-16 出版日期:2013-02-12 网络出版日期:2012-12-11
  • 通讯作者: 章元明, E-mail: soyzhang@njau.edu.cn
  • 基金资助:

    本研究由国家自然科学基金项目(30971848), 教育部新世纪优秀人才支持计划项目(NECT-05-0489), 江苏省自然科学基金项目(BK2008335)和中央高校基本科研业务费专项资金创新团队项目(KYT201002)资助。

Genetic Basics of Seed Traits in Soybean with Bayes Hierarchical Generalized Linear Model Method

YAN Ning,XIE Shang-Qian,GENG Qing-Chun,XU Yu,LI Guang-Jun,LIU Bing,WANG Xia,LI Qi-Gang,ZHANG Yuan-Ming   

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement / Nanjing Agricultural University, Nanjing 210095, China
  • Received:2012-05-31 Revised:2012-11-16 Published:2013-02-12 Published online:2012-12-11
  • Contact: 章元明, E-mail: soyzhang@njau.edu.cn

摘要:

以溧水中子黄豆(P1)和南农493-1(P2)组合的504个正反交F2:3~F2:7家系群体为材料, 调查大豆粒长、粒宽、粒厚、长宽比、长厚比、宽厚比和百粒重性状在2007—2011年的表型观测值, 扫描F2群体SSR分子标记信息, Bayes分层广义线性模型方法检测了上述性状的主效QTLQTL´环境(QE)互作、QTL´细胞质(QC)互作和QTL´QTL(QQ)互作。共检测到89个主效QTL33QE20QC35QQ互作。上述7个性状的主效QTL分别有710101919177; QQ互作分别有11060693, 没有检测到显性´显性互作; QE互作分别有5763624; QC互作分别有2138420对。主效、QQ互作、QC互作和QE互作QTL的总贡献率分别为12.42%~61.79%0~23.21%0.35%~1.51%0~14.16%, 表明主效QTL贡献最大, QQ互作次之, QE互作最小。各类QTL都有一因多效现象, 同一基因座可通过不同方式影响性状表达。这些结果揭示了大豆粒形性状的遗传基础, 为标记辅助育种提供了参考信息。

关键词: 大豆, 籽粒大小和形状, 上位性, 主效QTL, QTL×环境互作, QTL细胞质互作, Bayes分层广义线性模型

Abstract:

Seed size and shape traits in soybean play a crucial role in yield and appearance quality. In this study, an experiment was performed to detect main-effect quantitative trait loci (MQTL), QTL-by-environment (QE), QTL-by-cytoplasm (QC), and QTL-by-QTL (QQ) interactions for the soybean seed traits (length, width, thickness, length-to-width, length-to-thickness, width-to-thickness, and 100-seed weight) using Bayes hiearchical generalized linear model approach. Evaluation of these traits for the 504 F2:3–F2:7 familiesfrom the direct and reciprocal crosses of Lishuizhongzihuangdou ´ Nannong 493-1 was carried out in 2007–2011, respectively, and the 504 F2 plants were scanned by 152 SSR markers. As a result, a total of 89 MQTL, 35 QQ interactions, 33 QE interactions and 20 QC interactions were detected. As for the above seven traits, there were respectively 7, 10, 10, 19, 19, 17, and 7 MQTL; 1, 10, 6, 0, 6, 9, and 3 QQ interactions; 5, 7, 6, 3, 6, 2, and 4 QE interactions; and 2, 1, 3, 8, 4, 2, and 0 QC interactions. The total proportion of phenotypic variance explained by the above four types of QTL for each trait is 12.42–61.79%, 0–23.21%, 0.35–1.51%, and 0–14.16%, respectively, indicating that the most important genetic component is MQTL, the second one is epistasis, and the last one is QE interaction. Pleiotropic effects were observed in all kinds of QTL, while various types of QTL shared with one same locus were found to be response for a seed trait as well. These results revealed genetic basis of seed size and shape traits in soybean, and provide reference information for marker assisted breeding.

Key words: Soybean, Seed size and shape traits, Main-effect QTL, Epistasis, QTL-by-environment interaction, QTL-by-cytoplasm interaction, Bayes hierarchical generalized linear mode

[1]Lai Y-C(来永才), Li W(李炜), Wang Q-X(王庆祥), Li X-H(李霞辉), Qi N(齐宁), Lin H(林红). Innovation and utilization of new high isoflavone resource of wild soybean in Heilongjiang province: I. analysis of isoflavone content and relevant of characters. Soybean Sci (大豆科学), 2006, 25(4): 414–416 (in Chinese with English abstract)



[2]Wang S-M(王曙明). The effect of grain size within the genotype on soybean protein and oil content. Soybean Bull (大豆通报), 1996, (1): 7 (in Chinese)



[3]Rabiei B, Valizadeh M, Ghareyazie B, Moghaddam M, Ali A J. Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers. Euphytica, 2004, 137: 325–332



[4]Ayoub M, Symons S J, Edney M J, Mather D E. QTLs affecting kernel size and shape in a two-rowed by six-rowed barley cross. Theor Appl Genet, 2002, 105: 237–247



[5]Gegas V C, Nida A, Griffiths S, Simmonds J, Fish L, Orford S, Sayers L, Doonan J H, Snape J W. A genetic framework for grain size and shape variation in wheat. Plant Cell, 2010, 22: 1046–1056



[6]Zheng Y-L(郑有良), Lai Z-M(赖仲铭), Yang K-C(杨克诚). The relationship between maize seed traits and seed size and the study on the genetics. Sichuan Agric Univ (四川农业大学学报), 1985, 3(2): 73–79 (in Chinese)



[7]Salas P, Oyarzo-Llaipen J C, Wang D, Chase K, Mansur L. Genetic mapping of seed shape in three populations of recombinant inbred lines of soybean (Glycine max L. Merr.). Theor Appl Genet, 2006, 113: 1459–1466



[8]Gong L-H(宫李辉), Gao Z-Y(高振宇), Ma B-J(马伯军), Qian Q(钱前). Progress of genetic research on grain shape on rice. Chin Bull Bot (植物学报), 2011, 46(6): 597–605 (in Chinese with English abstract)



[9]Mao H L, Sun S Y, Yao J L, Wang C R, Yu S B, Xu C G, Li X H, Zhang Q F. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA, 2010, 107: 19579–19584



[10]Song X J, Huang W, Shi M, Zhu M Z, Lin H X. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet, 2007, 39: 623–630



[11]Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M. Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet, 2008, 40: 1023–1028



[12]Weng J F, Gu S H, Wan X Y, Gao H, Guo T, Su N, Lei C L, Zhang X, Cheng Z J, Guo X P, Wang J L, Jiang L, Zhai H Q, Wan J M. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res, 2008, 18, 1199–1209



[13]Nelson R L, Wang P. Variation and evaluation of seed shape in soybean. Crop Sci, 1989, 29: 147–150



[14]Cober E R, Voldeng H D, Fregeau-Reid J A. Heritability of seed shape and seed size in soybean. Crop Sci, 1997, 37: 1767–1769



[15]Liang H-Z(梁慧珍), Li W-D(李卫东), Wang H(王辉), Fang X-J(方宣钧). Genetic effects on seed traits in soybean. Acta Genet Sin (遗传学报), 2005, 32(11): 1199–1204 (in Chinese with English abstract)



[16]Liang H-J(梁慧珍), Wang S-F(王树峰), Yu Y-L(余永亮), Wang T-F(王庭峰), Gong P-T(巩鹏涛), Fang X-J(方宣钧), Liu X-Y(刘学义), Zhao S-J(赵双进), Zhang M-C(张孟臣), Li W-D(李卫东). Mapping quantitative trait loci for six seed shape traits in soybean. Henan Agric Sci (河南农业科学), 2008, 45(9): 54–60 (in Chinese)



[17]Xu Y, Li H N, Li G J, Wang X, Cheng L G, Zhang Y M. Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.). Theor Appl Genet, 2011, 122: 581–594



[18]Zhang W-Y(张文英), Cheng J-Q(程君奇), Zhu J(朱军), Wu W-R(吴为人). Epistasis and its application in genetics and breeding. China J Bioinform (生物信息学), 2004, 2: 39–41 (in Chinese with English abstract)



[19]Lei D-Y(雷东阳), Xie F-M(谢放鸣), Xu J-L(徐建龙), Chen L-Y(陈立云). QTLs mapping and epistasis analysis for grain shape and chalkiness degree of rice. Chin J Rice Sci (中国水稻科学). 2008, 22(3): 255–260 (in Chinese with English abstract)



[20]Jiang L-R(江良荣), Wang W(王伟), Huang J-Y(黄建勋), Huang R-Y(黄荣裕), Zheng J-S(郑景生), Huang Y-M(黄育民), Wang H-C(王侯聪). Analysis of epistatic and QE interaction effects of QTLs for grain shape in rice. Mol Plant Breed (分子植物育种), 2009, 7(4): 690–698 (in Chinese with English abstract)



[21]Wang W(王伟), Ye Z-Y(叶志云), Zheng J-S(郑景生), Huang Y-M(黄育民), Huang R-Y(黄荣裕), Wang H-C(王侯聪), Jiang L-R(江良荣). Mapping QTLs for rice grain shape with QTL×environment interactions and epistatic effects analysis. Acta Bot Boreal-Occident Sin (西北植物学报), 2010, 30(7): 1344–1350 (in Chinese with English abstract)



[22]Yi N, Banerjee S. Hierarchical generalized linear models for multiple quantitative trait locus mapping. Genetics, 2009, 181: 1101–1113



[23]Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statist Soc, Ser B (Methodological), 1995, 57: 289–300



[24]Lin Z-X(林忠旭), Feng C-H(冯常辉), Guo X-P(郭小平), Zhang X-L(张献龙). Genetic analysis of major QTLs and epistasis interaction for yield and fiber quality in upland cotton. Sci Agric Sin (中国农业科学), 2009, 42(9): 3036–3047 (in Chinese with English abstract)



[25]Nakagawa H, Tanaka A, Tanabata T, Ohtake M, Fujioka S, Nakamura H, Ichikawa H, Mori M. Short grain 1 decreases organ elongation and brassinosteroid response in rice. Plant Physiol, 2012, 158: 1208–1209



[26]Li J, Chu H, Zhang Y, Mou T, Wu C, Zhang Q, Xu J. The rice HGW gene encodes a ubiquitin-associated (UBA) domain protein that regulates heading date and grain weight. PloS one, 2012, 7: e34231



[27]Wang A, Garcia D, Zhang H, Feng K, Chaudhury A, Berger F, Peacock W J, Dennis E S, Luo M. The VQ motif protein IKU1 regulates endosperm growth and seed size in Arabidopsis. Plant J, 2010, 63: 670–679



[28]Hughes R, Spielman M, Schruff M C, Larson T R, Graham I A, Scott R J. Yield assessment of integument-led seed growth following targeted repair of auxin response factor 2. Plant Biotechnol J, 2008, 6(8): 758–769



[29]Wang Y, Zhang W Z, Song L F, Zou J J, Su Z, Wu W H. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol, 2008, 148: 1201–1211



[30]Johnson C S, Kolevski B, Smyth D R. TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell, 2002, 14: 1359–1375



[31]Debeaujon I, Nesi N, Perez P, Devic M, Grandjean O, Caboche M, Lepiniec L. Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. Plant Cell, 2003, 15: 2514–2531



[32]Niu Y(牛远), Xu Y(徐宇), Li G-J(李广军), Wang Y-Q(王云清), Liu X-F(刘晓芬), Li H-N(李河南), Wei S-P(魏世平), Zhang Y-M(章元明). Domestication of seed size and shape traits in soybean. Soybean Sci (大豆科学), 2012, 31(4): 68–75 (in Chinese with English abstract)

[1] 陈玲玲, 李战, 刘亭萱, 谷勇哲, 宋健, 王俊, 邱丽娟. 基于783份大豆种质资源的叶柄夹角全基因组关联分析[J]. 作物学报, 2022, 48(6): 1333-1345.
[2] 杨欢, 周颖, 陈平, 杜青, 郑本川, 蒲甜, 温晶, 杨文钰, 雍太文. 玉米-豆科作物带状间套作对养分吸收利用及产量优势的影响[J]. 作物学报, 2022, 48(6): 1476-1487.
[3] 王炫栋, 杨孙玉悦, 高润杰, 余俊杰, 郑丹沛, 倪峰, 蒋冬花. 拮抗大豆斑疹病菌放线菌菌株的筛选和促生作用及防效研究[J]. 作物学报, 2022, 48(6): 1546-1557.
[4] 于春淼, 张勇, 王好让, 杨兴勇, 董全中, 薛红, 张明明, 李微微, 王磊, 胡凯凤, 谷勇哲, 邱丽娟. 栽培大豆×半野生大豆高密度遗传图谱构建及株高QTL定位[J]. 作物学报, 2022, 48(5): 1091-1102.
[5] 李阿立, 冯雅楠, 李萍, 张东升, 宗毓铮, 林文, 郝兴宇. 大豆叶片响应CO2浓度升高、干旱及其交互作用的转录组分析[J]. 作物学报, 2022, 48(5): 1103-1118.
[6] 彭西红, 陈平, 杜青, 杨雪丽, 任俊波, 郑本川, 罗凯, 谢琛, 雷鹿, 雍太文, 杨文钰. 减量施氮对带状套作大豆土壤通气环境及结瘤固氮的影响[J]. 作物学报, 2022, 48(5): 1199-1209.
[7] 王好让, 张勇, 于春淼, 董全中, 李微微, 胡凯凤, 张明明, 薛红, 杨梦平, 宋继玲, 王磊, 杨兴勇, 邱丽娟. 大豆突变体ygl2黄绿叶基因的精细定位[J]. 作物学报, 2022, 48(4): 791-800.
[8] 李瑞东, 尹阳阳, 宋雯雯, 武婷婷, 孙石, 韩天富, 徐彩龙, 吴存祥, 胡水秀. 增密对不同分枝类型大豆品种同化物积累和产量的影响[J]. 作物学报, 2022, 48(4): 942-951.
[9] 杜浩, 程玉汉, 李泰, 侯智红, 黎永力, 南海洋, 董利东, 刘宝辉, 程群. 利用Ln位点进行分子设计提高大豆单荚粒数[J]. 作物学报, 2022, 48(3): 565-571.
[10] 周悦, 赵志华, 张宏宁, 孔佑宾. 大豆紫色酸性磷酸酶基因GmPAP14启动子克隆与功能分析[J]. 作物学报, 2022, 48(3): 590-596.
[11] 王娟, 张彦威, 焦铸锦, 刘盼盼, 常玮. 利用PyBSASeq算法挖掘大豆百粒重相关位点与候选基因[J]. 作物学报, 2022, 48(3): 635-643.
[12] 董衍坤, 黄定全, 高震, 陈栩. 大豆PIN-Like (PILS)基因家族的鉴定、表达分析及在根瘤共生固氮过程中的功能[J]. 作物学报, 2022, 48(2): 353-366.
[13] 张国伟, 李凯, 李思嘉, 王晓婧, 杨长琴, 刘瑞显. 减库对大豆叶片碳代谢的影响[J]. 作物学报, 2022, 48(2): 529-537.
[14] 宋丽君, 聂晓玉, 何磊磊, 蒯婕, 杨华, 郭安国, 黄俊生, 傅廷栋, 汪波, 周广生. 饲用大豆品种耐荫性鉴定指标筛选及综合评价[J]. 作物学报, 2021, 47(9): 1741-1752.
[15] 曹亮, 杜昕, 于高波, 金喜军, 张明聪, 任春元, 王孟雪, 张玉先. 外源褪黑素对干旱胁迫下绥农26大豆鼓粒期叶片碳氮代谢调控的途径分析[J]. 作物学报, 2021, 47(9): 1779-1790.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!