基于杂交群体解析玉米籽粒大小相关性状及其配合力的分子遗传机制

doi:10.3724/SP.J.1006.2022.13052

Abstract

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

LI Ting, WANG Ya-Peng, DONG Yuan, GUO Rui-Shi, LI Dong-Mei, TANG Ya-Ling, ZHANG Xing-Hua, XUE Ji-Quan, XU Shu-Tu. Dissecting the genetic basis of kernel size related traits and their combining ability based on a hybrid population in maize[J].Acta Agronomica Sinica, 2022, 48(10): 2451-2462.

Figures/Tables 8

Table 1

Fig. 1

Fig. 2

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 2

Table 3

Fig. 3

Fig. 4

Table 4

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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

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

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

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

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