Construction of high density genetic map and QTL mapping of yield related traits in soybean

doi:10.19802/j.issn.1007-9084.2021268

Abstract

Abstract:

To accelerate molecular marker-assisted breeding for soybean, a recombinant inbred lines （RILs） population （F_2:10） containing 168 lines was constructed from Dongnong 42 and Dongnong 50 for constructing a high density genetic map. The two parents are significantly different on yield. QTL analysis was carried out by using the compound interval mapping （CIM） method of R/qtl software combined with phenotypic data on yield-related traits at 6 environments in 2 years. Results showed that 660 316 SNP markers obtained by sequencing could be used to construct a high-density genetic map of soybean containing 6227 bin markers distributed in 20 linkage groups. The general and average map distances were 2739.15 cM and 0.44 cM respectively. 22 QTLs related to yield traits were mapped on 12 chromosomes. QTLs for number of four-seed-pod （NFSP）, number of pods per plant （NPPP）, seed weight per plant （SWPP）, 100-seed weight （HSW） were 5, 4, 5 and 8 respectively. There was a genomic region on each of the chromosomes 3 and 19. They were repeatedly located in 2 years, involving 6 major QTLs, namely qNFSP-19-1 （22.976%）, qNFSP-19-2 （11.977%）, qNFSP-19-3 （17.203%）, qHSW-3-1 （11.346%）, qHSW-3-2 （11.346%） and qHSW-3-3 （11.175%）, all these QTLs had negative additive effects. 7 QTLs for yield-related traits were newly mapped on chromosomes 3, 7, 11, 12 and 20, among which qHSW-3-3 （14.276%） had the highest phenotypic contribution, including qHSW-3-2 and qHSW-3-3 with repetitive mapping intervals. Compared with the results of previous co-mapping, more QTLs greatly shortened the mapping interval, which showed the accuracy of the high-density genetic map constructed in this study.

Key words: soybean, high density genetic map, number of four-seed-pod, pods per plant, seed weight per plant, 100-seed weight, QTL

CLC Number:

S565.1

Bo WANG, Ying-ying DONG, Xue FU, He-yu LIU, Xiang-chao ZHANG, Ji LIU, Fei-fei SHI, Xue ZHAO, Ying-peng HAN, Wen-bin LI, Wei-li TENG. Construction of high density genetic map and QTL mapping of yield related traits in soybean[J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2022, 44(6): 1228-1238.

Figures/Tables 9

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性状 Trait	年份 Year	地点 Site	亲本Parents		显著性Significance
性状 Trait	年份 Year	地点 Site	东农42 Dongnong 42	东农50 Dongnong 50	显著性Significance
四粒荚数 NFSP	2019	XY	9.80	40.57	**
		AC	11.11	39.50	**
		HL	10.80	33.14	ns
		平均值 Mean	10.57	37.74	**
	2020	XY	4.70	31.00	**
		AC	9.30	22.43	**
		HL	6.10	46.83	**
		平均值 Mean	6.70	33.42	**
单株荚数 NPPP	2019	XY	43.60	83.71	**
		AC	63.33	80.50	ns
		HL	71.20	73.14	ns
		平均值 Mean	59.38	79.12	**
	2020	XY	40.50	76.64	**
		AC	49.60	51.29	ns
		HL	68.20	97.25	*
		平均值 Mean	52.77	75.06	**
单株粒重 /g SWPP	2019	XY	14.48	11.08	ns
		AC	30.02	12.05	**
		HL	29.44	11.91	**
		平均值 Mean	24.65	11.68	**
	2020	XY	15.71	13.50	ns
		AC	23.97	8.03	**
		HL	30.35	18.39	**
		平均值 Mean	23.34	13.31	**
百粒重 /g HSW	2019	XY	17.56	7.33	**
		AC	19.54	6.36	**
		HL	19.80	9.23	**
		平均值 Mean	18.97	7.64	**
	2020	XY	18.68	7.22	**
		AC	19.69	6.28	**
		HL	20.83	8.29	**
		平均值 Mean	19.73	7.27	**

性状 Trait	年份 Year	地点 Site	平均值±标准偏差 Mean ± SD	方差 Variance	峰度 Kurtosis	偏度 Skewness	范围 Range	变异系数 /% Coefficient of variation
四粒荚数 NFSP	2019	XY	13.18±7.88	62.03	6.96	1.87	1.67~58.00	59.79
		AC	17.62±9.50	90.28	5.25	1.33	1.40~72.00	53.92
		HL	13.76±8.40	70.58	1.10	0.96	0.60~46.60	61.05
	2020	XY	9.65±5.39	29.08	4.08	1.28	0.80~37.80	55.85
		AC	15.38±7.31	53.49	0.61	0.59	1.40~39.80	47.53
		HL	15.30±10.13	102.71	1.64	1.30	0.20~50.00	66.21
单株荚数 NPPP	2019	XY	48.24±15.04	226.30	1.76	0.75	13.20~106.33	31.18
		AC	60.92±19.70	388.02	11.53	2.13	15.80~191.00	32.34
		HL	55.70±19.08	364.18	-0.17	0.16	14.25~114.20	34.25
	2020	XY	44.60±11.58	134.05	1.37	0.73	16.00~93.40	25.96
		AC	55.46±15.74	247.66	3.42	1.51	28.40~122.00	28.38
		HL	65.51±31.13	968.94	11.30	2.45	11.60~267.00	47.52
单株粒重 /g SWPP	2019	XY	12.38±4.31	18.56	0.06	0.27	1.70~24.08	34.81
		AC	18.15±5.95	35.39	0.76	0.37	3.10~40.79	32.78
		HL	15.98±6.75	45.54	-0.09	0.38	2.96~34.65	42.24
	2020	XY	13.01±3.36	11.30	0.23	0.48	4.61~21.89	25.83
		AC	17.63±5.45	29.65	3.18	1.27	7.90~41.54	30.91
		HL	21.22±9.78	95.67	4.93	1.43	1.74~74.00	46.09
百粒重 /g HSW	2019	XY	13.84±2.49	6.20	1.11	0.33	6.44~23.15	17.99
		AC	14.01±2.66	7.05	1.12	0.09	5.41~22.01	18.99
		HL	14.82±2.55	6.49	0.25	0.08	8.11~21.57	17.21
	2020	XY	13.86±2.73	7.47	0.74	0.39	6.99~23.13	19.70
		AC	13.93±2.77	7.70	-0.15	-0.02	5.79~21.56	19.89
		HL	15.66±2.91	8.45	0.00	0.23	7.66~23.61	18.58

地点 Site	性状 Trait	2019				2020
地点 Site	性状 Trait	四粒荚数 NFSP	单株荚数 NPPP	单株粒重/g SWPP	百粒重/g HSW	四粒荚数 NFSP	单株荚数 NPPP	单株粒重/g SWPP	百粒重/g HSW
XY	四粒荚数NFSP	1				1
	单株荚数NPPP	0.634**	1			0.418**	1
	单株粒重SWPP /g	0.493**	0.719**	1		0.402**	0.663**	1
	百粒重HSW /g	-0.162*	-0.255**	0.327**	1	-0.147	-0.328**	0.378**	1
AC	四粒荚数NFSP	1				1
	单株荚数NPPP	0.530**	1			0.330**	1
	单株粒重SWPP /g	0.495**	0.570**	1		0.387**	0.594**	1
	百粒重HSW /g	-0.018	-0.253**	0.443**	1	-0.009	-0.355**	0.359**	1
HL	四粒荚数NFSP	1				1
	单株荚数NPPP	0.409**	1			0.409**	1
	单株粒重SWPP /g	0.524**	0.794**	1		0.548**	0.857**	1
	百粒重HSW /g	0.121	-0.106	0.368**	1	-0.006	-0.206**	0.189*	1

样品 Sample	Q30 /%	GC含量 /% GC percentage	平均覆盖深度 Average coverage depth	覆盖率 Coverage ratio /%
样品 Sample	Q30 /%	GC含量 /% GC percentage	平均覆盖深度 Average coverage depth	1×	5×	10×
东农42 Dongnong 42	93.36	34.84	20.00	95.46	93.75	88.05
东农50 Dongnong 50	91.77	34.70	20.00	95.00	92.69	85.68
家系 Population	93.16	34.72	3.18	79.71	25.40	3.99

连锁群 Linkage group	总标记数 Total bin marker	遗传距离 /cM Total distance	标记间距离 /cM Average distance	最大间隔 /cM Max gap	间隔<5 cM /% Gaps< 5 cM
LG1	381	126.63	0.33	12.48	98.95
LG2	431	173.81	0.40	11.99	99.30
LG3	334	196.78	0.59	13.99	98.20
LG4	277	136.09	0.49	8.83	98.91
LG5	233	179.06	0.77	11.51	99.14
LG6	325	138.77	0.43	10.59	97.84
LG7	417	143.21	0.34	11.99	99.28
LG8	274	179.07	0.65	10.59	98.17
LG9	338	138.46	0.41	8.41	98.81
LG10	370	130.71	0.35	5.65	99.46
LG11	200	111.03	0.56	16.74	97.49
LG12	272	128.93	0.47	6.98	99.26
LG13	330	137.19	0.42	10.59	98.78
LG14	339	127.41	0.38	15.60	98.82
LG15	385	113.35	0.29	6.80	99.22
LG16	195	120.82	0.62	8.83	97.42
LG17	386	113.41	0.29	7.19	99.74
LG18	200	114.35	0.57	16.17	98.49
LG19	288	130.91	0.45	13.99	97.91
LG20	252	99.16	0.39	9.70	98.80
总计	6227	2739.15	0.44	16.74	98.70