Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction

doi:10.11923/j.issn.2095-4050.cjas2023-0092

Abstract

Abstract:

To explore the natural variations in regulating the maize kernel development and to assist in the genetic improvement of maize yield traits, in this study, 150 maize inbred lines with rich genetic variations were selected as materials for investigation. Combining 34,342 SNP markers and three models, a genome-wide association analysis was conducted on five grain-related traits. The results revealed that a total of 18 independent loci were significantly associated with the target traits, with each locus accounting for 12.24% to 15.41% of the phenotypic variations. Additionally, significant epistatic interactions were identified among four pairs of SNPs associated with kernel length, collectively explaining 5.32% of the phenotypic variations. By integrating the dynamic transcriptome data of kernel development in the B73 inbred line and functional annotations of genes, 19 candidate genes were predicted and classified into four categories: 6 enzymes, 3 ribosomal proteins, 1 transcription factor, and 9 other proteins. These candidate genes provide new genetic resources for deciphering the molecular mechanisms of maize kernel development and enhancing maize kernel size and yield. Through this research, we have not only uncovered the natural variations that regulate the development of corn kernels but also provided new genetic resources for the genetic improvement of corn yield traits. These findings are expected to bring new breakthroughs in corn breeding efforts, enhance corn production, and thereby better meet human needs for food.

Key words: maize, kernel size, yield, genome-wide association analysis, candidate genes prediction

CHEN Xinyi, LIU Chenyan, HUA Mingzhu, XU Xin, FENG Wenxiang, WANG Baohua, FANG Hui. Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction[J]. Journal of Agriculture, 2024, 14(4): 26-36.

Figures/Tables 8

References 81

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性状	自交系个数	最小值	最大值	平均值±标准差	变异系数	广义遗传力	置信区间
HKW/g	150	8.28	31.07	20.49 ± 4.12	20.11	0.995	0.994~0.997
KL/mm	150	7.37	10.00	8.75 ± 0.51	5.83	0.653	0.530~0.744
KW/mm	150	6.82	9.08	8.17 ± 0.37	4.53	0.916	0.886~0.938
KT/mm	150	3.97	6.12	4.79 ± 0.41	8.56	0.849	0.795~0.888
KV/mL	150	0.10	0.26	0.17 ± 0.03	17.65	0.523	0.354~0.647

性状	自交系个数	最小值	最大值	平均值±标准差	变异系数	广义遗传力	置信区间
HKW/g	150	8.28	31.07	20.49 ± 4.12	20.11	0.995	0.994~0.997
KL/mm	150	7.37	10.00	8.75 ± 0.51	5.83	0.653	0.530~0.744
KW/mm	150	6.82	9.08	8.17 ± 0.37	4.53	0.916	0.886~0.938
KT/mm	150	3.97	6.12	4.79 ± 0.41	8.56	0.849	0.795~0.888
KV/mL	150	0.10	0.26	0.17 ± 0.03	17.65	0.523	0.354~0.647

	HKW	KL	KW	KT	KV
HKW	1	4.62E-16	5.70E-16	3.25E-11	3.32E-31
KL	0.65	1	3.34E-05	2.05E-01	4.87E-12
KW	0.65	0.36	1	3.42E-02	1.03E-09
KT	0.55	0.12	0.19	1	2.23E-09
KV	0.82	0.57	0.52	0.51	1

	HKW	KL	KW	KT	KV
HKW	1	4.62E-16	5.70E-16	3.25E-11	3.32E-31
KL	0.65	1	3.34E-05	2.05E-01	4.87E-12
KW	0.65	0.36	1	3.42E-02	1.03E-09
KT	0.55	0.12	0.19	1	2.23E-09
KV	0.82	0.57	0.52	0.51	1

性状	标记	染色体	物理位置	P值	R²/%	候选基因_V3	候选基因_V4	功能注释	备注
KL	PUT-163a-4730462-2143	1	49131053	7.94E-05	12.51	GRMZM2G038015	Zm00001d028879	bZIP-transcription factor 24
KL	PZE-101070408	1	53158367	5.13E-05	13.56	GRMZM2G107463	Zm00001d028989	RING/U-box superfamily protein
HKW	SYN29761	1	90219767	2.75E-05	14.29	GRMZM2G154487	Zm00001d029887	Ribosomal L18p/L5e family protein
KV	PZE-102077877	2	60656421	5.47E-05	13.80	GRMZM2G016749	Zm00001d000124	Protein-serine/threonine phosphatase
KW	PZE-103124207	3	181695567	1.10E-05	15.41	GRMZM2G386991	Zm00001d042938	Serine/threonine-protein kinase AFC1
KL	ZM013522-0530	3	222667473	1.22E-05	15.26	GRMZM5G866024	Zm00001d044376	membrane protein
KT	SYNGENTA2236	4	5010855	8.07E-05	12.86	GRMZM2G101502	Zm00001d018506	Deoxyhypusine hydroxylase	条件分析
KL	SYN3700	5	216163416	1.93E-05	14.62	GRMZM2G101571	Zm00001d018507	bet1 sft1-related snare
KL	PZE-106060527	6	109295972	1.13E-05	15.25	GRMZM2G048194	Zm00001d037151	erwinia induced protein 1
KV	PZE-106082684	6	139912054	9.34E-05	12.71	GRMZM2G068496	Zm00001d037972	60S ribosomal protein L29	条件分析
KV	PZE-106082684	6	139912054	9.34E-05	12.71	GRMZM2G068323	Zm00001d037975	pentatricopeptide repeat-containing protein	条件分析
HKW	SYN38610	6	165943896	7.25E-05	12.74	GRMZM2G132929	Zm00001d039106	40S ribosomal protein S12-like
HKW	PZE-108019862	8	17889483	8.97E-05	12.47	GRMZM2G080722	Zm00001d008736	Monothiol glutaredoxin-S4, mitochondrial
KT	PZE-108040469	8	65972918	1.05E-05	15.35	GRMZM2G021331	Zm00001d009488	ATP synthase beta chain
KL	PZE-108113799	8	164939218	7.41E-05	14.74	GRMZM2G049269	Zm00001d012211	ankyrin-like protein
KL	PZE-109030021	9	33672066	7.05E-05	12.78	GRMZM2G065355	Zm00001d045724	heat shock factor-binding protein 1
KL	SYN32340	9	90842290	6.11E-05	13.20	GRMZM2G056166	Zm00001d046531	bri1-kd interacting protein 118
KL	PZE-109077339	9	124770857	2.27E-05	14.39	GRMZM2G113866	Zm00001d047335	sigma factor sigB regulation protein rsbQ
KL	PZE-110109454	10	148515533	9.38E-05	12.24	GRMZM2G173636	Zm00001d026639	acyl-binding domain-containing protein 6