Scientia Agricultura Sinica ›› 2018, Vol. 51 ›› Issue (5): 821-834.doi: 10.3864/j.issn.0578-1752.2018.05.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Association Studies of Plant Type Traits in Maize

LIU Kun1, ZHANG XueHai1, SUN GaoYang1, YAN PengShuai1, GUO HaiPing1, CHEN SiYuan2, XUE YaDong1, GUO ZhanYong1, XIE HuiLing1, TANG JiHua1, LI WeiHua1   

  1. 1College of Agronomy, HenanAgriculturalUniversity/Key Laboratory of Wheat and Maize Crops Science, Zhengzhou 450002; 2No.1 Middle School of Zhengzhou, Zhengzhou 450002
  • Received:2017-09-26 Online:2018-03-01 Published:2018-03-01

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Abstract: 【Objective】 Plant morphological traits are the basis of ideotype-based maize breeding which are closely related to photosynthetic efficiency, lodging resistance and grain yields. Genome-wide association studies (GWAS) of 558 629 SNPs with genome-wide coverage was used to elucidate the genetic basis of six plant morphological traits, including total number of leaves (LN), leaf number above ear (LNAN), the ratio of LNAN to LN (LNAN/LN), plantheight (PH), earheight (EH) and the ratio of EH to PH (EH/PH), which could provide theoretical basis in enhancing ideotype-based maize breeding and facilitating the genetic improvement of new maize varieties with high plant density and lodging resistance. 【Method】 In this study, a representative panel of 284 inbred lines planted in Zhengzhou and Xunxian, including temperate, subtropical and tropical materials, were used for association mapping.【Result】 All traits measured in the two locations exhibited an approximately normal distribution. Highly positive or negative correlations between paired traits were observed. Variance analysis of these traits indicated that significant variations were observed across environment, genotype and the genotype × environment interaction. When test with the optimal GWAS model, we found that Q model showed high type I errors (false positive), while Q+K model were too strict in reducing false positive. K model is the best in reducing false positive. Totally, 56 significant SNP-trait associations involving in 17 loci were identified for five traits (P≤3.99E-6), each locus can explain phenotypic variation ranging from 7.97% to 10.56%. Moreover, four loci were detected in both environments, indicating that these 4 loci were less affected by environment effects and could be stable in different environments. All potential candidate genes and their annotations within 100 kb (50 kb upstream and downstream of the lead SNP) of the loci were identified, in total, 80 candidate genes were found, including 42 genes that have functional annotation. For example，the gene GRMZM2G161293 encoding a protein that has acetylgluco-saminyl transferase is associated with plant height and ear height. It catalyzes the transfer of the amino group from N-acetyl glucosamine to glucose, which may improve yield by influencing the content of soluble sugars in maize kernels.【Conclusion】 The results indicated that K model having the best result in reducing the type I errors (false positive). Based on K model, a total of 17 loci associated with plant morphological traits were identified.

Key words: maize (Zea mays L.), genome-wide association study, plant type traits, ideotype

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