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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (10): 2451-2462.doi: 10.3724/SP.J.1006.2022.13052

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

Dissecting the genetic basis of kernel size related traits and their combining ability based on a hybrid population in maize

LI Ting1,2(), WANG Ya-Peng1,2, DONG Yuan1,2, GUO Rui-Shi1, LI Dong-Mei1, TANG Ya-Ling1, ZHANG Xing-Hua1,2, XUE Ji-Quan1,2, XU Shu-Tu1,2,*()   

  1. 1Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
    2Maize Engineering Technology Research Centre of Shaanxi Province, Yangling 712100, Shaanxi, China
  • Received:2021-09-07 Accepted:2022-02-25 Online:2022-10-12 Published:2022-03-22
  • Contact: XU Shu-Tu E-mail:ltstime@163.com;shutuxu@nwafu.edu.cn
  • Supported by:
    China Agriculture Research System (Maize, CARS-02-77) of MOF and MARA;Key Research and Development Program of Shaanxi Province(2021ZDLNY01-06)

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Abstract:

Combining ability is a crucial index for evaluating elite inbred lines and selecting superior hybrids during maize breeding processes. Kernel size related traits are important components of grain yield. Therefore, dissecting the genetic basis of kernel size related traits and their combining ability is beneficial for improving maize yield. In this study, we performed genome-wide association study (GWAS) of kernel size related traits and their combining ability using 246 hybrids breed by designed as NCII mating. The broad-sense heritability of kernel length (KL), kernel width (KW), and kernel thickness (KT) was 76.20%, 86.52%, and 81.14%, respectively. The correlation coefficient between each trait and their combining ability was more than 0.58, indicating there was significant positive correlation. Based on the efficient mixed-model association expedited (EMMAX) algorithm, we identified 31, 21, and 5 significant single nucleotide polymorphisms (SNPs) associated with the best linear unbiased estimation (BLUE), general combining ability (GCA), and special combining ability (SCA) of kernel size related traits, respectively. Among these significant SNPs, 10 SNPs were co-located both kernel size related traits and their combining ability. The effect analysis of co-located significant SNPs showed that three SNPs were additive, four were partial dominance and one was overdominance. Further, 17 candidate genes were predicted from candidate regions of co-located SNPs or SNPs with large effect, such as shrunken 1, emp6 and so on. The results further dissect the genetic architecture of maize kernel size related traits and their combining ability and provide useful information for improving grain yield in maize breeding.

Key words: maize, hybrids, kernel size, combining ability, genome-wide association study

Table 1

Descriptive statistics analysis and analysis of variance of kernel size related traits (mm)"

来源 Source 粒长 KL 粒宽 KW 粒厚 KT
均值±标准差 Mean ± SD 12.62 ± 0.66 7.55 ± 0.44 4.30 ± 0.23
变异系数 CV 5.21% 5.78% 5.38%
偏度 Skewness 0.08 0.30 0.24
峰度 Kurtosis 0.15 0.41 -0.25
母本一般配合力 GCA female 2.22*** 0.26*** 1.55***
父本一般配合力 GCA male 25.86*** 3.89*** 6.60***
特殊配合力 SCA 0.56*** 0.08*** 0.18***
母本一般配合力×环境 GCA female × Environment 0.44 0.05** 0.11
父本一般配合力×环境GCA male × Environment 0.57 0.04 0.22*
特殊配合力×环境 SCA × Environment 0.35 0.04 0.09
基因型方差 $\sigma _{\text{g}}^{2}$ 0.31 0.17 0.04
基因型×环境方差 $\sigma _{\text{ge}}^{2}$ 0.02 0.00 0.00
广义遗传力 H2 (%) 76.20 86.52 81.14

Fig. 1

Correlation analysis of kernel size related traits and combining ability A: correlation analysis of kernel size related traits in different environments. B: correlation analysis between kernel size related traits and their combining ability. *, **, and *** indicate significant correlation at P < 0.05, P < 0.01, and P < 0.001, respectively; KL: kernel length; KW: kernel width; KT: kernel thickness; XY: Xunyi; YL: Yulin; BLUE: best linear unbiased estimation; GCA: general combining ability; SCA: special combining ability."

Fig. 2

Distribution of significant SNPs associated with kernel size related traits and their combining ability Abbreviations are the same as those given in Fig. 1."

Table 2

Associated SNPs of kernel size related traits and their combining ability including general combining ability (GCA) and special combining ability (SCA)"

序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 位置
Position		 等位基因
Allele		 P值
P-value		 模型
Model		 表型解释率
R2 (%)
1 KL_BLUE Affx-291427653 2 172,900,382 A/C 1.17E-05 加性Additive 2.65
2 KL_BLUE Affx-291399192 2 174,990,230 C/T 6.00E-05 显性Dominance 5.20
3 KL_BLUE Affx-291415239 2 188,723,861 A/G 1.23E-04 加性Additive 3.36
4 KL_BLUE Affx-291421576 3 4,667,059 C/T 1.17E-04 显性Dominance 0.59
5 KL_BLUE Affx-291388159 4 161,189,573 G/T 9.25E-05 显性Dominance 7.87
6 KL_BLUE Affx-291414096 5 19,152,693 G/A 1.12E-04 显性Dominance 7.50
7 KL_BLUE Affx-291382102 5 45,936,956 A/T 6.34E-05 显性Dominance 0.75
8 KL_BLUE Affx-291430485 5 199,891,583 T/C 3.77E-05 显性Dominance 0.84
序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 位置
Position		 等位基因
Allele		 P值
P-value		 模型
Model		 表型解释率
R2 (%)
9 KL_GCA Affx-88981164 2 109,561,515 G/A 2.62E-05 加性Additive 25.52
10 KL_GCA Affx-291438859 2 147,075,651 C/T 1.25E-04 加性Additive 7.29
11 KL_GCA Affx-291381936 2 172,197,055 G/A 7.39E-05 加性Additive 13.35
12 KL_GCA Affx-291427653 2 172,900,382 A/C 7.93E-07 加性Additive 0.80
13 KL_GCA Affx-291383897 2 173,344,526 G/C 1.86E-05 加性Additive 0.90
14 KL_GCA Affx-291399192 2 174,990,230 C/T 3.45E-05 加性Additive 0.03
15 KL_GCA Affx-291400614 2 177,112,609 C/T 4.06E-05 加性Additive 1.11
16 KL_GCA Affx-291415239 2 188,723,861 A/G 4.76E-06 加性Additive 0.42
17 KL_GCA Affx-291419252 2 194,294,110 T/C 9.17E-06 加性Additive 0.02
18 KL_SCA Affx-291414096 5 19,152,693 G/A 6.68E-05 显性Dominance 3.54
19 KW_BLUE Affx-291445199 1 180,428,491 C/T 1.16E-04 显性Dominance 10.90
20 KW_BLUE Affx-158946352 1 224,324,098 G/A 5.83E-05 加性Additive 0.65
21 KW_BLUE Affx-291438736 1 292,427,178 C/A 4.06E-05
5.00E-11		 加性Additive
显性Dominance		 28.23
0.07
22 KW_BLUE Affx-291386203 2 28,660,634 C/A 3.98E-05
2.31E-05		 加性Additive
显性Dominance		 3.79
0.44
23 KW_BLUE Affx-291438094 2 235,818,735 C/G 1.09E-05 显性Dominance 0.07
24 KW_BLUE Affx-291404824 3 1,338,197 C/A 2.84E-05
8.58E-06		 加性Additive
显性Dominance		 6.41
12.47
25 KW_BLUE Affx-291426461 4 35,122,656 T/C 3.23E-05 显性Dominance 0.11
26 KW_BLUE Affx-159061154 5 2,145,982 T/G 8.59E-05 显性Dominance 0.15
27 KW_BLUE Affx-291435207 7 277,626 A/G 5.33E-05 加性Additive 12.96
28 KW_BLUE Affx-291438357 9 38,415,742 T/C 8.18E-05 显性Dominance 0.18
29 KW_GCA Affx-291445199 1 180,428,491 C/T 1.34E-04 加性Additive 16.83
30 KW_GCA Affx-158946352 1 224,324,098 G/A 1.36E-04 加性Additive 6.47
31 KW_GCA Affx-158948129 1 235,021,563 C/T 7.38E-05 加性Additive 10.69
32 KW_GCA Affx-291438736 1 292,427,178 C/A 4.28E-06 加性Additive 16.97
33 KW_GCA Affx-291385173 2 5,147,139 T/C 3.83E-05 加性Additive 1.67
34 KW_GCA Affx-291420744 5 80,480,359 A/C 3.51E-05 加性Additive 7.50
35 KW_GCA Affx-291401044 9 129,309,960 A/G 2.72E-05 加性Additive 8.28
36 KW_SCA Affx-291436386 2 27,498,155 C/T 1.11E-04 显性Dominance 2.92
37 KT_BLUE Affx-291413666 1 118,986,201 A/C 8.08E-05 显性Dominance 7.95
38 KT_BLUE Affx-159032175 1 262,226,149 T/C 6.04E-06 显性Dominance 0.37
39 KT_BLUE Affx-291390855 1 262,368,074 C/T 4.17E-05
1.60E-05		 加性Additive
显性Dominance		 12.47
7.33
40 KT_BLUE Affx-158839028 1 280,195,356 C/A 7.78E-05 显性Dominance 3.39
41 KT_BLUE Affx-291410051 1 285,592,051 C/T 5.51E-05 显性Dominance 4.21
42 KT_BLUE Affx-291443747 2 23,623,257 G/A 8.77E-05 加性Additive 25.58
43 KT_BLUE Affx-291388256 2 195,694,458 C/T 1.19E-04 显性Dominance 0.34
44 KT_BLUE Affx-291401517 2 235,207,369 G/A 1.26E-05 显性Dominance 0.26
45 KT_BLUE Affx-291441620 3 85,891,477 T/C 6.06E-06 显性Dominance 2.57
46 KT_BLUE Affx-291422512 9 11,615,037 G/A 1.36E-04 显性Dominance 0.53
47 KT_BLUE Affx-291445448 9 15,315,557 A/C 8.53E-05 显性Dominance 3.25
48 KT_BLUE Affx-291438777 9 107,428,822 G/A 2.59E-05 显性Dominance 0.04
49 KT_BLUE Affx-291378767 10 144,701,539 C/A 1.09E-04 显性Dominance 2.76
50 KT_GCA Affx-291399215 1 104,625,663 C/T 3.57E-05 加性Additive 21.69
序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 位置
Position		 等位基因
Allele		 P值
P-value		 模型
Model		 表型解释率
R2 (%)
51 KT_GCA Affx-291390855 1 262,368,074 C/T 7.69E-05 加性Additive 10.71
52 KT_GCA Affx-291418355 3 1,713,800 A/G 1.18E-04 加性Additive 9.51
53 KT_GCA Affx-291442108 4 12,611,068 G/A 9.26E-05 加性Additive 0.03
54 KT_GCA Affx-291425118 5 37,099,257 C/T 1.14E-04 加性Additive 4.83
55 KT_SCA Affx-291399798 3 11,407,826 G/A 9.19E-05 显性Dominance 3.52
56 KT_SCA Affx-291422512 9 11,615,037 G/A 4.99E-05 显性Dominance 5.84
57 KT_SCA Affx-291438777 9 107,428,822 G/A 8.20E-05 显性Dominance 1.66

Table 3

Effects analysis of co-located SNPs between BLUE and their combining ability including general combining ability (GCA) and special combining ability (SCA)"

序号
Number		 性状
Trait		 SNP名称
SNP marker		 染色体
Chr.		 位置
Position		 显性度
Dominance effect index		 效应
Effect
1 KL_BLUE, KL_GCA Affx-291427653 2 172,900,382 0.03 加性 Additive
2 KL_BLUE, KL_GCA Affx-291399192 2 174,990,230 -0.12 加性 Additive
3 KL_BLUE, KL_GCA Affx-291415239 2 188,723,861 -0.55 部分显性 Partial dominance
4 KL_BLUE, KL_SCA Affx-291414096 5 19,152,693 2.64 超显性 Overdominance
5 KW_BLUE, KW_GCA Affx-291445199 1 180,428,491 — —
6 KW_BLUE, KW_GCA Affx-158946352 1 224,324,098 -0.08 加性Additive
7 KW_BLUE, KW_GCA Affx-291438736 1 292,427,178 -0.57 部分显性 Partial dominance
8 KT_BLUE, KT_GCA Affx-291390855 1 262,368,074 — —
9 KT_BLUE, KT_SCA Affx-291422512 9 11,615,037 -0.60 部分显性 Partial dominance
10 KT_BLUE, KT_SCA Affx-291438777 9 107,428,822 -0.57 部分显性 Partial dominance

Fig. 3

Allele distribution and phenotypic difference of co-located SNPs between traits and their combine ability ** and *** indicate significant difference at P < 0.01 and P < 0.001, respectively. Abbreviations are the same as those given in Table 1."

Fig. 4

Functional enrichment analysis of genes expressed in kernel in the candidate interval. A: GO analysis; B: KEGG pathway analysis. BP: biological process; CC: cellular component; MF: biological process."

Table 4

Putative candidate genes of kernel size related traits and their combining ability including general combining ability (GCA) and special combining ability (SCA)"

序号
Number		 性状
Trait		 SNP标记
SNP marker		 染色体
Chr.		 候选基因
Candidate gene		 注释
Description
1 KT_GCA Affx-291399215 1 GRMZM2G025157 Putative pentatricopeptide repeat-containing protein
2 KW_BLUE, KW_GCA Affx-291445199 1 GRMZM2G085474 Thiolase1 (thl1)
3 KW_BLUE, KW_GCA Affx-158946352 1 GRMZM2G031572 Putative serine peptidase S28 family protein
4 KW_GCA Affx-158948129 1 GRMZM2G464680 Xyloglucan galactosyltransferase KATAMARI 1
5 KT_BLUE, KT_GCA Affx-291390855 1 GRMZM2G022997 Inositol hexakisphosphate and diphosphoinositol- pentakisphosphatekinase VIP2
6 KW_BLUE, KW_GCA Affx-291438736 1 GRMZM2G450920 Protein SCAR2
7 KT_BLUE Affx-291443747 2 GRMZM2G505380 Protein O-glucosyltransferase 1
8 KL_GCA Affx-88981164 2 GRMZM2G158043 Pullulanase-type starch debranching enzyme1 (zpu1)
9 KL_BLUE, KL_GCA Affx-291427653 2 GRMZM2G014106 Enhancer of polycomb-like transcription factor
10 KL_GCA Affx-291381936 2 GRMZM2G104546 Aspartate kinase homoserine dehydrogenase 2
11 KL_BLUE, KL_GCA Affx-291399192 2 AC203957.3_FG004 BZIP-transcription factor 40
12 KL_BLUE, KL_GCA Affx-291415239 2 GRMZM2G048392 Empty pericarp6 (emp6)
13 KW_BLUE Affx-291404824 3 GRMZM2G175218 Beta amylase4 (amyb4)
14 KL_BLUE, KL_SCA Affx-291414096 5 GRMZM2G081221 Protein phosphatase 1 regulatory inhibitor
15 KW_BLUE Affx-291435207 7 GRMZM5G800488 Laccase20 (lac20)
16 KT_BLUE, KT_SCA Affx-291422512 9 GRMZM2G089713 Sucrose synthase (shrunken1)
17 KT_BLUE, KT_SCA Affx-291438777 9 GRMZM2G048472 Homogentisate phytyltransferase VTE2-1
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