欢迎访问作物学报,今天是

作物学报 ›› 2014, Vol. 40 ›› Issue (01): 1-6.doi: 10.3724/SP.J.1006.2014.00001

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

玉米穗行数全基因组关联分析

张焕欣,翁建峰*,张晓聪,刘昌林,雍洪军,郝转芳,李新海*   

  1. 中国农业科学院作物科学研究所 / 作物分子育种国家工程实验室,北京100081
  • 收稿日期:2013-06-19 修回日期:2013-09-16 出版日期:2014-01-12 网络出版日期:2013-10-22
  • 通讯作者: 翁建峰, E-mail: jfweng@126.com; 李新海, E-mail: lixinhai@caas.cn
  • 基金资助:

    本研究由国家自然科学基金项目(31201219)和国家重点基础研究发展计划(973计划)项目(2011CB100106)资助。

Genome-wide Association Analysis of Kernel Row Number in Maize

ZHANG Huan-Xin,WENG Jian-Feng*,ZHANG Xiao-Cong,LIU Chang-Lin,YONG Hong-Jun,HAO Zhuan-Fang,LI Xin-Hai*   

  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences / National Engineer Laboratory of Crop Molecular Breeding, Beijing 100081, China
  • Received:2013-06-19 Revised:2013-09-16 Published:2014-01-12 Published online:2013-10-22
  • Contact: 翁建峰, E-mail: jfweng@126.com; 李新海, E-mail: lixinhai@caas.cn

摘要:

穗行数是玉米产量的重要组成性状,其遗传解析对高产育种具有指导意义。本文以203份主要玉米自交系为材料,2007年在新疆乌鲁木齐、吉林公主岭和海南三亚进行穗行数测定;采用分布于玉米基因组的41 101个单核苷酸多态性(SNP)标记对穗行数进行关联分析。共鉴定出9个与穗行数显著关联(P < 0.0001)SNP分别位于染色体框1.021.107.038.029.0610.038SNP位于已定位的数量性状座位(QTL)区间内。在显著SNP位点LD区域内发掘出4个候选基因,分别编码含F-box结构域的生长素受体蛋白、玉米kn1蛋白、AP2结构域蛋白和富亮氨酸重复的跨膜蛋白激酶。采用全基因组关联分析策略发掘穗行数基因位点及候选基因,将为克隆控制玉米产量性状基因奠定基础。

关键词: 玉米, 穗行数, 全基因组关联分析, 候选基因

Abstract:

Kernel row number (KRN) is one of grain yield components in maize (Zea mays L.). Investigation of its genetic architecture will help develop high-yield varieties in maize. In this study, the KRN in a panel of 203 maize inbred lines was detected in Urumqi of Xinjiang, Gongzhuling of Jilin, and Sanya of Hainan in 2007, and used to perform the genome-wide analysis for KRN using MaizeSNP50 BeadChip. A total of nine SNPs were found to be significantly associated with KRN at a threshold of P < 0.0001, which were on chromosome Bins 1.02, 1.10, 7.03, 8.02, 9.06, and 10.03, respectively. Eight of these SNPs were located in the QTL intervals reported previously.Meanwhile, four candidate genes were scanned, encoding auxin signaling F-box containing protein, kn1 protein, AP2 domain containing protein and leucine-rich repeat transmembrane protein kinase respectively. In summary, these identified genes and SNPs will offer essential information for cloning yield-related genes in maize.

Key words: Maize, Kernel row number, Genome-wide association analysis, Candidate gene

[1]Kerstetter R A, Laudencia-Chingcuanco D, Smith L G, Hake S. Loss-of-function mutations in the maize homeobox gene, knotted1, are defective in shoot meristem maintenance. Development, 1997, 124: 3045–3054



[2]Dhillon BS, Singh J. Estimation and inheritance of stability parameters of grain yield in maize. J Agric Sci, 1977, 88: 257–265



[3]Lima M L A, Souza C L, Bento D A V, Souza A P, Carlini-Garcia L A. Mapping QTL for grain yield and plant traits in a tropical maize population. Mol Breed, 2006, 17: 227–239



[4]Ma X Q, Tang J H, Teng W T, Yan J B, Meng Y J, Li J S. Epistatic interaction is an important genetic basis of grain yield and its components in maize. Mol Breed, 2007, 20: 41–51



[5]Lu M, Xie C X, Li X H, Hao Z F, Li M S, Weng J F, Zhang D G, Bai L, Zhang S H. Mapping of quantitative trait loci for kernel row number in maize across seven environments. Mol Breed, 2010, 28: 143–152



[6]Guo J J, Chen Z L, Liu Z P, Wang B B, Song W B, Li W, Chen J, Dai J G, Lai J S. Identification of genetic factors affecting plant density response through QTL mapping of yield component traits in maize (Zea mays L.). Euphytica, 2011, 182: 409–422



[7]谭巍巍, 李永祥, 王阳, 刘成, 刘志斋, 彭勃, 王迪, 张岩, 孙宝成, 石云素, 宋燕春, 杨德光, 王天宇, 黎裕. 在干旱和正常水分条件下玉米穗部性状QTL分析. 作物学报, 2011, 37: 235–248



Tan W W, Li Y X, Wang Y, Liu C, Liu Z Z, Peng B, Wang D, Zhang Y, Sun B C, Shi Y S, Song Y C, Yang D G, Wang T Y, Li Y. QTL mapping of ear traits of maize under different water regimes. Acta Agron Sin, 2011, 37: 235–248 (in Chinese with English abstract)



[8]江培顺, 张焕欣, 李博, 郝转芳, 吕香玲, 李明顺, 王宏伟, 慈晓科, 张世煌, 李新海, 翁建峰, 史振声. 玉米产量相关性状Meta-QTL及候选基因分析. 作物学报, 2013, 39: 969–978



Jiang P S, Zhang H X, Li B, Hao Z F, Lü X L, Li M S, Wang H W, Ci X K, Zhang S H, Li X H, Weng J F, Shi Z S. Analysis of Meta-QTL and candidate genes related to yield components in maize. Acta Agron Sin , 2013, 39: 969–978 (in Chinese with English abstract)



[9]Yu J M, Buckler E S. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol, 2006, 17: 155–160



[10]Zhu C S, Gore M, Buckler E S, Yu J M. Status and prospects of association mapping in plants. Plant Genome, 2008, 1: 5–20



[11]Huang X H, Zhao Y, Wei X H, Li C Y, Wang A H, Zhao Q, Li W J, Guo Y L, Deng L W, Zhu C R, Fan D L, Lu Y Q, Weng Q J, Liu K Y, Zhou T Y, Jing Y F, Si L Z, Dong G J, Huang T, Lu T T, Feng Q, Qian Q, Li J Y, Han B. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet, 2012, 44: 32–39



[12]Weng J F, Xie C X, Hao Z F, Wang J J, Liu C L, Li M S, Zhang D G, Bai L, Zhang S H, Li X H. Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines. PLoS One, 2011, 6: e29229



[13]Weng J F, Liu X J, Wang Z H, Wang J J, Zhang L, Hao Z F, Xie C X, Li M S, Zhang D G, Bai L, Liu C L, Zhang S H, Li X H. Molecular mapping of the major resistance quantitative trait locus qHS2.09 with simple sequence repeat and single nucleotide polymorphism markers in maize. Phytopathology, 2012, 102: 692–699



[14]Tian F, Bradbury P J, Brown P J, Hung H, Sun Q, Flint-Garcia S, Rocheford T R, McMullen M D, Holland J B, Buckler E S. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet, 2011, 43: 159–162



[15]Buckler E S, Holland J B, Bradbury P J, Acharya C B, Brown P J, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz J C, Goodman M M, Harjes C, Guill K, Kroon D E, Larsson S, Lepak N K, Li H H, Mitchell S E, Pressoir G, Peiffer J A, Rosas M O, Rocheford T R, Romay M C, Romero S, Salvo S, Villeda H S, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J M, Zhang Z W, Kresovich S, McMullen M D. The genetic architecture of maize flowering time. Science, 2009, 325: 714–718



[16]Brown P J, Upadyayula N, Mahone G S, Tian F, Bradbury P J, Myles S, Holland J B, Flint-Garcia S, McMullen M D, Buckler E S, Rocheford T R. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet, 2011, 7: e1002383



[17]Murray M G, Thompson W F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res, 1980, 8: 4321–4326



[18]Knapp S J, Stroup W W, Ross W M. Exact confidence intervals for heritability on a progeny mean basis. Crop Sci, 1985, 25: 192–194



[19]Pritchard J K, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000, 155: 945–959



[20]Hardy O J, Vekemans X. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes, 2002, 2: 618–620



[21]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



[22]刘宗华,汤继华, 卫晓轶,王春丽, 田国伟, 胡彦民, 陈伟程. 氮胁迫和正常条件下玉米穗部性状的QTL分析. 中国农业科学, 2007, 40: 2409–2417 (in Chinese with English abstract)



Liu Z H, Tang J H, Wei X Y, Wang C L, Tian G W, Hu Y M, Chen W C. QTL mapping of ear traits under low and high nitrogen conditions in maize. Sci Agric Sin, 2007, 40: 2409–2417 (in Chinese with English abstract)



[23]Smith L G, Greene B, Veit B, Hake S. A dominant mutation in the maize homeobox gene, knotted-1, causes its ectopic expression in leaf cells with altered fates. Development, 1992, 1l6: 21–30



[24]Kump K L, Bradbury P J, Wisser R J, Buckler E S, Belcher A R, Oropeza-Rosas M A, Zwonitzer J C, Kresovich S, McMullen M D, Ware D, Balint-Kurti P J, Holland J B. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet, 2011, 43: 163–168



[25]Poland J A, Bradbury P J, Buckler E S, Nelson R J. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA, 2011, 108: 6893–6898



[26]Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz J O. Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci USA, 2010, 107: 21199–21204



[27]Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R, Chao S, Dong Y, Schwarz P, Muehlbauer G J, Smith K P. Genome-wide association mapping of fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breed, 2011, 27: 439–454



[28]Flint-Garcia S A, Thornsberry J M, Buckler E S. Structure of linkage disequilibrium in plans. Annu Rev Plant Biol, 2003, 54: 357–374



[29]Barrett J C, Fry B, Maller J, Daly M J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 2005, 21: 263–265



[30]杨小红, 严建兵,郑艳萍, 余建明, 李建生. 植物数量性状关联分析研究进展. 作物学报, 2007, 33: 523–530



Yang X H, Yan J B, Zheng Y P, Yu J M, Li J S. Reviews of association analysis for quantitative traits in plants. Acta Agron Sin, 2007, 33: 523–530 (in Chinese with English abstract)



[31]Aranzana M J, Kim S, Zhao K Y, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C L, Toomajian C, Traw B, Zheng H G, Bergelson J, Dean C, Marjoram P, Nordborg M. Genome-wide association mapping in Arabidopsis thaliana identifies previously known genes responsible for variation in flowering time and pathogen resistance. PLoS Genet, 2005, 1: 0531–0539



[32]Huang X H, Wei X H, Sang T, Zhao Q, Feng Q, Zhao Y, Li C Y, Zhu C R, Lu T T, Zhang Z W, Li M, Fan D L, Guo Y L, Wang A H, Wang L, Deng L W, Li W J, Lu Y Q, Weng Q J, Liu K Y, Huang T, Zhou T Y, Jing Y F, Li W, Lin Z, Buckler E S, Qian Q, Zhang Q F, Li J Y, Han B. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42: 961–967



[33]Kepinski S, Leyser O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature, 2005, 435: 446–451



[34]Vollbrecht E, Reiser L, Hake S. Shoot meristem size is dependent on inbred background and presence of the maize homeobox gene, knotted1. Development, 2000, 127: 3161–3172



[35]Chuck G, Meeley R B, Hake S. The control of maize spikelet meristem fate by the APETALA2-like gene indeterminate spikelet1. Genes Dev, 1998, 12: 1145–1154



[36]Chuck G, Meeley R B, Hake S. Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1. Development, 2008, 135: 3013–3019



[37]Lee D Y, An G. Two AP2 family genes, supernumerary bract (SNB) and osindeterminate spikelet 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice. Plant J, 2012, 69: 445–461



[38]Bommert P, Lunde C, Nardmann J, Vollbrecht E, Running M, Jackson D, Hake S, Werr W. thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development, 2005, 132: 1235–1245



[39]Taguchi-Shiobara F, Yuan Z, Hake S, Jackson D. The fasciated ear2 gene encodes a leucine-rich repeat receptor-like protein that regulates shoot meristem proliferation in maize. Genes Dev, 2001, 15: 2755–2766



[40]Bommert P, Nagasawa N S, Jackson D. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet, 2013, 45: 334–337

[1] 习千辉, 徐梓瑗, 刘梦梦, 王宏艺, 郎凯琳, 井震海, 陈锋, 赵磊. 小麦籽粒铜含量的全基因组关联分析及候选基因预测[J]. 作物学报, 2026, 52(6): 1604-1617.
[2] 毛嘉琦, 黄朋雨, 赵佳佳, 郑兴卫, 武棒棒, 郝宇琼, 屈非, 刘成, 马朋涛, 郑军. 山西小麦品种白粉病抗性评价及抗病基因分子检测[J]. 作物学报, 2026, 52(6): 1669-1681.
[3] 刘恩波, 陈静, 李红星, 于宁宁, 任佰朝, 赵斌, 刘鹏, 张吉旺. 遮阴改变源-库平衡和调节碳水化合物代谢进而抑制夏玉米幼穗发育[J]. 作物学报, 2026, 52(6): 1891-1901.
[4] 梁进宇, 尹嘉德, 王红丽, 张国平, 侯慧芝, 董博, 马明生. 基于无人机高光谱和机器学习的旱地饲用玉米叶片氮含量估测[J]. 作物学报, 2026, 52(6): 1788-1801.
[5] 唐宽强, 李公允, 宋美毅, 赵雪, 常春玲. 大豆株高性状全基因组关联分析及预测模型构建[J]. 作物学报, 2026, 52(6): 1743-1756.
[6] 杨欣雨, 崔文涛, 迪力尼格尔·阿力木, 汪凯翔, 吴鹏昊, 任姣姣. 玉米穗上叶片数全基因组关联分析和全基因组选择[J]. 作物学报, 2026, 52(5): 1573-1590.
[7] 韩亚鑫, 何冠华, 张小琼, 张登峰, 李永祥, 刘旭洋, 王天宇, 黎裕, 邹华文, 李春辉. 基于RNA-Seq和BSA-Seq联合分析挖掘玉米侧根密度基因资源[J]. 作物学报, 2026, 52(5): 1341-1352.
[8] 闫安, 蒋昆炜, 王蓉圆, 田林, 张璐, 王韵, 徐建龙. 水稻剑叶小维管束数基因SVN7的鉴定与克隆[J]. 作物学报, 2026, 52(5): 1364-1372.
[9] 孙淑凤, 许振南, 黄嘉鑫, 翁建峰, 李新海. 玉米MAPK家族全基因组鉴定及其对拟轮枝镰孢菌感染的响应[J]. 作物学报, 2026, 52(5): 1291-1308.
[10] 张宁宁, 滕雨菲, 任娜娜, 魏兴卓, 闫书豪, 樊可心, 王永宏, 陈文康, 张兴华, 朱万超, 徐淑兔, 薛吉全. 201份玉米自交系抗旱表型评价及可塑性分析[J]. 作物学报, 2026, 52(5): 1309-1325.
[11] 张鸿蓉, 王菲儿, 李盼, 仇海龙, 朱静, 赵连豪, 南运有, 何蔚, 樊志龙, 胡发龙, 柴强, 殷文. 减量20%灌水与25%有机肥替代化肥提高青贮玉米产量的光合特性[J]. 作物学报, 2026, 52(5): 1487-1500.
[12] 杨扬, 常诗惠, 田红丽, 易红梅, 王璐, 任洁, 范亚明, 刘亚维, 王凤格, 赵久然. 不同生态区国审玉米品种的遗传多样性分析[J]. 作物学报, 2026, 52(5): 1352-1364.
[13] 蔡宏玮, 于爱忠, 姜科强, 王鹏飞, 王玉珑, 霍建喆, 庞小能, 尹波, 尚永盼. 干旱灌区有机肥替代部分化肥促进甜玉米产量提升的关键机制[J]. 作物学报, 2026, 52(4): 1166-1180.
[14] 田红丽, 杨扬, 范亚明, 易红梅, 郭丹丹, 王凤格, 赵久然. 适于玉米品种鉴定的一套三等位变异SNP新型标记组合[J]. 作物学报, 2026, 52(4): 993-1005.
[15] 杨亚莉, 徐明睿, 马越飞, 海艺蕊, 刘凯栋, 刘万茂, 孙颖. 玉米根尖及整根响应缺铁的转录组比较研究[J]. 作物学报, 2026, 52(4): 1006-1021.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!