玉米叶向值的全基因组关联分析

doi:10.3724/SP.J.1006.2020.93063

Abstract

Abstract:

Leaf orientation value is a comprehensive index reflecting the two characteristics of “straight” and “vertical” of leaves. The varieties with high leaf orientation value have straight and not curved leaves, and small angle, which are conducive to the wind ventilation and light transmission for maize population. When the planting density is high, it is easier to obtain high yield than the expanded plant-type. It is of great significance for molecular design breeding of ideal plant type to clarify the genetic basis of leaf orientation value. In this study, 285 diverse lines genotyped by the MaizeSNP50 chip were evaluated for leaf orientation in 2017 and 2018. The genome-wide association analysis (GWAS) were used to identified the SNPs, which were significant association with leaf orientation values. The analysis of variance showed that the significant variations were observed for leaf orientation value of different inbred lines (P < 0.01). In the selection of the optimal model, it was found that the Q + K model was the most suitable for the leaf orientation association analysis in this study. A total of 15 loci (P < 4.05E-5) were detected by GWAS, including 27 SNPs, explaining 5.54%-8.73% of phenotypic variation, and 15 candidate genes were mined in two years. Among them, site 2 in 1.07 bin was an important site found in this study, and its candidate gene might be Zm00001d032050 encoding cyclin dependent protein kinase, which needed to be further confirmed by map-based cloning.

Key words: maize, leaf orientation value, leaf angle, single nucleotide polymorphism, association analysis

PENG Bo,ZHAO Xiao-Lei,WANG Yi,YUAN Wen-Ya,LI Chun-Hui,LI Yong-Xiang,ZHANG Deng-Feng,SHI Yun-Su,SONG Yan-Chun,WANG Tian-Yu,LI Yu. Genome-wide association studies of leaf orientation value in maize[J].Acta Agronomica Sinica, 2020, 46(6): 819-831.

Figures/Tables 8

Table 1

Fig. 1

Table 2

Fig. 2

Fig. 3

Fig. 4

Table 3

Significant SNPs and candidate genes associated with leaf orientation value identified by GWAS in two years"

位点^a Locus^a	Bin	年份 Year	SNP	基因型 Genotype	物理位置^b Physical position	P值 P-value	贡献率 R²(%)	峰值SNP 物理位置^b Lead SNP physical position	QTL区间^b QTL region ^b		候选基因 Candidate gene	基因功能注释 Gene annotation
位点^a Locus^a	Bin	年份 Year	SNP	基因型 Genotype	物理位置^b Physical position	P值 P-value	贡献率 R²(%)	峰值SNP 物理位置^b Lead SNP physical position	-LD	+LD	候选基因 Candidate gene	基因功能注释 Gene annotation
1	1.02	BLUP	PUT-163a-149085801-877	[A/G]	28,638,770	9.25E-06	7.95	28,638,770	28,306,770	28,638,770	Zm00001d028265	细胞分裂素响应因子 Cytokinin response regulator
1	1.02	2017	PUT-163a-149085801-877	[A/G]	28,638,770	3.21E-06	8.73	28,638,770	28,306,770	28,638,770	Zm00001d028265	细胞分裂素响应因子 Cytokinin response regulator
2	1.07	BLUP	PZE-101164453	[T/C]	210,517,983	3.22E-05	6.94	211,113,165	210,781,165	211,445,165	Zm00001d032050	细胞周期蛋白依赖性蛋白激酶 Regulation of cyclin-dependent protein serine/threonine kinase activity
2	1.07	BLUP	PZE-101164815	[A/G]	210,772,541	1.16E-06	8.15
2	1.07	2017	PZE-101164815	[A/G]	210,772,541	9.67E-07	8.49
2	1.07	2018	PZE-101164815	[A/G]	210,772,541	2.71E-05	6.24
2	1.07	2017	SYN25384	[A/G]	211,113,165	3.97E-05	6.99
2	1.07	BLUP	SYN25375	[T/C]	211,116,324	1.90E-05	7.32
2	1.07	2017	SYN25375	[T/C]	211,116,324	3.78E-05	6.93
3	1.07	BLUP	PZE-101165699	[A/G]	211,785,378	2.04E-05	7.55	211,785,378	211,453,378	212,117,378	Zm00001d032078	细胞分裂周期相关蛋白激酶 Cell division cycle 2-related protein kinase 7
3	1.07	2017	PZE-101165699	[A/G]	211,785,378	3.02E-05	7.30	211,785,378	211,453,378	212,117,378	Zm00001d032078	细胞分裂周期相关蛋白激酶 Cell division cycle 2-related protein kinase 7
4	1.07	BLUP	PZE-101166565	[A/G]	212,687,705	1.20E-06	7.65	212,687,705	212,355,705	213,019,705	Zm00001d032100	果胶酶/果胶酶抑制剂 Pectinesterase/pectinesterase inhibitor 13
4	1.07	2017	PZE-101166565	[A/G]	212,687,705	5.31E-06	6.93
4	1.07	2018	PZE-101166565	[A/G]	212,687,705	9.69E-06	6.67
5	1.08	BLUP	PZE-101196520	[A/G]	248,302,322	1.38E-05	7.78	248,302,322	247,970,322	248,634,322	Zm00001d033047	含SPX结构域蛋白 SPX domain-containing protein 3
6	1.08	2017	PZE-101199858	[T/C]	252,942,320	2.99E-05	6.73	252,942,320	252,610,320	253,274,320	Zm00001d033180	油菜素内酯缺乏性矮秆基因 Brassinosteroid-deficient dwarf1,brd1
6	1.08	2017	PZE-101199859	[A/G]	252,942,792	2.99E-05	6.73	252,942,320	252,610,320	253,274,320	Zm00001d033180	油菜素内酯缺乏性矮秆基因 Brassinosteroid-deficient dwarf1,brd1
7	2.01	BLUP	SYN9223	[A/G]	3,825,340	3.71E-05	7.11	3,825,340	3,526,340	4,124,340	Zm00001d001968	细胞周期相关蛋白 Cyclin-related
8	2.04	BLUP	PZE-102062747	[A/C]	43,019,177	1.98E-05	7.91	43,019,177	42,720,177	43,318,177	Zm00001d003401	类似14-3-3蛋白 14-3-3-like protein GF14-6
9	2.04	BLUP	SYN29642	[T/C]	50,700,996	3.50E-05	6.15	50,700,996	50,401,996	50,999,996	Zm00001d003626	NAC-转录因子 NAC-transcription factor 76
10	2.07	2017	PZE-102150850	[T/G]	203,858,592	3.50E-05	6.82	203,858,592	203,559,592	204,157,592	Zm00001d006293	NLP转录因子 NLP-transcription factor 17
11	2.07	BLUP	PZE-102152182	[A/G]	205,338,006	3.24E-05	5.54	205,338,006	205,039,006	205,637,006	Zm00001d006348	生长调节因子 Growth-regulating factor 9
12	5.06	BLUP	PZE-105142621	[A/G]	201,997,615	9.76E-06	7.70	201,997,615	201,615,615	202,379,615	Zm00001d017618	ABI3-VP1-转录因子 ABI3-VP1-transcription factor 16
12	5.06	2017	PZE-105142621	[A/G]	201,997,615	1.72E-05	7.52	201,997,615	201,615,615	202,379,615	Zm00001d017618	ABI3-VP1-转录因子 ABI3-VP1-transcription factor 16
13	7.02	BLUP	PZE-107043106	[A/G]	87,913,892	3.32E-05	8.24	87,913,892	87,468,892	88,358,892	Zm00001d020041	参与细胞壁果胶代谢蛋白 Cell wall pectin metabolic process
14	10.03	2017	PZE-110020884	[T/C]	28,391,702	2.32E-05	7.65	28,391,702	27,697,702	29,085,702	Zm00001d023927	锌指CCCH结构域蛋白 Zinc finger CCCH domain-containing protein 30
15	10.04	BLUP	PZE-110053328	[A/G]	100,750,723	4.02E-05	6.73	100,750,723	100,056,723	101,444,723	Zm00001d025033	TCP转录因子 TCP-transcription factor 40

Table 3

Fig. 5

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年份 Year	均值 Mean	变异范围 Range	标准差 SD	偏度 Skewness	峰度 Kurtosis	相关系数Correlation coefficient
年份 Year	均值 Mean	变异范围 Range	标准差 SD	偏度 Skewness	峰度 Kurtosis	2017	2018
2017	59.45	12.99-86.28	13.77	-0.58	0.13
2018	63.86	17.05-90.00	13.11	-0.79	0.59	0.75^**
BLUP	61.58	23.46-82.65	11.14	-0.63	0.30	0.95^**	0.90^**

变异来源 Variation source	方差分量 Variance	遗传力 H²(%)
基因型 Genotype	141.46^**	87.86
年份Year	8.97^**
基因型×年份 Genotype×year	21.41^**
重复Replication	14.63
残差Residual	35.32

Genome-wide association studies of leaf orientation value in maize

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