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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (7): 1228-1238.doi: 10.3724/SP.J.1006.2021.03048


Genome-wide association study of ear cob diameter in maize

MA Juan, CAO Yan-Yong, LI Hui-Yong*()   

  1. Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
  • Received:2020-08-14 Accepted:2020-12-01 Online:2021-07-12 Published:2021-01-04
  • Contact: LI Hui-Yong E-mail:lihuiyong1977@126.com
  • Supported by:
    This study was supported by the Science and Technology Project of Henan Province(182102110368);the Science-Technology Foundation for Outstanding Young Scientists of Henan Academy of Agricultural Sciences(2020YQ04)


Maize ear cob diameter is an important trait impacting the yield of grain and cob, and the analysis of its genetic mechanism will provide a guidance for high-yield breeding. In this study, the genotypes of 309 inbred lines were identified by genotyping-by-sequencing technology. FarmCPU (fixed and random model circulating probability unification), MLMM (multiple loci mixed linear model), and CMLM (compressed mixed linear model) were used to identify significant single nucleotide polymorphisms (SNP) for ear cob diameter of Yuanyang of Henan province, Dancheng of Henan province, Yucheng of Henan province, Sanya of Hainan province in 2017 and 2019, and best linear unbiased estimate environment. A total of 12 significant SNP for ear cob diameter were detected at P < 8.60E-07. S4_29277313 was detected from Yuanyang in 2017 using FarmCPU and MLMM. The phenotypic variance explained of S1_29006330, S2_170889116, S2_2046026464, and S4_83821463 ranged from 10.23% to 14.17%, and were considered major-effect SNP. In addition, S1_29006330 was mapped in the interval of known QTL for ear cob diameter. A total of 17 candidate genes were identified. Among them, WAKL14 (wall-associated receptor kinase-like 14), transcription factor ZIM35 (zinc-finger protein expressed in inflorescence meristem 35), HMGA (HMG-Y-related protein A), histone-lysine N-methyltransferase ATX4 (Arabidopsis trithorax 4), and XTH32 (xyloglucan endotransglucosylase/hydrolase protein 32) might be important genes for ear cob diameter. The identification of four major-effect SNP and five candidate genes can provide an information for molecular marker-assisted breeding, fine mapping, and gene cloning.

Key words: maize, genome-wide association study (GWAS), FarmCPU, ear cob diameter

Table 1

Multi-environment analysis of variance"

Degree of freedom
Sum of square
Mean of square
区组/环境Block/Environment 9 0.77 0.086 1.65 0.0970
基因型Genotype 308 184.95 0.60 11.55 <0.0001
环境Environment 4 4.84 1.21 23.28 <0.0001
Genotype and environment interaction
1036 170.71 0.16 3.17 <0.0001
误差Error 1694 88.04 0.052

Fig. 1

Correlation analysis and histograms for ear cob diameter in multi-environments Histograms are showed in diagonal. Correlation values and significant levels represented by asterisk are showed in upper triangular matrix. Significant levels 0.05, 0.01, and 0.001 are denoted by *, **, and ***, respectively. Scatter plots of ear cob diameter are showed in lower triangular matrix. SY, DC, YC, and YY represent Sanya, Dancheng, Yucheng, and Yuanyang, respectively. 2017 and 2019 denote years."

Fig. 2

Manhattan plots and quantile-quantile plots for significant SNP for ear cob diameter A and B: FarmCPU in BLUE environment; C and D: FarmCPU in Dancheng in 2017; E and F: FarmCPU in Sanya in 2017; G and H: FarmCPU in Yucheng in 2017; I and J: FarmCPU in Yuanyang in 2017; K and L: MLMM in Yuanyang in 2017."

Table 2

Significant SNP for ear cob diameter and candidate genes using different methods in different environments"

方法Method 标记名称
Marker name
Position (Mb)
bin P
MAF 表型变异解释率
Phenotypic variance explained (%)
Candidate genes
FarmCPU S1_143964620 1 143.96 1.05 1.82E-08 0.47 0.34 YY2017 intergenic Zm00001d030556 (organic cation/carnitine transporter 7 OCT7); Zm00001d030557 (alanine aminotransferase 2 ALT2)
FarmCPU S1_29006330 1 29.01 1.02 1.36E-07 0.34 13.10 SY2017 intergenic Zm00001d028279; Zm00001d028280 (wall-associated receptor kinase-like 14WAKL14)
FarmCPU S1_5537879 1 5.54 1.01 2.15E-07 0.37 3.27 BLUE intronic Zm00001d027451 (S-adenosyl-L-methionine-dependent methyltransferases superfamily protein)
FarmCPU S1_88127156 1 88.13 1.05 3.53E-07 0.27 0.0010 YY2017 intergenic Zm00001d029812 (threonine synthase 1 TS1); Zm00001d029814 (xyloglucan endotransglucosylase/hydrolase protein XTH32)
FarmCPU S2_170090146 2 170.09 2.06 6.12E-07 0.14 3.02 DC2017 intergenic Zm00001d005339; Zm00001d005342
FarmCPU S2_170889116 2 170.89 2.06 1.83E-08 0.11 14.17 DC2017 intronic Zm00001d005358 (nuclear pore complex protein GP210)
FarmCPU S2_204602646 2 204.60 2.07 8.45E-08 0.14 10.23 BLUE exonic Zm00001d006323 (histone-lysine N-methyltransferase ATX4)
FarmCPU S3_170875493 3 170.88 3.06 1.12E-09 0.11 8.55 BLUE intronic Zm00001d042528 (chromatin assembly factor 1 subunit FAS1)
FarmCPU S4_29277313 4 29.28 4.04 7.28E-08 0.09 0.01 YY2017 exonic Zm00001d049399 (putative nucleolin-like family protein)
FarmCPU S4_83821463 4 83.82 4.05 2.84E-07 0.23 12.83 YC2017 intergenic Zm00001d050365 (ZIM-transcription factor 35 ZIM35); Zm00001d050368 (HMG-Y-related protein A HMGA)
FarmCPU S5_17720377 5 17.72 5.03 5.46E-08 0.37 0.81 BLUE intronic Zm00001d013694 (single myb histone 6)
FarmCPU S7_127839936 7 127.84 7.02 5.41E-09 0.29 8.10 SY2017 exonic Zm00001d020679
MLMM S4_29277313 4 29.28 4.04 7.96E-07 0.09 0.01 YY2017 exonic Zm00001d049399 (putative nucleolin-like family protein)

Fig. S1

Manhattan plots and quantile-quantile plots for genome-wide association analysis for ear cob diameter using CMLM method in different environments DC, YC, SY, and YY represent Dancheng, Yucheng, Sanya, and Yuanyang, respectively. 2017 and 2019 denote in 2017 and in 2019."

Fig. S2

Manhattan plots and quantile-quantile plots for no significant SNP for ear cob diameter using MLMM and FarmCPU DC, YC, SY, and YY represent Dancheng, Yucheng, Sanya, and Yuanyang, respectively. 2017 and 2019 denote in 2017 and in 2019."

Fig. S3

Expression profiles of 17 candidate genes in different tissues retrieved from maize GDB"

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