玉米叶夹角性状的全基因组关联分析与关键位点优异等位变异挖掘

doi:10.3724/SP.J.1006.2022.23019

Abstract

Abstract:

Leaf angle (LA) is one of the important components of the canopy structure in maize, which can directly affect the distribution of light and CO₂ in the canopy and the light capture efficiency of the population, thus affecting the yield of maize. In order to analysis the genetic basis of maize LA traits, an association panel including 854 maize inbred lines was used to analyze the first (ULA1), second (ULA2), and third (ULA3) upper leaf angle of ears in five environments, and then 2795 single nucleotide polymorphic (SNP) markers distributed on 10 chromosomes of maize genome were used for genome-wide association analysis (GWAS) of LA traits based on FarmCPU (fixed and random model circulating probability unification) model. Eighty-one significant SNP associations were identified, among which 26, 27, and 28 significant SNPs associated with ULA1, ULA2, and ULA3, and phenotypic variation explained (PVE) for each SNP was 0.03%-9.68%, 0.06%-9.30%, and 0.01%-8.23%, respectively. We further identified 17 heigh-confidence SNPs repeatedly detected for specific trait, among which three loci were firstly reported in this study, 14 loci located within the intervals that had been previously mapped, and nine SNPs were associated with more than one LA trait. Seven SNPs with PVE > 5% were classified as major SNPs, and thus nine germplasms combining the seven elite alleles with small LAs were isolated. Through searching the candidate regions of the 17 high-confidence SNPs, a total of 131 candidate genes were predicated, and a key gene DRL1 known to regulate LA of maize that located 70 kb downstream of PZE-101039301 on chromosome 1 was also identified as one of candidate genes. In summary, the genetic loci and candidate genes identified by this study will be useful for revealing the genetic mechanism of maize LA traits, and provide clues for cloning LA correlated genes. The identified elite alleles and germplasm resources can be used to increase maize yield by molecular marker-assisted selection of LA traits.

Key words: maize, leaf angle, genome-wide association study, candidate gene, elite allele

QIN Wen-Xuan, BAO Jian-Xi, WANG Yan-Bo, MA Ya-Jie, LONG Yan, LI Jin-Ping, DONG Zhen-Ying, WAN Xiang-Yuan. Genome-wide association study of leaf angle traits and mining of elite alleles from the major loci in maize[J].Acta Agronomica Sinica, 2022, 48(11): 2691-2705.

Figures/Tables 9

Fig. S1

Table 1

Fig. 1

Fig. S2

Fig. 2

Table S1

Summary of the significant SNPs associated with different LA traits"

性状 Trait	标记名称 Marker name	染色体 Chromosome	位置 Position (bp)	P值 P-value	表型变异率 PVE (%)	环境/BLUP Environment/BLUP
ULA1	PZB02058.1	1	28,614,062	2.11E-06	3.67	BLUP
	PZE-101063113	1	46,668,336	1.34E-05	5.28	21ZC
	PZE-101073494	1	56,920,858	5.31E-06	2.65	21BJ
	PZE-101256077	1	305,013,865	5.41E-08	2.58	20BJ/21BJ/BLUP
	PZE-102000560	2	837,383	1.57E-09	0.84	20BJ/BLUP
	SYN2580^a	2	31,809,511	3.22E-06	1.54	21BJ
	PZE-102079155	2	63,417,366	1.96E-06	3.64	21ZC
	PZE-102142045	2	194,956,148	1.23E-06	7.09	19BJ
	PZE-103016432	3	8,535,602	1.41E-10	4.61	19BJ
	PZE-103049573	3	53,869,130	3.25E-06	7.18	BLUP
	PZE-104023748	4	28,367,320	3.04E-07	6.31	20BJ/BLUP
	PZE-104062792	4	127,297,691	8.02E-06	0.11	21BJ
	SYN11091	4	172,531,224	1.83E-07	1.26	19BJ/20ZC/BLUP
	PZE-104119909	4	201,188,940	6.31E-07	5.57	19BJ
	PZE-104123484	4	204,948,076	5.48E-06	4.44	20ZC
	PZE-104144719	4	238,721,563	2.85E-06	1.13	21ZC
	PZE-105039536	5	25,111,571	3.56E-06	6.80	20BJ/21BJ/BLUP
	SYN23915	6	121,768,114	1.84E-06	0.97	20BJ
	PZE-107010573	7	7,544,684	3.53E-06	0.17	20BJ/20ZC
	PZE-107010578^c	7	7,546,222	5.29E-06	0.10	19BJ
	PZE-107060629	7	119,797,398	2.65E-06	0.10	20BJ
	PZE-108002532	8	2,930,186	8.55E-06	0.03	20ZC
	PZE-108052985	8	96,363,878	8.70E-09	1.37	20BJ/20ZC
	PZE-109031124	9	37,396,449	5.35E-06	0.17	19BJ/21BJ/BLUP
	PZE-109086476	9	137,669,212	4.74E-06	9.68	19BJ/20BJ/20ZC/21ZC/BLUP
	SYN23715	10	126,322,856	1.61E-05	3.48	20ZC/21ZC
ULA2	PZE-101039301	1	26,700,206	1.24E-07	4.30	21BJ/BLUP
	PZE-101075097	1	59,163,811	1.13E-06	2.99	21BJ
	PZE-101256077	1	305,013,865	1.48E-05	2.52	21BJ
	PZE-102006385	2	3408,488	1.00E-05	3.67	20BJ
	SYN2580^a	2	31,809,511	1.46E-07	1.97	21BJ
	PZE-102079155	2	63,417,366	3.66E-07	4.21	20ZC/21ZC
	PZE-102142045	2	194,956,148	1.33E-05	7.65	19BJ/20BJ
	PZE-102191957^b	2	241,700,492	7.97E-07	0.06	21ZC
	PZE-103016432	3	8,535,602	1.07E-05	5.65	19BJ/20BJ/20ZC/21ZC/BLUP
	PZE-104023748	4	28,367,320	5.63E-07	6.90	19BJ/20ZC
	PZE-104068824	4	140,064,999	1.35E-05	0.93	19BJ
	SYN11091	4	172,531,224	3.58E-06	0.54	19BJ/21BJ
	PZE-104123484	4	204,948,076	2.90E-07	6.49	20BJ/20ZC
	PZE-104126415	4	208,894,785	8.65E-06	7.13	21ZC
	PZE-105042765	5	31,030,693	4.17E-06	1.03	19BJ
	PZE-107010573	7	7,544,684	4.73E-06	0.10	19BJ/20BJ
	PZE-107010578^c	7	7,546,222	8.28E-06	0.11	20ZC
	PZE-108052985	8	96,363,878	2.60E-07	1.45	20ZC/21BJ/BLUP
	PZE-108091532	8	153,166,307	1.08E-06	6.11	20ZC
	PZE-109031124	9	37,396,449	1.16E-09	0.41	19BJ/20BJ/21BJ/BLUP
	PZE-109038841	9	72,089,497	1.13E-05	2.47	20ZC
	PZE-109041138	9	65,843,923	4.94E-06	0.96	21ZC
	PZE-109042223	9	62,588,395	7.38E-06	3.05	21ZC
	PZE-109086476	9	137,669,212	6.54E-06	9.30	20BJ/20ZC/21BJ/21ZC
	PZE-110036140^d	10	68,224,892	2.21E-07	0.22	19BJ
	PZE-110064304	10	121,007,535	1.12E-08	0.11	21ZC
	SYN15051^e	10	125,014,193	1.62E-07	2.19	21ZC
ULA3	PZE-101039301	1	26,700,206	4.81E-07	4.15	21BJ
	PZE-101061168	1	45,273,264	7.12E-06	3.98	21BJ/BLUP
	PZE-101101518	1	101,087,313	6.86E-07	2.71	21BJ
	PZE-101256077	1	305,013,865	3.19E-06	3.34	21ZC
	PZE-102079155	2	63,417,366	2.87E-06	3.80	21BJ/21ZC
	PZE-102191957^b	2	241,700,492	1.47E-05	0.01	21ZC
	PZE-103016432	3	8,535,602	2.96E-07	7.46	19BJ/20BJ/20ZC/21ZC/BLUP
	PZE-103087199	3	145,604,315	9.49E-06	7.82	21BJ
	PZE-103118170	3	179,372,004	1.52E-05	4.25	21ZC
	PZE-104023748	4	28,367,320	1.36E-06	5.13	21BJ
	SYN11091	4	172,531,224	4.11E-06	0.35	21BJ
	PZE-105042690	5	30,864,455	5.59E-07	2.52	21BJ
	PZE-105077135	5	88,521,036	3.23E-06	5.73	20BJ
	PZE-105157980	5	211,658,642	1.69E-05	5.00	21BJ
	ZM013489-0395	5	217,943,859	5.55E-06	0.15	19BJ
	PZE-106000325	6	713,929	7.45E-06	0.17	21BJ
	PZE-106036880	6	87,796,537	1.97E-06	0.02	19BJ
	PZE-107010573	7	7,544,684	4.02E-06	0.13	20BJ/21ZC/BLUP
	PZE-107047280	7	99,863,965	2.07E-07	0.03	21BJ
	SYN15862	8	2,200,273	1.58E-07	0.01	20BJ
	PZE-108052985	8	96,363,878	1.11E-05	1.09	20BJ
	PZE-108091532	8	153,166,307	1.15E-07	7.13	20ZC/21BJ/BLUP
	PZE-109031124	9	37,396,449	7.79E-06	0.72	19BJ/20BJ/21BJ
	PZE-109039325	9	70,992,241	4.68E-06	5.15	21BJ
	PZE-109086476	9	137,669,212	5.43E-06	8.23	BLUP
	PZE-110036140^d	10	68,224,892	1.23E-05	0.18	19BJ
	SYN15051^e	10	125,014,193	4.40E-07	2.21	21ZC
	SYN23715	10	126,322,856	6.89E-06	4.11	21BJ/BLUP

Table S1

Table 2

Fig. 3

Table 3

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性状 Trait	环境 Environment	均值 Mean (°)	标准差 Standard deviation	方差 Variance	偏度 Skewness	峰度 Kurtosis	变异系数 Variation coefficient (%)	变异范围 Rang of variations (°)	遗传力 h²(%)
穗上第1叶夹角 ULA1	19BJ	23.79	8.741	76.40	1.13	3.18	36.74	5.60-97.85	88.8
	20BJ	16.93	8.673	75.22	1.10	3.37	51.23	0.05-83.85
	20ZC	17.00	8.333	69.44	0.97	3.43	49.02	0.10-80.10
	21BJ	18.21	8.453	71.46	0.75	1.21	46.43	0.25-59.80
	21ZC	19.08	8.177	66.86	0.71	1.02	42.85	0.05-62.30
穗上第2叶夹角 ULA2	19BJ	21.40	8.881	78.87	1.25	3.59	41.49	5.50-96.85	90.4
	20BJ	15.23	8.646	74.75	1.21	3.42	56.78	0.05-82.93
	20ZC	16.57	8.997	80.94	1.04	2.86	54.29	0.00-81.90
	21BJ	16.65	8.972	80.50	1.07	2.48	53.87	0.00-81.10
	21ZC	15.55	8.030	64.48	0.97	1.76	51.63	0.05-55.30
穗上第3叶夹角 ULA3	19BJ	20.98	9.502	90.29	1.35	3.40	45.29	5.30-90.75	90.7
	20BJ	14.41	9.057	82.03	1.29	3.80	62.86	0.00-81.65
	20ZC	15.93	9.972	99.44	1.30	4.44	62.62	0.00-97.90
	21BJ	16.64	9.686	93.81	1.42	5.57	58.22	0.05-107.95
	21ZC	14.61	8.591	73.80	1.49	4.73	58.80	0.00-76.85

自交系 Inbred line	ULA1 (°)					ULA2 (°)					ULA3 (°)
自交系 Inbred line	19BJ	20BJ	20ZC	21BJ	21ZC	19BJ	20BJ	20ZC	21BJ	21ZC	19BJ	20BJ	20ZC	21BJ	21ZC
B241	14.43	6.35	6.65	7.54	7.18	9.40	2.09	5.55	4.46	5.27	10.57	4.35	5.16	5.24	6.71
B292	9.48	4.57	2.56	5.70	5.41	8.78	1.66	1.62	5.65	3.26	8.57	3.33	2.34	2.68	2.87
B630	13.15	3.57	2.73	5.97	7.51	9.61	6.08	6.38	5.61	4.52	10.46	2.24	3.99	7.17	5.07
B631	14.71	4.22	6.16	10.17	9.38	11.63	4.00	6.60	4.46	4.58	9.86	2.47	2.81	4.95	5.51
B634	12.65	4.47	4.86	5.56	10.35	10.43	2.77	5.71	5.08	3.76	10.37	1.63	2.80	4.21	2.97
B635	9.68	2.15	2.71	6.08	4.60	7.84	4.12	5.31	4.83	5.93	7.80	2.81	2.82	6.36	5.51
B638	11.15	2.20	3.40	2.58	9.48	7.42	2.76	4.96	5.17	4.10	7.10	1.92	2.53	2.20	4.60
B640	13.85	5.00	4.97	4.72	11.23	11.55	4.12	6.52	6.96	5.20	10.52	3.74	2.46	5.66	4.60
B709	12.20	6.46	6.04	9.26	9.18	11.38	4.68	6.76	2.88	5.11	10.02	3.94	4.35	6.08	4.97

Genome-wide association study of leaf angle traits and mining of elite alleles from the major loci in maize

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