东北大豆种质群体百粒重QTL-等位变异的全基因组解析

doi:10.3864/j.issn.0578-1752.2020.09.003

Abstract

Abstract:

【Objective】A genome-wide association study in the Northeast China soybean germplasm population was conducted for a relatively thorough detection of the QTL-allele constitution of 100-seed weight, which may provide a theoretical basis for soybean breeding for seed size improvement. 【Method】In the present study, a total of 290 soybean accessions that were frequently used for soybean breeding and production in the Northeast China were tested in 2013 and 2014 for 100-seed weight at four locations, including Keshan, Mudanjiang, Jiamusi and Changchun, which are all in the second sub-ecoregion of the Northeast China. RAD-seq (restriction site-associated DNA sequencing) was used for SNP genotyping, and 82 966 high-quality SNPs were obtained after filtering and imputation. According to the RTM-GWAS (restricted two-stage multi-locus genome-wide association analysis) method, firstly a total of 15 546 multi-allelic SNPLDBs were constructed, and then a multi-locus model was used for genome-wide association study of 100-seed weight. The genes near (within 50kb) the detected SNPLDBs were analyzed, and candidate genes for 100-seed weight were identified and annotated according to Chi-square test of independence between the SNPs within genes and the detected SNPLDBs. Finally, genetic differentiation among maturity groups were investigated based on the detected QTL-allele system of 100-seed weight. 【Result】The 100-seed weight of the present population ranged from 18.3 to 20.7 g, and the trait heritability was 92.3%. A total of 76 SNPLDBs were detected to be associated with 100-seed weight, among which there were 15 SNPLDBs with non-significant main effect and the 61 SNPLDBs with significant main effect explained 65.40% phenotypic variation. There were 68 SNPLDBs that had significant interaction effect with environment and explained 17.46% phenotypic variation. In addition, 34 out of 76 detected SNPLDBs overlapped 30 previously reported QTLs and 42 SNPLDBs were novel loci. A total of 137 candidate genes for 100-seed weight were annotated in the detected SNPLDB regions, and functional annotation showed that these genes were not only involved in regulation of 100-seed weight, but also involved in primary metabolism, translation, protein modification, material transport, stress response and signal transduction, etc. Although there was no obvious difference in the 100-seed weight among different maturity groups, genetic differentiation analysis showed varying changes of allele emergence and exclusion in QTL-allele structure of 100-seed weight among maturity groups. 【Conclusion】The RTM-GWAS method used in the present study provided a relatively thorough detection of genome-wide QTLs and their multiple alleles for 100-seed weight in the Northeast China soybean germplasm population. The 100-seed weight of the Northeast China soybean germplasm population was controlled by a large number of QTLs with large significant interaction effect with environment, and there was also abundant multiple allelic variation in these QTLs. The QTL-allele matrix established from RTM-GWAS provided an efficient tool for population genetics and evolution study.

Key words: soybean [Glycine max (L.) Merr.], 100-seed weight, RTM-GWAS, QTL-allele matrix, candidate gene

XiaoShuai HAO,MengMeng FU,ZaiDong LIU,JianBo HE,YanPing WANG,HaiXiang REN,DeLiang WANG,XingYong YANG,YanXi CHENG,WeiGuang DU,JunYi GAI. Genome-Wide QTL-Allele Dissection of 100-Seed Weight in the Northeast China Soybean Germplasm Population[J].Scientia Agricultura Sinica, 2020, 53(9): 1717-1729.

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Figures/Tables 6

Table 1

Table 2

Fig. 1

Table 3

SNPLDBs significantly associated with 100-seed weight in soybean"

QTL	AN	主效QTL		QTL×Env. ^a		QTL	AN	主效QTL		QTL×Env. ^a
QTL	AN	-lgP	R² (%)	-lgP	R² (%)	QTL	AN	-lgP	R² (%)	-lgP	R² (%)
q-SW-1-1	2	-	-	6.07	0.10	q-SW-12-1	2	7.95	0.08	6.99	0.11
q-SW-1-2	2	-	-	3.47	0.06	q-SW-12-2	8	4.34	0.07	4.63	0.24
q-SW-1-3	2	-	-	2.55	0.05	q-SW-12-3	4	5.30	0.06	20.46	0.35
q-SW-2-1	5	2.87	0.04	7.60	0.21	q-SW-12-4	2	2.27	0.02	3.83	0.07
q-SW-2-2	3	-	-	2.85	0.06	q-SW-12-5	2	-	-	3.50	0.06
q-SW-2-3	5	203.54	2.40	11.07	0.26	q-SW-13-1	6	150.15	1.76	20.04	0.42
q-SW-2-4	2	-	-	2.29	0.05	q-SW-13-2	7	76.04	0.90	46.13	0.80
q-SW-2-5	2	13.60	0.14	-	-	q-SW-13-3	5	28.30	0.33	14.53	0.31
q-SW-2-6	2	3.00	0.03	-	-	q-SW-13-4	4	102.12	1.16	10.74	0.23
q-SW-3-1	3	5.73	0.06	-	-	q-SW-14-1	7	-	-	7.12	0.26
q-SW-3-2	6	3.19	0.05	12.21	0.31	q-SW-14-2	6	192.85	2.28	19.05	0.41
q-SW-3-3	5	307.65	4.26	18.50	0.37	q-SW-14-3	2	63.12	0.69	-	-
q-SW-3-4	4	-	-	4.81	0.14	q-SW-14-4	2	-	-	2.26	0.05
q-SW-4-1	6	19.08	0.24	5.81	0.21	q-SW-15-1	6	34.07	0.41	7.51	0.24
q-SW-4-2	5	14.91	0.18	10.54	0.26	q-SW-15-2	6	40.33	0.48	15.05	0.35
q-SW-4-3	2	307.65	10.56	-	-	q-SW-16-1	3	213.17	2.49	3.98	0.10
q-SW-4-4	6	59.53	0.70	12.31	0.31	q-SW-16-2	4	-	-	11.03	0.23
q-SW-6-1	2	35.63	0.38	3.29	0.06	q-SW-16-3	2	2.74	0.02	2.41	0.05
q-SW-6-2	6	8.46	0.11	8.63	0.26	q-SW-16-4	5	20.46	0.24	14.44	0.31
q-SW-6-3	2	2.61	0.02	2.41	0.05	q-SW-16-5	7	29.99	0.37	19.95	0.45
q-SW-6-4	7	29.03	0.36	23.57	0.50	q-SW-17-1	5	53.76	0.62	7.77	0.21
q-SW-6-5	8	7.57	0.12	6.58	0.27	q-SW-17-2	5	2.98	0.04	26.98	0.48
q-SW-6-6	3	35.92	0.40	3.54	0.09	q-SW-18-1	5	145.14	1.69	4.18	0.16
q-SW-6-7	4	49.75	0.56	8.91	0.20	q-SW-18-2	2	-	-	2.29	0.05
q-SW-7-1	5	12.92	0.16	15.52	0.33	q-SW-18-3	6	262.05	3.16	31.38	0.57
q-SW-7-2	2	147.28	1.66	2.36	0.05	q-SW-18-4	7	17.23	0.22	13.01	0.35
q-SW-7-3	6	11.66	0.15	10.25	0.28	q-SW-18-5	2	-	-	5.50	0.09
q-SW-8-1	2	-	-	4.40	0.08	q-SW-18-6	4	200.62	2.35	10.23	0.22
q-SW-8-2	3	90.82	1.02	4.07	0.10	q-SW-18-7	5	228.35	2.71	88.81	1.24
q-SW-8-3	2	-	-	-	-	q-SW-19-1	8	15.85	0.21	10.59	0.32
q-SW-8-4	2	45.35	0.49	-	-	q-SW-19-2	7	178.86	2.12	14.09	0.37
q-SW-8-5	4	114.44	1.31	8.39	0.19	q-SW-19-3	7	54.88	0.64	16.95	0.38
q-SW-9-1	2	-	-	2.12	0.05	q-SW-19-4	6	74.96	0.87	11.80	0.30
q-SW-9-2	6	8.40	0.11	10.50	0.28	q-SW-19-5	5	23.13	0.27	5.86	0.18
q-SW-9-3	2	24.99	0.26	4.68	0.08	q-SW-20-1	8	307.65	5.77	55.70	0.97
q-SW-9-4	6	59.00	0.69	17.45	0.39	q-SW-20-2	5	34.46	0.40	13.88	0.30
q-SW-9-5	6	95.80	1.11	14.16	0.34	LC-QTL	83	18	52.15
q-SW-10-1	5	6.28	0.08	3.34	0.14	SC-QTL	205	43	13.25
q-SW-10-2	2	307.65	4.35	7.36	0.11	总Total	328	61	65.40	68	17.46
q-SW-10-3	2	89.96	0.99	-	-

Table 3

Table 4

Large contribution QTLs and candidate genes for 100-seed weight"

QTL	R² (%)	候选基因 Candidate gene	基因本体生物学过程 Gene ontology biological process
q-SW-3-3	4.43	Glyma03g31790	囊泡介导的运输Vesicle-mediated transport
		Glyma03g31810	线粒体mRNA修饰Mitochondrial mRNA modification
		Glyma03g31820	微管细胞骨架组织Microtubule cytoskeleton organization
		Glyma03g31940	甲壳素响应Response to chitin
		Glyma03g32040	高尔基体内囊泡介导转运Intra-Golgi vesicle-mediated transport
q-SW-4-3	10.93	Glyma04g38830	细胞分裂素代谢Cytokinin metabolic
		Glyma04g38870	甲基转移酶活性Methyltransferase activity
		Glyma04g38955	糖介导的信号通路Sugar mediated signaling pathway
q-SW-8-5	1.36	Glyma08g44800	RRNA加工RRNA processing
		Glyma08g44820	蛋白水解Proteolysis
		Glyma08g44960	未知Unknown
		Glyma08g44921	跨膜运输Transmembrane transport
q-SW-9-5	1.16	Glyma09g41070	液泡运输Vacuolar transport
		Glyma09g41140	肌醇六磷酸磷酸酯的生物合成过程Myo-inositol hexakisphosphate biosynthetic process
		Glyma09g41150	胚胎发育以种子休眠结束Embryo development ending in seed dormancy
		Glyma09g41260	氧化应激响应Response to oxidative stress
		Glyma09g41320	鸟嘌呤运输Guanine transport
		Glyma09g41121	未知Unknown
q-SW-13-1	1.83	Glyma13g08170	翻译调控Regulation of translation
q-SW-13-4	1.21	Glyma13g29011	种子萌发Seed germination
q-SW-14-2	2.37	Glyma14g08040	嘧啶核糖核苷酸生物合成Pyrimidine ribonucleotide biosynthetic
		Glyma14g08050	缺氧响应Response to hypoxia
		Glyma14g08070	种子萌发正调控Positive regulation of seed germination
		Glyma14g08220	脱落酸应激响应Response to abscisic acid stimulus
		Glyma14g08075	未知Unknown
		Glyma14g08145	未知Unknown
q-SW-16-1	2.58	Glyma16g06320	未知Unknown
q-SW-18-1	1.75	Glyma18g10460	新陈代谢Metabolic
		Glyma18g10470	防御反应Defense response
q-SW-18-3	3.28	Glyma18g16720	蛋白质折叠Protein folding
		Glyma18g16761	蛋白水解Proteolysis
q-SW-18-6	2.44	Glyma18g36455	未知Unknown
q-SW-18-7	2.81	Glyma18g52250	盐胁迫响应Response to salt stress
		Glyma18g52260	转录调控Regulation of transcription
		Glyma18g52290	碳水化合物代谢Carbohydrate metabolic
		Glyma18g52350	Basipetal生长素运输Basipetal auxin transport

Table 4

Table 5

The 100-seed weight QTL-allele changes among maturity groups"

QTL	a1	a2	a3	a4		a5	a6	a7	a8		QTL	a1	a2	a3	a4	a5	a6	a7	a8		QTL	a1	a2	a3	a4	a5	a6	a7	a8
1-1	yz										7-3			X	yz						14-4	yz
1-2		y									8-1		z								15-1				X
1-3		yz									8-2			z							15-2	z	z
2-1	z					z					8-3	XYZ	yz		XZ						16-1
2-2	z	yz									8-4	xyz	XYZ	XYZ	XYZ	XYZ	xyz				16-2			XY	yz
2-3	X			XY		z					8-5	xyz	xyz	xyz	xyz						16-3
2-4	XZ										9-1	z									16-4	yz
2-5		z									9-2	xy	z								16-5	yz	z
2-6	yz										9-3		XY								17-1		XY			z
3-1	XY		XYZ	Y							9-4				XYZ	y	z				17-2	z				y
3-2	X		XZ								9-5			yz							18-1	XYZ	y			z
3-3	yz		yz								10-1	X			XY						18-2		z
3-4		z		y							10-2		X								18-3	y		z		z	yz
4-1		yz	yz	yz		z					10-3		z								18-4				yz	yz	yz	XY
4-2	z	yz		yz							12-1										18-5	yz
4-3	z										12-2	z	XZ		yz		z	z	yz		18-6	yz	yz	y
4-4	YZ	yz	xz			z	z				12-3	yz	z								18-7				z
6-1											12-4		yz								19-1							X
6-2	z						X				12-5	z									19-2		z	xyz	z
6-3		XZ									13-1				z	yz	z				19-3			XY			XY
6-4			z	yz			z				13-2	z	yz		XZ	z					19-4	yz		yz		z	YZ
6-5		yz	y			yz		y	yz		13-3			z	XYZ	z					19-5					z
6-6	yz	yz									13-4			z	yz						20-1	XZ	X		z	y	yz	XY	X
6-7			xyz								14-1	yz		z		z					20-2	y				y
7-1	XYZ			z							14-2	XYZ	XY		yz
7-2											14-3		xy
熟期组 Maturity group					等位变异总数 Total allele					继承等位变异 Inherent allele						变化等位变异 Changed allele				新生等位变异 Emerged allele						汰除等位变异 Excluded allele
熟期组 Maturity group					Allele no.			QTL no.		Allele no.				QTL no.		Allele no.		QTL no.		Allele no.				QTL no.		Allele no.			QTL no.
Ⅰ+Ⅱ					292 (147, 145)			76
0 vs.Ⅰ+Ⅱ					321 (162, 159)			76		287 (144, 143)				76		39 (21,18)		30		34 (18,16)				25		5 (3,2)			5
00 vs. 0					250 (125,125)			76		247 (123, 124)				76		77(41,36)		49		3 (2,1)				2		74 (39,35)			49
000 vs. 00					208 (105,103)			76		189 (96,93)				76		80(38,42)		52		19 (9,10)				17		61(29,32)			44
0+00+000 vs.Ⅰ+Ⅱ					324 (163, 161)			76		288 (144, 144)				76		40 (22,18)		31		36 (19,17)				27		4(3,1)			4

Table 5

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模型Model	变异来源Source	自由度DF	均方MS	F	p
基因型×年份×地点 Genotype×Year×Location	年份Year	1	835.46	81.59	<0.001
	地点Location	3	3156.29	493.80	<0.001
	区组（年份,地点） Block(Year, Location)	24	2.59	1.86	0.0068
	基因型Genotype	289	146.47	13.74	<0.001
	基因型×年份Genotype×Year	289	9.10	2.65	<0.001
	基因型×地点Genotype×Location	867	5.22	1.41	<0.001
	基因型×年份×地点Genotype×Year×Location	849	3.70	2.65	<0.001
	误差Error	6791	1.40
基因型×环境 Genotype×Environment	环境Environment	7	1978.57	308.84	<0.001
	区组（环境） Block(Environment)	24	2.59	1.86	0.0068
	基因型Genotype	289	147.00	28.15	<0.001
	基因型×环境Genotype×Environment	2005	5.24	3.75	<0.001
	误差Error	6791	1.40

Genome-Wide QTL-Allele Dissection of 100-Seed Weight in the Northeast China Soybean Germplasm Population

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类型 Type	百粒重100-seed weight (g)															N	平均数 Mean	变幅 Range	遗传率 h²
类型 Type	7	9	11	12	14	16	17	19	21	23	24	26	28	29	31	N	平均数 Mean	变幅 Range	遗传率 h²
环境Environment
长春CC		1	1	0	0	9	45	75	85	52	14	4	4			290	20.3	9.7-28.2	0.642
佳木斯JMS	1	2	10	3	1	1	17	57	93	68	28	4	4	0	1	290	20.7	8.1-32.0	0.780
克山KS	3	2	0	1	5	45	91	83	49	9	1	0	1			290	18.3	6.4-28.2	0.777
牡丹江MDJ		2	0	0	0	10	48	98	85	39	4	3	0	1		290	19.9	6.7-28.9	0.726
Mean		1	1	0	0	7	53	89	90	39	5	4	0	1		290	19.8	8.2-29.5	0.923
熟期组Maturity
MG0					1	2	25	55	51	16	4	1				155	19.9	13.6-25.6
MG00			1	0	0	0	6	11	15	10	2					45	20.3	9.9-24.8
MG000							3	3	5	3	1					15	20.4	18.8-21.8
MGI+II						2	9	33	25	6						75	19.7	15.6-22.7
MG0+00+000			1	0	1	2	34	69	71	29	7	1				215	20.0	9.9-25.6

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