栽培大豆×半野生大豆高密度遗传图谱构建及株高QTL定位

doi:10.3724/SP.J.1006.2022.14063

Abstract

Abstract:

In this study, 252 plants and their parents of Fengshou 24 × Tongjiao 83-611 were genotyped by SNP160K DNA-chip. A high-density genetic linkage map with a total length of 3661.46 cM was constructed, composing of 5861 SNP markers. Seven QTLs of plant height were detected by inclusive composite interval mapping (ICIM), and each one explained 2.56%-10.41% of the variation in plant height. qPH-6-1 had the highest contribution rate of phenotypic variation and dominant effect, explaining 10.41% of plant height variation, and the additive and dominant effects are -1.72 and 18.94, respectively. The contribution rate of qPH-18-1 was the second, explaining 9.64% of plant height variation, but qPH-18-1 has the highest additive effect, reaching -12.42. 11 plants with qPH-6-1 and qPH-18-1 genotypes Q6Q6/Q18Q18 were screened in F₂ population with an average plant height of 167.00 cm, and 16 plants with 2-locus genotypes q6q6/q18q18 were screened out with an average plant height of 91.25 cm. The addition of 23 SNP markers inside and outside the qPH-18-1 locus interval narrowed the locus interval from 766.97 kb to 66.03 kb, containing eight genes. Combined with gene annotation and relative expression difference analysis, it was hypothesized that Glyma.18G279800 and Glyma.18G280200 might be associated with plant height of soybean. This study provides a molecular reference base and genetic basis for the improvement of soybean plant architecture.

Key words: soybean, plant height, SNP, genetic linkage map, QTLs mapping, candidate gene

YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height[J].Acta Agronomica Sinica, 2022, 48(5): 1091-1102.

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引物名称 Primer name	基因编号 Gene ID	上游引物 Forward primer (5'-3')	下游引物 Reverse primer (5'-3')	产物长度 Product length (bp)
Fbox	Glyma.12G051100	CTAATGGCAATTGCAGCTCTC	AGATAGGGAAATTGTGCAGGT	93
Q2795	Glyma.18G279500	GTAGCAGCCATGGAAGCGATAC	AGATTTGTCTCGGTGGGGAAC	122
Q2796	Glyma.18G279600	CTGCTGGCTATGATGCACAGTCA	AGGTTCATATCCACCTCCACTACG	122
Q2797	Glyma.18G279700	TACATGCGTGGTTCGCCTTGC	TGTATGTTAGAGGGTGGGGAAAGG	135
Q2798	Glyma.18G279800	CCTTGATGAGCCAGATGAGAAATG	CATAGTACATGGTTAAGTCAGGAAC	170
Q2799	Glyma.18G279900	CATCACCACCACAAGTAGTTTGG	GATTTTGAGAGTTCATTGGAACTG	132
Q2800	Glyma.18G280000	GATCCTCTCCAGAAACATTGAGATG	GGGTTATTATGTGGCTCTACTTGTG	128
Q2802	Glyma.18G280200	GTACATGCAAGGACCCTCTTGG	TCACTGCTCTAACACACTGGCG	124

标记名称 Marker name	上游引物 Forward sequence (5'-3')	下游引物 Reverse sequence (5'-3')	物理位置 Physical position (bp)
BARCSOYSSR_18_1842	TGAAATGGAGGAGAAAATGGA	GTCCGGGGAAACTGAACC	56,015,746-56,015,789
BARCSOYSSR_18_1843	TCGTTCGCAAAGAAAAATCC	TTGGCAACAATGGAGTCTCA	56,035,543-56,035,596
BARCSOYSSR_18_1844	TGCAAGGCATTGATCTGATT	AGAGGCGTCCTTCTGTTGTT	56,063,881-56,063,916
BARCSOYSSR_18_1845	TCATTGAGCCGAATCTTTTAAT	CGTGCACATGGTGAGACATA	56,066,436-56,066,463
BARCSOYSSR_18_1846	CTTTTAACGATTGGGTTGGG	CTTCGGCCTTAGACTTTTCG	56,068,160-56,068,221
BARCSOYSSR_18_1848	CGGTGTTGCTGACTATTGTCCT	GGCTTTTGTAAACTGCTGGC	56,110,310-56,110,343
BARCSOYSSR_18_1849	TCTCGTCCCCGTATAAGGCT	GGCGGATTGGAGAGAACATA	56,110,482-56,110,503
BARCSOYSSR_18_1850	AAATGCATTCGTGGCTTTCT	TGGGTATTATTTGGCAAGCAC	56,138,357-56,138,410

性状 Trait	亲本Parent		群体Population
性状 Trait	丰收24 Fengshou 24	通交83-611 Tongjiao 83-611	幅度 Range	均值 Mean	标准差 SD	峰度 Kurtosis	偏度 Skewness
株高Plant height (cm)	90.67±3.67	191.17±6.91	60.00-230.00	144.28	30.65	0.36	-0.54

染色体号 Chromosome-ID	标记数量 Number of markers	总图距 Total distance (cM)	平均图矩 Average distance (cM)
1	277	170.23	0.61
2	338	220.66	0.65
3	344	158.81	0.46
4	379	195.95	0.52
5	312	176.98	0.57
6	310	209.66	0.68
7	236	170.11	0.72
8	250	203.31	0.81
9	304	192.14	0.63
10	354	200.50	0.57
11	268	195.60	0.73
12	150	118.50	0.79
13	261	227.96	0.87
14	276	152.34	0.55
15	272	162.66	0.60
16	244	177.84	0.73
17	455	185.47	0.41
18	285	195.06	0.68
19	240	177.67	0.74
20	306	170.02	0.56
合计Total	5861	3661.46	0.62

QTL	染色体 Chr.	标记区间 Marker flanking	位置 Position (cM)	区间长度 Length (cM)	LOD	贡献率 PVE (%)	加性效应 Add	显性效应 Dmo	已报道位点 Reported
qPH-6-1	6	Gm06_18957454-Gm06_17916496	57	3.00	9.24	10.41	-1.72	18.94	Rossi et al., 2013^[4]
qPH-8-1	8	Gm08_9294990-Gm08_9210707	143	10.00	2.57	2.56	2.45	-9.12	—
qPH-10-1	10	Gm10_8606306-Gm10_7981987	134	7.00	3.00	2.95	4.30	-8.25	—
qPH-13-1	13	Gm13_38753560-Gm13_37989992	56	6.00	4.16	4.73	-9.04	3.38	Pathan et al., 2013^[25]
qPH-13-2	13	Gm13_28621502-Gm13_28455484	115	3.00	2.70	2.67	-2.20	9.56	Li et al., 2009^[26]
qPH-18-1	18	Gm18_56044812-Gm18_56811782	16	6.00	8.58	9.64	-12.42	1.84	Kim et al., 2012^[12]
qPH-20-1	20	Gm20_33777405-Gm20_33894103	56	1.00	3.77	4.05	-8.10	-1.49	Chapman et al., 2003^[27]

Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height

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聚合纯合提升株高基因型的QTL QTL of polymerized homozygous genotypes with increase plant height					聚合纯合降低株高基因型的QTL QTL of polymerized homozygous genotypes with reduce plant height
位点数 No. of QTL	植株数量 No. of plants	平均株高 Average height (cm)	分组 Group	P值 P-value	位点数 No. of QTL	植株数量 No. of plants	平均株高 Average height (cm)	分组 Group	P值 P-value
0	36	131.39±4.48	AC	对照Control	0	35	170.86±3.30	a	对照Control
1	64	139.45±3.89	AB	0.548	1	61	154.18±3.19	b	0.013^*
2	74	146.49±3.28	BD	0.043^*	2	70	137.14±3.18	c	0.000^*
3	26	154.23±4.78	DE	0.010^*	3	33	125.00±4.99	d	0.000^*
4	15	166.67±5.66	E	0.000^*	4	15	133.00±7.49	cd	0.000^*
5	3	160.00±10.00	—	—	5	4	115.00±10.41	cd	0.000^*

基因编号 Gene ID	基因注释 Gene annotation	同源基因 Homologous gene
Glyma.18G279500	后期促进复合物3 (APC3, CDC27) Anaphase-promoting complex subunit 3 (APC3, CDC27)	Phvul.008G021500 AT2G20000
Glyma.18G279600	—	—
Glyma.18G279700	—	—
Glyma.18G279800	在Pmr5和Cas1p中发现的GDSL/SGNH类酰基酯酶家族(PC-酯酶) GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase); PMR5 N terminal Domain (PMR5N)	Phvul.008G021200 AT5G15900
Glyma.18G279900	在Pmr5和Cas1p中发现的GDSL/SGNH类酰基酯酶家族(PC-酯酶) GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase); PMR5 N terminal Domain (PMR5N)	Phvul.008G021100
Glyma.18G280000	—	—
Glyma.18G280100	与F27J15.22相关; 油质蛋白 F27J15.22-RELATED; Oleosin	—
Glyma.18G280200	富脯氨酸受体样蛋白激酶perk8 Proline-rich receptor-like protein kinase perk8	AL7G52030

芯片名称 SNP-chip name	亲本间SNP数 No. of parental SNPs	图谱标记数 No. of markers	图谱总长 Total distance (cM)	标记间平均距离 Average distance (cM)
BARCSoySNP6K	1133-2585	1063-2283	1908.7-2834	1.10-1.80
SoyaSNP180K	23,429-28,385	1570-8967	3454-5050	0.50-2.2
SNP160K	48,248	5861	3661.46	0.62

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