夏大豆重组自交系群体遗传图谱构建及开花期QTL分析

doi:10.3864/j.issn.0578-1752.2020.04.002

中国农业科学 ›› 2020, Vol. 53 ›› Issue (4): 683-694.doi: 10.3864/j.issn.0578-1752.2020.04.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

夏大豆重组自交系群体遗传图谱构建及开花期QTL分析

曹永策^1,²,李曙光²,张新草¹,孔杰杰²,赵团结²()

1 延安大学生命科学学院/陕西省红枣重点实验室(延安大学),陕西延安 716000
2 南京农业大学大豆研究所/国家大豆改良中心/农业部大豆生物学与遗传育种重点实验室(综合)/作物遗传与种质创新国家重点实验室/江苏省现代作物生产协同创新中心,南京 210095

收稿日期:2019-07-31 接受日期:2019-09-29 出版日期:2020-02-16 发布日期:2020-03-09
联系方式: 曹永策,E-mail：caoyongce@yau.edu.cn。
基金资助:
延安大学博士科学研究启动项目(YDBK2018-02);陕西省教育厅科学研究专项计划(19JK0959);延安大学科学研究专项计划(YDQ2018-23)

Construction of Genetic Map and Mapping QTL for Flowering Time in A Summer Planting Soybean Recombinant Inbred Line Population

YongCe CAO^1,²,ShuGuang LI²,XinCao ZHANG¹,JieJie KONG²,TuanJie ZHAO²()

1 College of Life Science, Yan’an University/Shaanxi Key Laboratory of Chinese Jujube (Yan’an University), Yan’an 716000, Shaanxi
2 Soybean Research Institute, Nanjing Agricultural University/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General),Ministry of Agriculture/State Key Laboratory for Crop Genetic and Germplasm Enhancement/ Jiangsu Collaborative Innovation Center for Modern Crop Production,Nanjing 210095

Received:2019-07-31 Accepted:2019-09-29 Published:2020-02-16 Online:2020-03-09

摘要/Abstract

摘要：

【背景】开花期是大豆重要的生育期性状,不仅决定了大豆品种的适种范围,而且对大豆的产量和品质有重要影响。江淮地区是中国重要的大豆产区,目前对该地区夏大豆开花期性状遗传基础研究相对较少。【目的】利用2个夏大豆材料杂交衍生的重组自交系群体对开花期进行QTL定位,为分子标记辅助选择育种和基因克隆提供依据。【方法】以科丰35（KF35）和南农1138-2（NN1138-2）为亲本,构建了含91个家系（F_2:8）的重组自交系群体（NJK3N-RIL）,在6个环境下调查开花期性状数据。利用限制位点相关DNA测序（restriction-site associated DNA sequencing,RAD-seq）技术对群体亲本及家系材料进行SNP标记分型,并利用窗口滑动法进行bin标记划分。利用bin标记构建该群体的遗传图谱,结合多年多点的表型数据,使用QTL Network 2.2软件中的基于混合线性模型的复合区间作图法（mixed-model based composite interval mapping,MCIM）和Windows QTL Cartographer V2.5_011软件中的复合区间作图法（composite interval mapping,CIM）对开花期性状进行QTL分析。【结果】在大豆全基因组范围内共获得36 778个高质量SNP标记,被划分为1 733个bin标记。利用1 733个bin标记构建了一张覆盖大豆20条染色体遗传图谱,图谱长度为2 362.4 cM,标记间平均遗传距离为1.4 cM。利用MCIM法共检测到9个控制开花期的加性QTL、2对上位性QTL和1个环境互作QTL,3种效应累积贡献率分别为63.9%、4.6%和2.1%。利用CIM法共检测到10个控制开花期的QTL,其中qFT-8-1、qFT-11-1、qFT-15-1、qFT-16-1能在3个及以上环境检测到。综合2种分析方法,共检测到12个开花期QTL,其中qFT-8-1、qFT-11-1、qFT-15-1、qFT-16-1、qFT-16-2、qFT-20-1和qFT-20-2等能够被2种方法检测到。同时qFT-5-1、qFT-8-1、qFT-8-2、qFT-13-1、qFT-15-1和qFT-20-2等是本研究新检测到的开花期QTL。【结论】夏大豆开花期遗传构成复杂,但加性QTL效应占绝对优势,上位性互作及环境互作效应对开花期影响较小。qFT-8-1、qFT-11-1、qFT-15-1、qFT-16-1能够被2种方法在多个环境中检测到,是NJK3N-RIL群体中控制开花期的重要位点。

关键词: 大豆, 开花期, 遗传图谱, QTL

Abstract:

【Background】 Flowering time (FT) is an important agronomic trait, which determines the planting range of cultivars and has a significant influence on the yield and quality of soybean. The Chinese Jiang-Huai valley is an important soybean producing area. However, little is known about the genetic basis of flowering time in these genotypes. 【Objective】 The objectives of this study were to map mapping quantitative trait loci (QTLs) and identify stable and reliable loci that can be used for molecular marker-assisted selection (MAS) and map-based gene cloning, and then dissect the genetic basis of flowering time in summer planting soybean. 【Method】 A recombinant inbred lines (RIL) population containing 91 lines (F_2:8) developed by crossing KF35 with NN1138-2 was planted in six environments to investigate phenotypic data. Restriction-site associated DNA sequencing (RAD-seq) technology was used to genotype all lines and their parents. And then bin markers were obtained by window sliding method based on the SNP markers and used to construct the genetic map. The mixed-model based composite interval mapping (MCIM) method in the software of QTL Network 2.2 and the composite interval mapping (CIM) method in the software of Windows QTL Cartographer V2.5_011 were used to reveal the effects of the QTLs of FT. 【Result】 A total of 36778 high-quality SNP markers were obtained in the whole soybean genome, and further divided into 1733 bin markers. A high-density genetic map with 1733 bin markers was constructed that spanned 2362.4 cM of the soybean genome with an average marker distance of 1.4 cM. Nine additive QTLs, two pairs of epistatic QTLs and one environmental interaction QTL were detected by MCIM method. The cumulative contribution of additive, epistatic and environmental interaction effects were 63.9%, 4.6% and 2.1%, respectively. Ten QTLs were detected by CIM method, and four of them, qFT-8-1, qFT-11-1, qFT-15-1 and qFT-16-1 could be detected in three or more environments. Altogether, 12 QTLs controlling FT were mapped using MCIM and CIM methods. Six of them, qFT-8-1, qFT-11-1, qFT-15-1, qFT-16-1, qFT-16-2, qFT-20-1 and qFT-20-2 could be detected by two methods. Six novel QTLs, qFT-5-1, qFT-8-1, qFT-8-2, qFT-13-1, qFT-15-1 and qFT-20-2 were detected in this study. 【Conclusion】 The genetic composition of FT in summer planting soybean is relatively complex. However, the additive effect was dominant, epistatic interaction and environmental interaction had little effect on FT. Four QTLs, qFT-8-1, qFT-11-1, qFT-15-1 and qFT-16-1 can be detected by two methods and in multiple environments, which are important loci for controlling FT in NJK3N-RIL population.

Key words: soybean, flowering time, genetic map, QTL

曹永策, 李曙光, 张新草, 孔杰杰, 赵团结. 夏大豆重组自交系群体遗传图谱构建及开花期QTL分析[J]. 中国农业科学, 2020, 53(4): 683-694.

YongCe CAO, ShuGuang LI, XinCao ZHANG, JieJie KONG, TuanJie ZHAO. Construction of Genetic Map and Mapping QTL for Flowering Time in A Summer Planting Soybean Recombinant Inbred Line Population[J]. Scientia Agricultura Sinica, 2020, 53(4): 683-694.

图/表 8

表1

图1

表2

图2

表3

图3

表4

表5

NJK3N-RIL群体不同环境中开花期QTL分析"

位点 QTL	染色体 Chromosome	遗传位置 Position (cM)	相邻标记 Flank markers	LOD	置信区间 Confidence interval (cM)	加性效应 Additive (d)	贡献率 R² (%)	环境 Environment	报道位点 Reported locus
qFT-5-1	5	69.4	bin398-bin399	4.4	67.5—71.8	-0.6	9.9	2014JP	Novel
qFT-6-1	6	108.3	bin482-bin483	3.8	106.9—109.5	0.6	5.0	2013JP	First flower 1-1
qFT-8-1	8	105.2	bin670-bin671	4.5	99.2—108.2	0.8	9.1	2013FY	Novel
		107.2	bin671-bin672	3.2	102.9—108.4	0.5	6.6	2012JP
		106.2	bin670-bin671	4.6	100.9—111.3	0.6	9.0	2014YC
qFT-8-2	8	123.1	bin685-bin686	4.8	121.4—125.2	0.7	9.4	2012FY	Novel
		123.1	bin685-bin686	3.8	121.3—125.2	0.6	5.9	2013JP
qFT-11-1	11	84.6	bin927-bin928	12.7	84.2—85.8	1.3	34.3	2012JP	First flower 11-2
		84.5	bin927-bin928	14.2	83.6—87.5	1.5	39.6	2012FY
		87.2	bin930-bin931	18.2	86.5—88.4	1.9	49.6	2013FY
		88.2	bin930-bin931	8.6	86.8—89.2	1.0	18.5	2014YC
		92.9	bin932-bin933	9.4	89.0—95.6	1.1	17.7	2013JP
qFT-15-1	15	130.1	bin1290-bin1291	9.3	127.4—133.5	0.9	23.0	2014JP	Novel
		134.6	bin1291-bin1292	4.5	130.6—136.8	0.7	7.6	2013JP
		134.6	bin1291-bin1292	4.6	131.0—138.3	0.6	8.3	2014YC
		135.4	bin1292-bin1293	4.0	130.6—138.8	0.6	8.6	2012JP
qFT-16-1	16	21.3	bin1313-bin1314	5.6	17.2—26.1	0.9	10.8	2013FY	First flower 13-7
		22.3	bin1313-bin1314	4.7	21.7—25.0	0.6	10.9	2014JP
		23.3	bin1313-bin1314	7.9	21.1—26.3	0.9	18.1	2012FY
		24.3	bin1313-bin1314	11.1	21.2—26.3	1.0	24.8	2014YC
		26.7	bin1315-bin1316	13.9	23.9—28.0	1.3	28.9	2013JP
		32.7	bin1320-bin1321	5.2	31.9—33.6	0.7	11.5	2012JP
qFT-16-2	16	66.2	bin1359-bin1360	3.4	65.9—69.6	0.7	6.2	2013FY	First flower 9-3
qFT-20-1	20	44.8	bin1682-bin1683	10.3	43.8—45.4	1.1	19.1	2013JP	First flower 21-2
qFT-20-2	20	97.3	bin1728-bin1729	5.3	94.7—99.0	0.7	11.9	2014JP	Novel

表5

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环境 Environment	亲本 Parents		NJK3N-RIL群体
环境 Environment	科丰35 KF35 (d)	南农1138-2 NN1138-2 (d)	均值±标准差 Mean ± SD (d)	变幅 Range (d)	偏度 Skewness	峰度 Kurtosis	变异系数 CV (%)
2012JP	36.8 ± 2.4	39.8 ± 1.5	37.7 ± 1.9	31.0—41.3	-0.5	0.3	5.2
2012FY	48.3 ± 2.3	54.0 ± 4.6	51.1 ± 2.0	47.7—57.3	0.3	-0.3	4.0
2013JP	40.7 ± 3.1	50.5 ± 3.7	44.8 ± 2.4	40.0—50.7	0.3	-0.4	5.3
2013FY	41.0± 0.0	51.3 ± 2.0	47.1 ± 2.5	43.0—53.7	0.9	0.6	5.4
2014JP	40.3 ± 2.3	47.0 ± 1.3	49.3 ± 1.9	37.7—48.7	-0.4	1.0	4.2
2014YC	35.3 ± 0.6	45.7 ± 1.2	42.1 ± 2.6	35.7—48.3	0.4	0.1	6.2

染色体 Chromosome	SNP数目 SNP numbers	bin标记数目 bin numbers	遗传图谱长度 Linkage distance (cM)	标记间平均距离 Mean distance of adjacent markers(cM)
Chr. 01	528	57	110.3	1.9
Chr. 02	1127	114	146.4	1.3
Chr. 03	3521	81	110.2	1.4
Chr. 04	1272	90	126.4	1.4
Chr. 05	1333	73	94.5	1.3
Chr. 06	1497	87	133.6	1.5
Chr. 07	1700	85	132.1	1.6
Chr. 08	1111	109	144.5	1.3
Chr. 09	1030	85	140.7	1.7
Chr. 10	3435	95	123.9	1.3
Chr. 11	2256	85	126.4	1.5
Chr. 12	733	65	115.5	1.8
Chr. 13	2264	104	125.5	1.2
Chr. 14	1752	81	80.1	1.0
Chr. 15	2008	88	148.6	1.7
Chr. 16	2384	84	85.4	1.0
Chr. 17	2220	84	118.0	1.4
Chr. 18	4513	110	98.2	0.9
Chr. 19	695	71	96.8	1.4
Chr. 20	1399	85	105.5	1.2
总计Total	36778	1733	2362.4	1.4

位点 QTL	染色体 Chromosome	两侧标记 Flank markers	位置 Position (cM)	QTL置信区间 Confidence interval (cM)	物理区间 1-LOD interval (Mb)	加性效应 A (d)	h²_A (%)	加性与环境互作效应 AE (d)	h²_AE (%)	报道位点 Reported locus
qFT-8-1	8	bin670-bin671	98.2	95.6—102.2	36.6—41.3	0.4	3.2			新位点 Novel
qFT-10-1	10	bin875-bin876	123.3	122.0—123.3	48.6—49.3	-0.5	4.8			First flower 24-4
qFT-11-1	11	bin928-bin929	85.8	84.6—86.5	14.9—15.6	0.7	9.9	0.6(2013FY) -0.8(2014JP)	4.6	First flower 11-2
qFT-13-1	13	bin1093-bin1094	68.0	66.8—68.5	28.4—29.5	0.4	3.0			新位点 Novel
qFT-15-1	15	bin1289-bin1290	130.1	128.1—130.1	48.1—49.0	0.6	7.9			新位点 Novel
qFT-16-1	16	bin1313-bin1314	24.2	21.2—27.7	3.8—5.0	0.7	10.5			First flower 13-7
qFT-16-2	16	bin1357-bin1358	64.3	62.2—66.2	31.1—32.0	0.6	7.2			First flower 9-3
qFT-20-1	20	bin1688-bin1689	47.7	46.8—48.3	34.3—34.5	0.7	12.0			First flower 21-2
qFT-20-2	20	bin1727-bin1728	95.8	95.2—96.8	44.0—44.5	0.5	5.4			新位点 Novel

上位性QTL对 Epistatic QTL pairs	位点 QTL	相邻标记 Flanking marker	位置 position (cM)	置信区间 Confidence interval (cM)	上位性效应 AA (d)	h²_AA (%)	上位性与环境互作效应 AAE (d)	h²_AAE (%)
1	qFT-11-1	bin928-bin929	85.8	84.6—86.5	-0.2	0.6	-0.3*(2013FY) 0.2(2014JP)	0.8
	qFT-16-1	bin1313-bin1314	24.2	21.2—27.7			-0.3*(2013FY) 0.2(2014JP)
2	qFT-13-1	bin1093-bin1094	68.0	66.8—68.5	0.3	1.5
	qFT-16-2	bin1357-bin1358	64.3	62.2—66.2

夏大豆重组自交系群体遗传图谱构建及开花期QTL分析

Construction of Genetic Map and Mapping QTL for Flowering Time in A Summer Planting Soybean Recombinant Inbred Line Population

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