大豆巢式关联作图群体蛋白质含量的遗传解析

doi:10.3864/j.issn.0578-1752.2020.09.005

Abstract

Abstract:

【Objective】Soybean is an important cash crop, a major source of plant protein and oil for human diet. As a major objective of soybean breeding, protein content is a complex trait controlled by multiple genes with varying genetic effects interacting with environment. A genome-wide association study (GWAS) was conducted to dissect the genetic architecture of protein content in a soybean nested association mapping (NAM) population, and the detected genetic constitution can be further used for molecular design in soybean breeding for high protein content. 【Method】Four soybean recombinant inbred line (RIL) populations (Linhe×M8206, Zhengyang×M8206, M8206×Tongshan and M8206×WSB) with a common parent (M8206) as a NAM population were constructed, genotyped with RAD-seq (restriction-site-associated DNA sequencing) and tested under multiple locations in 2012 - 2014. Protein content was measured at full maturity (R8) stage. The restricted two-stage multi-locus GWAS (RTM-GWAS) procedure was used to dissect the genetic architecture of seed protein content of the population. 【Result】The protein content varied widely in the population with trait heritability estimated as high as 85.00%. The analysis of variance for protein content showed significant differences across genotypes, environments and genotype-by-environment interactions. A total of 90 QTLs were detected to be associated with protein content, with 20 loci being novel ones. The phenotypic variation explained by each QTL ranged from 0.06% to 3.99%, with a sum of 45.60%. The number of alleles at each locus ranged from 2 to 5, and the allele effects ranged from -2.434% to 2.845%, while most of them were between -1.000% and 1.000%. From the detected QTLs, 73 candidate genes were annotated. Among these candidate genes, Glyma18g03540 involved in cysteine biosynthetic process, and Glyma20g24830 involved in glycine and aromatic amino acid family metabolic process. The two genes may be selected for further functional study. Based on the QTL-allele matrix of protein content, the predicted transgressive potential of cross progeny was as high as 56.5%. 【Conclusion】A total of 90 QTLs for protein content were detected with 20 loci being novel, from which 73 candidate genes were annotated, indicating that protein content is a complex trait conferred by multiple genes or a gene network.

Key words: soybean [Glycine max (L.) Merr.], nested association mapping population (NAM), protein content, restricted two-stage multi-locus genome-wide association analysis

ShuGuang LI,YongCe CAO,JianBo HE,WuBin WANG,GuangNan XING,JiaYin YANG,TuanJie ZHAO,JunYi GAI. Genetic Dissection of Protein Content in a Nested Association Mapping Population of Soybean[J].Scientia Agricultura Sinica, 2020, 53(9): 1743-1755.

Figures/Tables 7

Table 1

Table 2

Fig. 1

Table 3

QTLs associated with the protein content detected in the soybean NAM population"

QTL	染色体 Chr.	位置 Position (bp)	等位变异 No. allele	-lgP	R²(%)	SoyBase QTL^a	GWAS QTL^b
qProt-6-1	6	5723944—5861193	3	89.2	3.99	30-5, 005, 007, 015	[16-17]
qProt-7-2	7	7895394—7951423	4	54.5	2.46	33-5	[18]
qProt-20-8	20	45758806—45958325	5	52.6	2.42
qProt-19-3	19	45138372—45336506	5	39.9	1.85	2-2, 36-31	[19]
qProt-6-4	6	13682742—13879752	4	38.4	1.74	34-2	[20,17]
qProt-2-2	2	8795893—8902236	4	37.8	1.71	21-4	[20]
qProt-5-5	5	38956925—39141177	4	36.1	1.64	2-1, 9-1, 12-1, 34-1, 011, 014
qProt-18-1	18	2346289—2531952	5	31.1	1.45	26-12, 28-5, 36-25	[21]
qProt-8-5	8	31139492—31248131	5	27.6	1.30
qProt-14-2	14	6415938—6607451	3	23.2	1.02	1-6, 4-10, 45-1	[21]
qProt-13-1	13	5277987—5435217	3	22.5	0.99	36-21
qProt-1-3	1	52165879—52301103	3	21.6	0.95	36-9	[5]
qProt-4-2	4	47959591—48019889	5	19.3	0.92	4-2, 37-2	[21]
qProt-16-3	16	34706667—34803913	5	19.1	0.91	41-6
qProt-10-1	10	3262276	2	19.2	0.79	41-11	[22]
qProt-20-4	20	18696597—18710242	3	17.7	0.73	1-3, 1-4, 3-12, 10-1, 11-1, 30-1, 31-1, 36-26, 37-8, 47-8, 003	[23]
qProt-13-4	13	39868073—40038639	5	14.8	0.72	26-11
qProt-6-7	6	20701467—20900668	5	13.9	0.68	012
qProt-6-9	6	41656522—41677922	3	13.9	0.61
QTL	染色体 Chr.	位置 Position (bp)	等位变异 No. allele	-lgP	R²(%)	SoyBase QTL^a	GWAS QTL^b
qProt-7-4	7	18234251	2	14.3	0.58	47-1
qProt-6-3	6	10921339—11119531	3	12.9	0.57
qProt-14-3	14	9912397—10112026	3	12.9	0.57	21-8
qProt-9-1	9	35965266—36048472	4	12.0	0.56	5-3, 33-3, 34-6, 35-4, 36-28, 36-29, 36-30, 37-11
qProt-11-1	11	5786106—5983572	5	11.1	0.55	3-2, 16-1, 34-7, 36-2, 37-1	[20-23]
qProt-2-1	2	4025110	2	12.9	0.52		[24]
qProt-5-2	5	1708219	2	12.4	0.50
qProt-5-3	5	32642277—32673061	3	11.4	0.50	36-1
qProt-7-1	7	176227—372535	5	10.1	0.50
qProt-19-2	19	39675711—39753005	4	9.2	0.44	30-7, 36-32
qProt-20-3	20	10292622—10303142	4	9.2	0.44	1-3, 1-4, 3-12, 10-1, 11-1, 30-1, 36-26, 37-8, 47-8	[25]
qProt-6-6	6	16510997—16689830	4	9.1	0.43	21-3, 26-7, 35-1, 36-7, 36-8
qProt-10-3	10	43721962—43903254	5	8.3	0.42	27-5	[1,26]
qProt-20-6	20	34459783—34480867	4	8.6	0.41	26-5, 34-11	[26]
qProt-1-4	1	54251785—54443212	5	7.9	0.40	36-9	[22]
qProt-8-3	8	23303969—23383404	3	9.2	0.40
qProt-1-1	1	2560155—2683983	4	8.2	0.39		[21-22]
qProt-15-1	15	3194114	2	9.5	0.38	30-3	[1,16]
qProt-1-2	1	4621764—4727603	5	7.1	0.37		[21]
qProt-15-3	15	50539746—50738644	5	7.1	0.37
qProt-14-5	14	16634057—16648499	3	7.5	0.33
qProt-16-1	16	4780910	2	8.2	0.32	4-7	[6,25]
qProt-8-1	8	7846414—8000705	5	5.8	0.31	26-1, 30-4, 34-4, 34-5, 013, 016
qProt-16-5	16	37249323—37294601	4	6.5	0.31	41-6
qProt-18-4	18	51679638—51878009	4	6.2	0.30	34-9
qProt-8-6	8	46434966—46595148	3	6.5	0.28	14-1, 21-1	[25]
qProt-3-1	3	1011738	2	7.1	0.27	010
qProt-3-2	3	39567898—39600101	5	4.9	0.27	36-34, 21-9, 36-37
qProt-5-1	5	1531632—1531635	2	6.8	0.26
qProt-18-3	18	5553907—5635734	2	6.7	0.26	47-6
qProt-1-5	1	55836890—55889699	3	5.8	0.25
qProt-4-1	4	41014079	2	6.5	0.25
qProt-2-5	2	49426511—49624658	4	5.0	0.24	37-4
qProt-16-4	16	34859125—35032972	5	5.5	0.24	41-6	[27]
qProt-13-2	13	18987333-18987363	2	6.0	0.23	26-13, 36-20, 36-21, 36-23	[5]
qProt-15-2	15	4817369	2	6.1	0.23	30-3	[18,27-29]
qProt-6-11	6	48032833—48165768	4	4.4	0.22	13-2
qProt-6-2	6	6233427—6256962	2	5.6	0.21	30-5, 31-4, 005, 007, 015
QTL	染色体 Chr.	位置 Position (bp)	等位变异 No. allele	-lgP	R²(%)	SoyBase QTL^a	GWAS QTL^b
qProt-6-8	6	22700125—22889619	4	4.2	0.21
qProt-8-4	8	27091794—27092100	3	4.9	0.21
qProt-11-3	11	36538681—36538733	2	5.6	0.21	26-6
qProt-20-7	20	42051825—42200759	5	3.8	0.21
qProt-12-1	12	36587265	2	5.5	0.20	5-2, 21-10, 33-1
qProt-17-1	17	33206802—33271301	4	4.1	0.20	36-14, 36-16
qProt-6-5	6	14689566—14795226	4	3.8	0.19	34-2	[1]
qProt-6-10	6	42894533—43089859	4	3.7	0.19	24-1
qProt-14-1	14	4726017—4860851	4	3.7	0.19	1-6, 4-11, 45-1	[22]
qProt-20-2	20	5157137	2	4.5	0.16	1-3, 1-4, 3-12, 10-1, 11-1, 30-1, 36-26, 37-8, 47-8
qProt-3-3	3	44249912—44442395	3	3.4	0.15	36-35, 27-4
qProt-6-12	6	48187414	2	4.2	0.15	13-2	[20-21]
qProt-8-2	8	8219073—8363193	5	2.4	0.15	26-1, 30-4, 34-4, 34-5, 013, 016	[6,26]
qProt-14-4	14	13291266	2	4.2	0.15
qProt-18-8	18	62050016—62248618	5	2.5	0.15	30-10
qProt-20-9	20	46154443	2	4.2	0.15
qProt-3-4	3	44486103—44672295	4	3.3	0.14	36-35, 27-4
qProt-18-2	18	2963699—3158571	5	2.2	0.14	20-1, 47-6	[6]
qProt-20-5	20	33207484—33279787	3	2.9	0.13	1-1, 1-2, 15-1, 26-5, 34-11, 39-4	[30]
qProt-7-3	7	18234233	2	3.5	0.12	47-1
qProt-7-5	7	35580968—35653659	3	2.8	0.12	41-9
qProt-18-7	18	60127020—60312441	5	1.9	0.12	3-10, 30-10
qProt-2-4	2	47360405	2	3.2	0.11	40-5	[23]
qProt-11-2	11	7962963	2	3.2	0.11
qProt-16-2	16	33179205	2	3.1	0.11
qProt-13-3	13	36897211	2	3.0	0.10	6-2, 24-2
qProt-18-5	18	52822014	2	3.0	0.10	3-8, 28-2
qProt-18-6	18	54160848	2	2.9	0.10	3-9
qProt-2-3	2	12237524	2	2.6	0.09	36-12
qProt-19-1	19	37053052—37053084	2	2.4	0.08
qProt-20-1	20	1315771—1315813	2	2.5	0.08	26-3, 26-4, 37-7, 37-9, 41-4
qProt-5-4	5	38098083	2	2.1	0.07	12-1, 011, 014	[6]
qProt-10-2	10	40629142—40629143	2	1.9	0.06	27-5, 40-1
LC QTL		10	42		19.58
SC QTL		80	261		26.06
总计Total		90	303		45.64	67(119)	33(45)

Table 3

Fig. 2

Table 4

Fig. 3

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变异来源Source of variation	自由度Degree of freedom	均方Mean square	F 值F value	P值P value
环境Environment	4	3652.54	49.46	<0.01
重复（环境）Replicate (Environment)	10	71.82	40.08	<0.01
基因型Genotype	622	33.05	6.79	<0.01
基因型×环境Genotype × Environment	2467	4.95	2.76	<0.01
误差Error	5589	1.79
总计Total	8692

组合 Cross	观测值 Observation		独立模型 Independence model		连锁模型 Linkage model
组合 Cross	Y1	Y2	均值 Mean	P5	P95	均值 Mean	P5	P95
蒙8206×临河 (LM)	36.3	47.8	42.1	33.1	51.1	42.0	37.8	46.3
蒙8206×正阳 (LZ)	36.3	44.7	40.5	35.8	45.2	40.5	37.1	43.9
蒙8206×通山 (MT)	36.3	45.1	40.7	35.8	45.6	40.7	37.5	43.9
蒙8206×WSB (MW)	36.3	42.9	39.6	34.3	45.0	39.6	36.4	42.7
临河×正阳 Linhe×Zhengyang	47.8	44.7	46.3	36.4	56.1	46.2	41.5	50.9
临河×通山Linhe×Tongshan	47.8	45.1	46.4	36.3	56.5	46.5	42.2	50.8
临河×WSB Linhe×WSB	47.8	42.9	45.4	35.7	54.8	45.3	40.6	50.2
正阳×通山 Zhengyang×Tongshan	44.7	45.1	44.9	39.9	49.8	44.9	41.7	48.1
正阳×WSB Zhengyang×WSB	44.7	42.9	43.8	36.7	50.7	43.8	39.6	48.0
通山×WSB Tongshan×WSB	45.1	42.9	44.0	36.9	51.1	44.0	39.9	48.1

Genetic Dissection of Protein Content in a Nested Association Mapping Population of Soybean

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环境 Env.^a	组中值Mid-point																	平均值 Mean	变幅 Range	CV^b (%)	h² (%)
环境 Env.^a	32.0	33.0	34.0	35.0	36.0	37.0	38.0	39.0	40.0	41.0	42.0	43.0	44.0	45.0	46.0	47.0	48.0	平均值 Mean	变幅 Range	CV^b (%)	h² (%)
FY2012	0	0	0	0	0	7	18	54	100	118	162	92	49	13	5	1	0	41.0	36.1—46.5	3.0	81.0
JP2012	0	0	0	0	1	8	23	36	70	133	124	106	66	24	18	2	2	41.4	35.9—47.8	3.0	82.2
JP2013	0	0	0	0	0	1	3	12	32	76	118	133	113	73	40	17	1	42.5	36.6—47.2	3.1	80.6
JP2014	0	0	0	0	0	4	18	41	91	107	139	121	60	22	14	4	0	41.3	36.6—46.6	3.6	76.9
YC2014	3	7	22	26	48	54	85	99	103	76	53	28	9	3	4	2	0	38.5	31.5—46.1	3.5	90.0
均值Mean	0	0	0	0	0	3	15	58	85	162	147	97	40	13	2	1	0	40.9	36.6—46.0	3.3	85.0

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