Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (01): 1-6.doi: 10.3724/SP.J.1006.2014.00001


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 Online:2014-01-12 Published:2013-10-22
  • Contact: 翁建峰, E-mail: jfweng@126.com; 李新海, E-mail: lixinhai@caas.cn


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] TIAN Tian, CHEN Li-Juan, HE Hua-Qin. Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis [J]. Acta Agronomica Sinica, 2022, 48(6): 1372-1388.
[2] WANG Dan, ZHOU Bao-Yuan, MA Wei, GE Jun-Zhu, DING Zai-Song, LI Cong-Feng, ZHAO Ming. Characteristics of the annual distribution and utilization of climate resource for double maize cropping system in the middle reaches of Yangtze River [J]. Acta Agronomica Sinica, 2022, 48(6): 1437-1450.
[3] YANG Huan, ZHOU Ying, CHEN Ping, DU Qing, ZHENG Ben-Chuan, PU Tian, WEN Jing, YANG Wen-Yu, YONG Tai-Wen. Effects of nutrient uptake and utilization on yield of maize-legume strip intercropping system [J]. Acta Agronomica Sinica, 2022, 48(6): 1476-1487.
[4] CHEN Jing, REN Bai-Zhao, ZHAO Bin, LIU Peng, ZHANG Ji-Wang. Regulation of leaf-spraying glycine betaine on yield formation and antioxidation of summer maize sowed in different dates [J]. Acta Agronomica Sinica, 2022, 48(6): 1502-1515.
[5] SHAN Lu-Ying, LI Jun, LI Liang, ZHANG Li, WANG Hao-Qian, GAO Jia-Qi, WU Gang, WU Yu-Hua, ZHANG Xiu-Jie. Development of genetically modified maize (Zea mays L.) NK603 matrix reference materials [J]. Acta Agronomica Sinica, 2022, 48(5): 1059-1070.
[6] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[7] XU Jing, GAO Jing-Yang, LI Cheng-Cheng, SONG Yun-Xia, DONG Chao-Pei, WANG Zhao, LI Yun-Meng, LUAN Yi-Fan, CHEN Jia-Fa, ZHOU Zi-Jian, WU Jian-Yu. Overexpression of ZmCIPKHT enhances heat tolerance in plant [J]. Acta Agronomica Sinica, 2022, 48(4): 851-859.
[8] LIU Lei, ZHAN Wei-Min, DING Wu-Si, LIU Tong, CUI Lian-Hua, JIANG Liang-Liang, ZHANG Yan-Pei, YANG Jian-Ping. Genetic analysis and molecular characterization of dwarf mutant gad39 in maize [J]. Acta Agronomica Sinica, 2022, 48(4): 886-895.
[9] YAN Yu-Ting, SONG Qiu-Lai, YAN Chao, LIU Shuang, ZHANG Yu-Hui, TIAN Jing-Fen, DENG Yu-Xuan, MA Chun-Mei. Nitrogen accumulation and nitrogen substitution effect of maize under straw returning with continuous cropping [J]. Acta Agronomica Sinica, 2022, 48(4): 962-974.
[10] XU Ning-Kun, LI Bing, CHEN Xiao-Yan, WEI Ya-Kang, LIU Zi-Long, XUE Yong-Kang, CHEN Hong-Yu, WANG Gui-Feng. Genetic analysis and molecular characterization of a novel maize Bt2 gene mutant [J]. Acta Agronomica Sinica, 2022, 48(3): 572-579.
[11] SONG Shi-Qin, YANG Qing-Long, WANG Dan, LYU Yan-Jie, XU Wen-Hua, WEI Wen-Wen, LIU Xiao-Dan, YAO Fan-Yun, CAO Yu-Jun, WANG Yong-Jun, WANG Li-Chun. Relationship between seed morphology, storage substance and chilling tolerance during germination of dominant maize hybrids in Northeast China [J]. Acta Agronomica Sinica, 2022, 48(3): 726-738.
[12] QU Jian-Zhou, FENG Wen-Hao, ZHANG Xing-Hua, XU Shu-Tu, XUE Ji-Quan. Dissecting the genetic architecture of maize kernel size based on genome-wide association study [J]. Acta Agronomica Sinica, 2022, 48(2): 304-319.
[13] YAN Yan, ZHANG Yu-Shi, LIU Chu-Rong, REN Dan-Yang, LIU Hong-Run, LIU Xue-Qing, ZHANG Ming-Cai, LI Zhao-Hu. Variety matching and resource use efficiency of the winter wheat-summer maize “double late” cropping system [J]. Acta Agronomica Sinica, 2022, 48(2): 423-436.
[14] ZHANG Qian, HAN Ben-Gao, ZHANG Bo, SHENG Kai, LI Lan-Tao, WANG Yi-Lun. Reduced application and different combined applications of loss-control urea on summer maize yield and fertilizer efficiency improvement [J]. Acta Agronomica Sinica, 2022, 48(1): 180-192.
[15] YU Rui-Su, TIAN Xiao-Kang, LIU Bin-Bin, DUAN Ying-Xin, LI Ting, ZHANG Xiu-Ying, ZHANG Xing-Hua, HAO Yin-Chuan, LI Qin, XUE Ji-Quan, XU Shu-Tu. Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize [J]. Acta Agronomica Sinica, 2022, 48(1): 138-150.
Full text



No Suggested Reading articles found!