Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (9): 1695-1709.doi: 10.3864/j.issn.0578-1752.2022.09.001


Genome-Wide Association Analysis of Yield and Combining Ability Based on Maize Hybrid Population

LI ZhouShuai(),DONG Yuan,LI Ting,FENG ZhiQian,DUAN YingXin,YANG MingXian,XU ShuTu,ZHANG XingHua*(),XUE JiQuan*()   

  1. College of Agronomy, Northwest A&F University/Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Yangling 712100, Shaanxi
  • Received:2021-12-10 Revised:2022-02-08 Online:2022-05-01 Published:2022-05-19
  • Contact: XingHua ZHANG,JiQuan XUE;;


【Objective】By analyzing the yield of the hybrids from the inbred lines bred from the Shaan A and Shaan B group, the combining ability of the inbred lines were evaluated, genome-wide association analysis, and mining associated loci for yield and its combining ability conducted. It will provide references for improving maize inbred lines selected from Shaan A group and Shaan B group and applying them in varieties breeding. 【Method】Based on NCⅡ genetic design, 85 excellent inbred lines from Shaan A group and Shaan B group were used to construct a hybrid population containing 246 F1. Then, the yield of the hybrid population was tested in three environments to evaluate their general combining ability (GCA) and special combining ability (SCA). Using the 6H90K maize array to detect the parental genotypes, 63 879 high-quality SNPs were obtained, which were used to analyze the genetic characteristics of parental lines. According to the parental genotypes, 55 951 high-quality SNPs were inferred in the hybrid population for genome-wide association analysis of hybrid yield, GCA, and SCA using additive model and non-additive model. Meanwhile, candidate genes around the significant SNPs were screened and annotated based on the maize B73 reference genome.【Result】The yield in the three environments accorded to the normal distribution with wide variation, the broad-sense heritability of yield was 59.04%, and the environmental effect was significant. There was significant positive correlation between hybrid yield and combining ability, and the correlation between hybrid yield and SCA (r=0.95) was higher than that between hybrid yield and GCA (r=0.62). The genetic characteristic of Shaan A group and Shaan B group was different, and inbred lines from Shaan A group have higher general combining ability. Totally, five, seven and nine significant SNPs were detected (-log10(P)>3.86) for GCA, hybrid yield and SCA, respectively. Among them, four SNPs were co-located in hybrid yield and SCA. Ultimately, 17 associated SNPs were anchored. Dominant allele analysis of different trait-associated loci showed that four GCA-associated SNPs were controlled by additive effects, and the F1 BLUE-associated loci could be divided into 4 types mainly by the dominant effect, and the heterozygous genotype is the favorite allele or sub-optimal allele for yield in F1. Through functional annotation, the candidate genes were specifically expressed in maize growth and kernel establishment, for example, GRMZM2G165828 and GRMZM2G057557 were related to maize kernel development. 【Conclusion】Based on this study, we consider that GCA and SCA jointly affect the yield of hybrids, and the effect of SCA is greater. Moreover, GCA and SCA may have different genetic basis, and GCA can be increased with the accumulation of favorable alleles. Using the genome-wide association analysis in the F1 hybrid population can carry out genetic analysis related to combining ability, mine the genetic loci related to yield and combining ability, and accelerated the application of the associated loci in molecular breeding.

Key words: maize, hybrids, general combining ability, special combining ability, genome-wide association analysis

Supplementary table 1

Materials list of 85 maize inbred lines"

Table 1

Descriptive statistical analysis and analysis of variance of yield in hybrid population"

FF value
1 5095.60 12917.48 9527.95 1243.25 -0.60 0.96 0.13 59.04 6.60** 6318.72** 3.89**
2 4286.95 12709.47 9286.99 1437.99 -0.64 0.63 0.15
1 12325.73 20036.29 15794.53 1367.89 0.17 0.20 0.09
2 12066.87 20488.13 15533.07 1441.90 0.20 0.36 0.09
1 9401.12 20342.91 14038.85 1889.22 0.41 0.25 0.13
2 10093.17 19664.45 14115.04 1783.91 0.26 -0.04 0.13
BLUE 10775.45 17180.75 13831.91 988.61 -0.28 0.59 0.07

Table 2

Basic statistical analysis of combining ability"

相关系数 Correlation coefficient
GCA 82 -565.87 316.87 172.54 -0.68 0.49 0.51*** 0.62***
SCA 246 -1772.11 1621.62 520.94 -0.30 0.65 0.95***

Fig. 1

Comparison analysis of the yield for testers and their F1 hybrids"

Fig. 2

Evaluation of GCA about 82 tested lines from Shaan A group and Shaan B group"

Fig. 3

Clustering and Principal component analysis of 85 parents"

Fig. 4

Manhattan chart of genome-wide association analysis results of yield and combining ability A: GCA of the tested lines; B: BLUE of F1 yield based on additive model; C: BLUE of F1 yield based on dominance model; D: SCA of hybrid based on additive model; E: SCA of hybrid based on dominance model"

Table 3

Significant associated SNPs of yield and combining ability"

Position (bp)
P value
PVE (%)
GCA Affx-291398318 1 296696400 A/G 0.36 1.02E-04 23.37
GCA Affx-291395842 2 228845613 T/C 0.22 1.13E-04 11.91
GCA Affx-291375443 4 80111618 G/A 0.12 7.12E-05 12.29
GCA Affx-291425877 4 155406944 G/A 0.29 2.77E-05 8.26
GCA Affx-159192088 4 176561593 C/A 0.41 1.31E-04 7.97
F1_ADD ●Affx-291424805 10 146974725 T/C 0.24 6.27E-05 1.55
F1_DOM Affx-88979942 2 4377056 G/A 0.31 1.07E-04 1.75
F1_DOM ■Affx-291385286 2 24634902 T/G 0.37 8.43E-05 4.12
F1_DOM ▲Affx-88980445 2 28002879 G/A 0.42 1.36E-04 0.43
F1_DOM Affx-158919359 4 153499376 C/T 0.08 9.46E-05 5.96
F1_DOM Affx-291394192 10 146837618 A/C 0.43 8.24E-05 3.30
F1_DOM ★Affx-291431456 10 4152732 C/T 0.47 3.52E-05 3.57
SCA_ADD ●Affx-291424805 10 146974725 T/C 0.24 2.82E-05 1.77
SCA_DOM Affx-291423507 1 8628332 C/T 0.44 3.13E-05 1.21
SCA_DOM ■Affx-291385286 2 24634902 T/G 0.37 3.78E-05 3.26
SCA_DOM ▲Affx-88980445 2 28002879 G/A 0.42 6.80E-06 1.22
SCA_DOM Affx-291382512 2 194691551 G/A 0.49 9.30E-05 0.92
SCA_DOM Affx-158945854 2 193402735 A/C 0.49 3.64E-05 1.76
SCA_DOM Affx-291445414 7 805187 G/C 0.42 1.13E-04 1.42
SCA_DOM Affx-291393021 10 1148101 C/T 0.31 1.06E-04 6.31
SCA_DOM ★Affx-291431456 10 4152732 C/T 0.47 6.97E-05 3.15

Table 4

Effect analysis of significant SNPs"

Position (bp)
Favorable bases in different traits
SNP effect
SNP_1 GCA Affx-291398318 Chr.1:296696400 A/G AA*** AA*** AA*** A
SNP_2 GCA Affx-291395842 Chr.2:228845613 T/C CC** CC** CC** A
SNP_3 GCA Affx-291375443 Chr.4:80111618 G/A GG** \ \ \
SNP_4 GCA Affx-291425877 Chr.4:155406944 G/A AA** GA/GG GA A=D
SNP_5 GCA Affx-159192088 Chr.4:176561593 C/A CC CC CC A
SNP_6 CO_ADD Affx-291424805 Chr.10:146974725 T/C CC*** TC TC* D
SNP_7 CO_DOM Affx-291431456 Chr.10:4152732 C/T TT TT/CC* TT/CC* A
SNP_8 CO_DOM Affx-291385286 Chr.2:24634902 T/G GG TG* TG** D
SNP_9 CO_DOM Affx-88980445 Chr.2:28002879 G/A AA GA* GA* D
SNP_10 F1BLUE Affx-88979942 Chr.2:4377056 G/A GG** GG* AA/GG A
SNP_11 F1BLUE Affx-158919359 Chr.4:153499376 C/T CC** CC*** CC** A
SNP_12 F1BLUE Affx-291394192 Chr.10:146837618 A/C CC* AC** AC* D
SNP_13 SCA Affx-291423507 Chr.1:8628332 C/T TT* CT CT* D
SNP_14 SCA Affx-291382512 Chr.2:194691551 G/A AA/GG GA* GA** D
SNP_15 SCA Affx-158945854 Chr.2:193402735 A/C CC AC* AC** D
SNP_16 SCA Affx-291445414 Chr.7:805187 G/C CC GC* GC** D
SNP_17 SCA Affx-291393021 Chr.10:1148101 C/T CC CC/CT*** CC/CT*** A=D

Fig. 5

Favorable allele analysis of significant SNPs"

Fig. 6

Enrichment of favorable alleles for GCA in tested lines"

Table 5

Prediction of candidate gene"

Position (bp)
Candidate genes
SNP_1 GCA Chr.1:296696400 AC206957.1_FG005 转座元件Transposable_element
SNP_2 GCA Chr.2:228845613 GRMZM2G559383 -
SNP_3 GCA Chr.4:80111618 GRMZM2G175827(Zm00001d050350) Kan3转录因子Kan3 transcription factor
SNP_4 GCA Chr.4:155406944 GRMZM2G137029(Zm00001d051447) F-box蛋白PP2-A13 F-box protein PP2-A13
SNP_5 GCA Chr.4:176561593 GRMZM2G097081(Zm00001d052102) AP2-EREBP-转录因子57
AP2-EREBP-transcription factor 57(ereb57)
SNP_6 CO_ADD Chr.10:146974725 GRMZM2G149932(Zm00001d026580) 外泌素家族蛋白 Exostosin family protein
SNP_7 CO_DOM Chr.10:4152732 GRMZM2G101928(Zm00001d023342) -
SNP_8 CO_DOM Chr.2:24634902 GRMZM2G124371(Zm00001d002876) 具有FYVE锌指结构域的染色体凝聚(RCC1)家族的调控因子 Regulator of chromosome condensation (RCC1) family with FYVE zinc finger domain
SNP_9 CO_DOM Chr.2:28002879 GRMZM2G133012(Zm00001d002980) -
SNP_10 F1BLUE Chr.2:4377056 GRMZM2G363066(Zm00001d002013) 水稻凝集素蛋白激酶家族蛋白同源基因 OsRLCK168, homologous gene of lectin protein kinase family protein
SNP_11 F1BLUE Chr.4:153499376 GRMZM2G101388 转座元件Transposable_element
SNP_12 F1BLUE Chr.10:146837618 GRMZM2G464157(Zm00001d026572) 羧酯酶SOBER1 Carboxylesterase SOBER1
SNP_13 SCA Chr.1:8628332 GRMZM2G474258(Zm00001d027598) CCT结构域相关基因(cct101) CO CO-LIKE TIMING OF CAB1 protein domain101(cct101)
SNP_14 SCA Chr.2:194691551 GRMZM2G079109(Zm00001d006153) 1-酰基甘油-3-磷酸O-酰基转移酶 1-acylglycerol-3-phosphate O-ac= yltransferase
SNP_15 SCA Chr.2:193402735 GRMZM2G378215 -
SNP_16 SCA Chr.7:805187 GRMZM2G165828(Zm00001d018615) 类似于谷氨酸受体3.4前体(配体门控离子通道3.4)(AtGLR 4) Similar to Glutamate receptor 3.4 precursor (Ligand-gated ion channel 3.4) (AtGLR4)
SNP_17 SCA Chr.10:1148101 GRMZM2G057557(Zm00001d023220) 外膜OMP85家族蛋白
Outer membrane OMP85 family protein
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