山西谷子种质资源株高全基因组关联分析

doi:10.3724/SP.J.1006.2024.44070

Abstract

Abstract:

A suitable plant height can effectively enhance the nutrient utilization efficiency and lodging resistance of millet. This study utilized 313 local millet varieties from Shanxi as an association group. Plant height was investigated in five different environments, followed by whole-genome deep resequencing. After quality control of the data, 3,160,066 SNP markers uniformly distributed across the nine chromosomes of millet were obtained for genome-wide association analysis (GWAS) of plant height. Eight QTL loci significantly associated with plant height were identified, with each locus explaining 7.13% to 12.08% of the phenotypic variation. Within the 25 kb upstream and downstream confidence intervals of these eight stable QTL loci, forty candidate genes were discovered. Integrating gene annotation information, six candidate genes were identified to be primarily involved in hormone synthesis, cell division regulation, signal transduction, and carbohydrate metabolism. Haplotype analysis revealed that the superior haplotype Hap2 of the candidate gene Millet_GLEAN_10031852 can effectively reduce plant height.

Key words: foxtail millet, plant height, genome-wide association analysis, haplotypes, candidate genes

YANG Shi-Jie, WANG Hua-Zhi, PAN Yi-Min, HUANG Rui, HOU Sen, QIN Hui-Bin, MU Zhi-Xin, WANG Hai-Gang. Genome-wide association analysis for plant height in foxtail millet (Setaria italica L.) germplasm resources in Shanxi, China[J].Acta Agronomica Sinica, 2024, 50(12): 2984-2997.

Figures/Tables 7

Table 1

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 2

Stable QTL loci and the candidate genes identified in this study"

QTL标记 QTL marker	染色体 Chr.	QTL 区间 QTL region (bp)	QTN标记 QTN marker	P值 P-value	性状环境 Trait environment	表型解释率 Phenotypic variation explained (%)	候选基因 Candidate gene	基因功能注释 Gene annotation
qPM3_1	3	18,916,296-18,966,346	PMG_18941296	7.45E-06	18JZ/19JZ/20JZ/20DT/BLUE	9.69	Millet_GLEAN_10028058	Myb DNA结构域 Myb-like DNA-binding domain
			PMG_18941340	5.59E-07	18JZ/19JZ/20JZ/20DT/BLUE	9.69
			PMG_18941346	5.59E-07	18JZ/19JZ/20JZ/20DT/BLUE	9.69
qPM5_2	5	1,178,009-1,236,158	PMG_1203009	9.72E-07	20YC/BLUE	10.78	Millet_GLEAN_10034090	细胞分裂素反应因子4 Cytokinin response factor 4
			PMG_1207247	8.24E-06	20YC/BLUE	9.71	Millet_GLEAN_10034089	s位点凝集素蛋白激酶家族蛋白 s-locus lectin protein kinase family protein
			PMG_1208529	7.19E-08	20YC/BLUE	9.63	Millet_GLEAN_10034086	s位点凝集素蛋白激酶家族蛋白 s-locus lectin protein kinase family protein
			PMG_1210670	7.22E-07	20YC/BLUE	8.42	Millet_GLEAN_10034085	富亮氨酸重复蛋白激酶家族蛋白 Leucine-rich repeat protein kinase family protein
			PMG_1210687	7.22E-07	20YC/BLUE	8.40	Millet_GLEAN_10034088	s位点凝集素蛋白激酶家族蛋白 s-locus lectin protein kinase family protein
			PMG_1210696	7.19E-08	20DT/20YC/BLUE	8.43
			PMG_1210700	7.19E-08	20DT/20YC/BLUE	8.43
			PMG_1211104	7.22E-07	20YC/BLUE	9.63
			PMG_1211147	7.22E-07	20YC/BLUE	9.12
			PMG_1211158	7.22E-07	20YC/BLUE	9.12
qPM6_2	6	29,775,230-29,825,230	PMG_29800230	6.82E-06	20JZ/20DT/BLUE	8.39	Millet_GLEAN_10001507	受体样蛋白41 Receptor like protein 41
							Millet_GLEAN_10001508	转移酶家族 Transferase family
							Millet_GLEAN_10001510	转移酶家族 Transferase family
							Millet_GLEAN_10001511	QWRF家族 QWRF family
qPM7_1	7	13,431,973-13,481,973	PMG_13456973	6.18E-09	18JZ/19JZ/20JZ/20DT/BLUE	9.69	Millet_GLEAN_10031850	LEA富含羟基脯氨酸糖蛋白家族 LEA hydroxyproline-rich glycoprotein family
							Millet_GLEAN_10031851	肽酶M20/M25/M40家族蛋白 Peptidase M20/M25/M40 family protein
							Millet_GLEAN_10031852	肽酶M20/M25/M40家族蛋白 Peptidase M20/M25/M40 family protein
							Millet_GLEAN_10031853	肽酶M20/M25/M40家族蛋白 Peptidase M20/M25/M40 family protein
							Millet_GLEAN_10031849	NDR1/HIN1-蛋白2 NDR1/HIN1-like protein 2
							Millet_GLEAN_10031855	Dcp1 脱酶家族 Dcp1-like decapping family
qPM7_2	7	29,921,803-29,971,803	PMG_29946803	6.82E-06	19JZ/20JZ/BLUE	8.17	Millet_GLEAN_10037443	抗病蛋白 Disease resistance protein
							Millet_GLEAN_10037449	蛋白酪氨酸激酶 Protein tyrosine kinase
							Millet_GLEAN_10037450	含有LRR和NB-ARC结构域的抗病蛋白 LRR and NB-ARC domains-containing disease resistance protein
							Millet_GLEAN_10037452	含NB-ARC结构域的抗病蛋白 NB-ARC domain-containing disease resistance protein
							Millet_GLEAN_10037453	溴域末端外转录调控 Bromodomain extra-terminal - transcription regulation
qPM8_1	8	32,285,639-32,335,639	PMG_32310639	7.45E-06	18JZ/19JZ/20JZ/20DT/BLUE	9.68	Millet_GLEAN_10007111	BURP 域 BURP domain
							Millet_GLEAN_10007109	多铜氧化酶家族 The multicopper oxidase family
							Millet_GLEAN_10007108	蛋白激酶结构域 Protein kinase domain
							Millet_GLEAN_10007107	BURP结构域蛋白 BURP domain-containing protein
							Millet_GLEAN_10007105	胞苷转移酶 Cytidylyltransferase-like
qPM9_1	9	906,306-956,306	PMG_931306	6.40E-10	18JZ/20YC/BLUE	12.08	Millet_GLEAN_10004992	Prolycopene异构酶 Prolycopene isomerase
							Millet_GLEAN_10004994	FAD/NAD(P)结合氧化还原酶家族蛋白 FAD/NAD(P)-binding oxidoreductase family protein
							Millet_GLEAN_10004995	蛋白激酶超家族 The protein kinase superfamily
							Millet_GLEAN_10004996	SPFH域/ Band 7家族 SPFH domain / Band 7 family
							Millet_GLEAN_10004999	磷脂酶D Phospholipase D delta
							Millet_GLEAN_10004993	肽酶C13家族 Peptidase C13 family
qPM9_2	9	1,033,570-1,109,794	PMG_1058570	8.46E-06	19JZ/20JZ/BLUE	7.17	Millet_GLEAN_10005900	肽酶抑制剂I9 Peptidase inhibitor I9
			PMG_1073463			10.65	Millet_GLEAN_10005901	铵转运蛋白家族 Ammonium Transporter Family
			PMG_1076745			7.57	Millet_GLEAN_10005902	丝氨酸苏氨酸蛋白激酶 Serine threonine-protein kinase
			PMG_1076759			7.57	Millet_GLEAN_10005904	argonaute家族 the argonaute family
			PMG_1077324			7.94	Millet_GLEAN_10005905	丝氨酸苏氨酸蛋白激酶 Serine threonine-protein kinase
			PMG_1077758			7.13	Millet_GLEAN_10005908	转录因子GHD7 Transcription factor GHD7
			PMG_1083194			10.60	Millet_GLEAN_10005911	烟酸转磷酸核糖基酶 Nicotinate phosphoribosyl transferase
			PMG_1084794			8.43	Millet_GLEAN_10005912	植物纤维素合成酶 Plant cellulose synthase subfamily

Table 2

Fig. 5

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环境 Environment	均值±标准差 Mean ± SD	变异系数 CV (%)	变异范围 Range	偏度 Skewness	峰度 Kurtosis	遗传力 H²
18JZ	118.71±19.06	16.06	44.20-167.20	-0.63	0.24	0.96
19JZ	109.57±16.33	14.90	55.80-156.80	-0.38	-0.09
20JZ	118.33±20.82	17.59	70.00-154.00	-0.50	-0.03
20DT	120.39±15.57	12.93	40.80-163.60	-0.57	0.06
20YC	124.84±14.63	11.71	66.30-164.40	-0.62	0.84

Genome-wide association analysis for plant height in foxtail millet (Setaria italica L.) germplasm resources in Shanxi, China

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