Crops ›› 2024, Vol. 40 ›› Issue (1): 31-39.doi: 10.16035/j.issn.1001-7283.2024.01.005

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Multi-Locus Genome-Wide Association Study and Genomic Prediction for General Combining Ability of Maize Ear Diameter

Ma Juan(), Huang Lu, Yu Ting, Guo Guojun, Zhu Weihong, Liu Jingbao   

  1. Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
  • Received:2022-06-07 Revised:2022-09-22 Online:2024-02-15 Published:2024-02-20

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Abstract:

Ear diameter is an important trait for ear in maize, and general combining ability (GCA) is an important index to evaluate parental mating ability in hybrid breeding. A total of 537 F1 hybrid combinations derived from NCII genetic mating design were used as materials. Seven multi-locus genome-wide association study (MGWAS) methods were used to conduct mapping analysis of ear diameter GCA in Xinxiang, Zhoukou, and combined environment, and the effects of different significant loci from MGWAS methods as fixed effects on the prediction accuracy of ear diameter GCA were studied, which will provide a guidance for the breeding utilization of genomic selection (GS) for key loci of ear diameter GCA. The results showed that a total of 18 significant SNPs (P<8.52E-07) were detected for the GCA effect of ear diameter, of which six loci were simultaneously detected using two to five MGWAS methods and three of them were detected in two environments. Five GS random effect models were used in the three environments, and the prediction accuracy of ear diameter GCA ranged from 0.32 to 0.44. The genomic prediction ability of GCA of ear diameter could be effectively enhanced in all three environments by adding significant loci as fixed effects into the prediction model, increasing the prediction accuracy to 0.38-0.64.

Key words: Maize, Ear diameter, General combining ability, Multi-locus genome-wide association study, Genomic selection, Fixed effect model

Fig.1

Statistic analysis of effect values of general combining ability for ear diameter (a)“×”denotes means, the same below; (c)“***”indicates significant correlation at P < 0.001 level."

Table 1

Analysis of variance and heritability for GCA of ear diameter"

来源
Source		 自由度
Degree of freedom		 均方
Mean of square		 F值
F value		 P值
P value
环境Environment 1 39.42 341.33 0.00
重复Replicate 1 0.92 7.98 0.0048
GCAL 122 0.54 4.65 0.00
GCAT 7 13.64 118.16 0.00
特殊配合力Special combining ability 407 0.26 2.22 0.00
环境:GCAL Environment: GCAL 122 0.26 2.29 3.67E-12
环境:GCAT Environment: GCAT 7 0.75 6.47 1.80E-07
环境:特殊配合力Environment: special combining ability 358 0.22 1.88 1.28E-14
残差Residuals 1019 0.12
GCA遗传力Heritability of GCA 0.88

Table 2

Significant loci identified using multi-locus genome-wide association study and candidate genes for GCA of ear diameter"

环境Environment 方法Method 标记Marker P值P value r2 (%) 预测基因Predicted gene
新乡Xinxiang FASTmrMLM 6_153041534 1.02E-07 15.94 Zm00001d038274
FASTmrMLM 10_3824944 1.09E-10 21.08 Zm00001d023343
pLARmEB 10_3824944 9.21E-09 11.90 Zm00001d023343
pLARmEB 10_142762498 2.40E-07 10.34 Zm00001d026284
ISIS EM-BLASSO 7_131856309 1.29E-07 8.32 Zm00001d020772
ISIS EM-BLASSO 10_3824944 1.51E-11 17.93 Zm00001d023343
周口Zhoukou mrMLM 1_186729735 8.18E-08 6.05 Zm00001d031338
pLARmEB 1_36247066 1.87E-10 12.85 Zm00001d028477
pLARmEB 2_196663320 1.87E-07 5.17 Zm00001d001001
pLARmEB 3_234977211 5.12E-08 16.21 Zm00001d044689
pLARmEB 10_2775283 2.66E-10 13.86 Zm00001d023314
ISIS EM-BLASSO 10_2775283 4.79E-08 22.04 Zm00001d023314
BLINK 10_2775283 1.91E-14 － Zm00001d023314
BLINK 1_36247066 9.40E-12 － Zm00001d028477
BLINK 3_234977211 1.31E-10 － Zm00001d044689
BLINK 2_196663320 9.31E-08 － Zm00001d001001
BLINK 7_127910914 8.28E-07 － Zm00001d020682, Zm00001d020683
FarmCPU 3_234977211 2.83E-12 － Zm00001d044689
FarmCPU 1_36247066 4.42E-07 － Zm00001d028477
综合环境Combined environment BLINK 10_3824944 4.06E-12 － Zm00001d023343
BLINK 10_139188724 6.17E-08 － －
BLINK 1_73368818 8.25E-08 － Zm00001d029499
FarmCPU 3_38863628 6.55E-09 － Zm00001d040341
mrMLM 2_25913905 1.18E-08 5.07 Zm00001d002889
mrMLM 10_3824944 1.80E-12 15.57 Zm00001d023343
FASTmrMLM 10_3824944 1.12E-10 18.12 Zm00001d023343
FASTmrEMMA 3_38952028 4.16E-07 0.00 Zm00001d040341, Zm00001d040342
pLARmEB 2_196663320 1.26E-08 7.02 Zm00001d001001
pLARmEB 6_153041644 1.79E-08 11.01 Zm00001d038274
pLARmEB 7_131856309 1.09E-08 7.08 Zm00001d020772
pLARmEB 10_3824944 4.79E-16 20.65 Zm00001d023343
pLARmEB 10_142058950 9.42E-08 7.62 Zm00001d026252
ISIS EM-BLASSO 3_38863604 1.14E-07 9.89 Zm00001d040341
ISIS EM-BLASSO 7_131856309 8.15E-09 8.60 Zm00001d020772
ISIS EM-BLASSO 10_3824944 4.33E-11 18.12 Zm00001d023343

Fig.2

Prediction accuracy for GCA of ear diameter using different random effect models"

Fig.3

The effect of significant loci as fixed effect on the prediction accuracy of GCA for ear diameter Except GBLUP and RKHS represent random effect models, the others are the combinations of MGWAS and predicted methods, which represent fixed effect models."

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