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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (6): 819-831.doi: 10.3724/SP.J.1006.2020.93063


Genome-wide association studies of leaf orientation value in maize

PENG Bo1,ZHAO Xiao-Lei1,WANG Yi1,YUAN Wen-Ya1,LI Chun-Hui2,LI Yong-Xiang2,ZHANG Deng-Feng2,SHI Yun-Su2,SONG Yan-Chun2,WANG Tian-Yu2,*(),LI Yu2,*()   

  1. 1Tianjin Crop Research Institute / Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin 300384, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2019-12-03 Accepted:2020-01-15 Online:2020-06-12 Published:2020-02-17
  • Contact: Tian-Yu WANG,Yu LI E-mail:wangtianyu@caas.cn;liyu03@caas.cn
  • Supported by:
    National Natural Science Foundation of China(31601308);Innovative Research and Experiment Project for Young Researchers(2018004);Tianjin Natural Science Foundation(19JCZDJC34500);President’s Fund of Tianjin Academy of Agricultural Sciences(17007)


Leaf orientation value is a comprehensive index reflecting the two characteristics of “straight” and “vertical” of leaves. The varieties with high leaf orientation value have straight and not curved leaves, and small angle, which are conducive to the wind ventilation and light transmission for maize population. When the planting density is high, it is easier to obtain high yield than the expanded plant-type. It is of great significance for molecular design breeding of ideal plant type to clarify the genetic basis of leaf orientation value. In this study, 285 diverse lines genotyped by the MaizeSNP50 chip were evaluated for leaf orientation in 2017 and 2018. The genome-wide association analysis (GWAS) were used to identified the SNPs, which were significant association with leaf orientation values. The analysis of variance showed that the significant variations were observed for leaf orientation value of different inbred lines (P < 0.01). In the selection of the optimal model, it was found that the Q + K model was the most suitable for the leaf orientation association analysis in this study. A total of 15 loci (P < 4.05E-5) were detected by GWAS, including 27 SNPs, explaining 5.54%-8.73% of phenotypic variation, and 15 candidate genes were mined in two years. Among them, site 2 in 1.07 bin was an important site found in this study, and its candidate gene might be Zm00001d032050 encoding cyclin dependent protein kinase, which needed to be further confirmed by map-based cloning.

Key words: maize, leaf orientation value, leaf angle, single nucleotide polymorphism, association analysis

Table 1

Basic stastical analysis and correlation coefficients of leaf orientation value in two years"

相关系数Correlation coefficient
2017 2018
2017 59.45 12.99-86.28 13.77 -0.58 0.13
2018 63.86 17.05-90.00 13.11 -0.79 0.59 0.75**
BLUP 61.58 23.46-82.65 11.14 -0.63 0.30 0.95** 0.90**

Fig. 1

Frequency distribution of leaf orientation value in two years A: Year of 2017; B: Year of 2018; C: BLUP for combined 2 years. "

Table 2

Analysis of variance (ANOVA) for leaf orientation value in two years"

Variation source
H2 (%)
基因型 Genotype 141.46** 87.86
年份Year 8.97**
基因型×年份 Genotype×year 21.41**
重复Replication 14.63
残差Residual 35.32

Fig. 2

Picture of whole-genome LD in the panel of 285 lines"

Fig. 3

Quantile-quantile (QQ) plots resulting from GWAS results using three methods for leaf orientation value in two years A: Year of 2017; B: Year of 2018; C: BLUP for combined two years. Green spot: Q model; blue spot: K model; purple spot: Q+K model. "

Fig. 4

Manhattan plots resulting from GWAS results using Q+K methods for leaf orientation value in two years A: Year of 2017; B: Year of 2018; C: BLUP for combined two years. Green spots: the Manhattan plots of 50 SNPs in the upstream and downstream of lead SNP at site 2 in two years. "

Table 3

Significant SNPs and candidate genes associated with leaf orientation value identified by GWAS in two years"

Bin 年份
SNP 基因型
Physical position
R2 (%)
Lead SNP physical position
QTL区间b QTL region b 候选基因
Candidate gene
Gene annotation
1 1.02 BLUP PUT-163a-149085801-877 [A/G] 28,638,770 9.25E-06 7.95 28,638,770 28,306,770 28,638,770 Zm00001d028265 细胞分裂素响应因子
Cytokinin response regulator
1 1.02 2017 PUT-163a-149085801-877 [A/G] 28,638,770 3.21E-06 8.73
2 1.07 BLUP PZE-101164453 [T/C] 210,517,983 3.22E-05 6.94 211,113,165 210,781,165 211,445,165 Zm00001d032050 细胞周期蛋白依赖性蛋白激酶
Regulation of cyclin-dependent protein serine/threonine kinase activity
2 1.07 BLUP PZE-101164815 [A/G] 210,772,541 1.16E-06 8.15
2 1.07 2017 PZE-101164815 [A/G] 210,772,541 9.67E-07 8.49
2 1.07 2018 PZE-101164815 [A/G] 210,772,541 2.71E-05 6.24
2 1.07 2017 SYN25384 [A/G] 211,113,165 3.97E-05 6.99
2 1.07 BLUP SYN25375 [T/C] 211,116,324 1.90E-05 7.32
2 1.07 2017 SYN25375 [T/C] 211,116,324 3.78E-05 6.93
3 1.07 BLUP PZE-101165699 [A/G] 211,785,378 2.04E-05 7.55 211,785,378 211,453,378 212,117,378 Zm00001d032078 细胞分裂周期相关蛋白激酶
Cell division cycle 2-related protein kinase 7
3 1.07 2017 PZE-101165699 [A/G] 211,785,378 3.02E-05 7.30
4 1.07 BLUP PZE-101166565 [A/G] 212,687,705 1.20E-06 7.65 212,687,705 212,355,705 213,019,705 Zm00001d032100 果胶酶/果胶酶抑制剂
Pectinesterase/pectinesterase inhibitor 13
4 1.07 2017 PZE-101166565 [A/G] 212,687,705 5.31E-06 6.93
4 1.07 2018 PZE-101166565 [A/G] 212,687,705 9.69E-06 6.67
5 1.08 BLUP PZE-101196520 [A/G] 248,302,322 1.38E-05 7.78 248,302,322 247,970,322 248,634,322 Zm00001d033047 含SPX结构域蛋白
SPX domain-containing protein 3
6 1.08 2017 PZE-101199858 [T/C] 252,942,320 2.99E-05 6.73 252,942,320 252,610,320 253,274,320 Zm00001d033180 油菜素内酯缺乏性矮秆基因 Brassinosteroid-deficient dwarf1,brd1
6 1.08 2017 PZE-101199859 [A/G] 252,942,792 2.99E-05 6.73
7 2.01 BLUP SYN9223 [A/G] 3,825,340 3.71E-05 7.11 3,825,340 3,526,340 4,124,340 Zm00001d001968 细胞周期相关蛋白
8 2.04 BLUP PZE-102062747 [A/C] 43,019,177 1.98E-05 7.91 43,019,177 42,720,177 43,318,177 Zm00001d003401 类似14-3-3蛋白
14-3-3-like protein GF14-6
9 2.04 BLUP SYN29642 [T/C] 50,700,996 3.50E-05 6.15 50,700,996 50,401,996 50,999,996 Zm00001d003626 NAC-转录因子
NAC-transcription factor 76
10 2.07 2017 PZE-102150850 [T/G] 203,858,592 3.50E-05 6.82 203,858,592 203,559,592 204,157,592 Zm00001d006293 NLP转录因子
NLP-transcription factor 17
11 2.07 BLUP PZE-102152182 [A/G] 205,338,006 3.24E-05 5.54 205,338,006 205,039,006 205,637,006 Zm00001d006348 生长调节因子
Growth-regulating factor 9
12 5.06 BLUP PZE-105142621 [A/G] 201,997,615 9.76E-06 7.70 201,997,615 201,615,615 202,379,615 Zm00001d017618 ABI3-VP1-转录因子
ABI3-VP1-transcription factor 16
12 5.06 2017 PZE-105142621 [A/G] 201,997,615 1.72E-05 7.52
13 7.02 BLUP PZE-107043106 [A/G] 87,913,892 3.32E-05 8.24 87,913,892 87,468,892 88,358,892 Zm00001d020041 参与细胞壁果胶代谢蛋白
Cell wall pectin metabolic process
14 10.03 2017 PZE-110020884 [T/C] 28,391,702 2.32E-05 7.65 28,391,702 27,697,702 29,085,702 Zm00001d023927 锌指CCCH结构域蛋白
Zinc finger CCCH domain-containing protein 30
15 10.04 BLUP PZE-110053328 [A/G] 100,750,723 4.02E-05 6.73 100,750,723 100,056,723 101,444,723 Zm00001d025033 TCP转录因子
TCP-transcription factor 40

Fig. 5

Distribution of the loci significantly association with leaf orientation value detected in this study on chromosomes and the comparison with the results of previous studies Bin with bold on the chromosomes represents the site detected in this study that is significantly association with leaf orientation value. "

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