Construction of Genetic Map and Mapping QTL for Flowering Time in A Summer Planting Soybean Recombinant Inbred Line Population
CAO YongCe1,2, LI ShuGuang2, ZHANG XinCao1, KONG JieJie2, ZHAO TuanJie,21 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
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 (F2:8) 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. Keywords：soybean;flowering time;genetic map;QTL
PDF (475KB)元数据多维度评价相关文章导出EndNote|Ris|Bibtex收藏本文 本文引用格式 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 doi:10.3864/j.issn.0578-1752.2020.04.002 CAO YongCe, LI ShuGuang, ZHANG XinCao, KONG JieJie, ZHAO TuanJie. Construction of Genetic Map and Mapping QTL for Flowering Time in A Summer Planting Soybean Recombinant Inbred Line Population[J]. Scientia Acricultura Sinica, 2020, 53(4): 683-694 doi:10.3864/j.issn.0578-1752.2020.04.002
利用SPSS 20.0（SPSS Inc.,Chicago,IL,USA）软件对表型数据进行描述性统计,包括性状在环境下的变异范围、平均值、标准差、变异系数和正态分布检验等。使用SAS 9.3（SAS Institute Inc. 2011）软件的Proc GLM过程进行多环境联合方差分析,估计方差分量用来评估性状在群体中的广义遗传率。广义遗传率计算公式如下：
采用限制性酶切位点相关的DNA测序（restriction- site Associated DNA sequencing,RAD-Seq）技术,对NJK3N-RIL群体进行全基因组SNP开发,然后根据亲本和家系的基因型开发bin标记用于构建遗传图谱,具体方法参考HAN等[37]和HUANG等[38]方法。采用JoinMap 4.0软件构建遗传图谱,以标记间LOD值大于3进行连锁群划分,采用Regression mapping算法和Kosambi函数计算连锁群内标记的线性排列以及标记间的遗传距离（centiMorgan,cM）[39]。
Table 1 表1 表1不同环境下NJK3N-RIL群体及其亲本开花期（天）性状描述性统计 Table 1Results of descriptive statistics of flowering time (days) in NJK3N-RIL population grown in different environments
Table 3 表3 表3NJK3N-RIL群体开花期加性及QTL与环境互作效应的分析 Table 3Additive QTLs and QTL-by-environment interaction effect for flowering time in the NJK3N-RIL population
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)
h2A (%)
加性与环境 互作效应 AE (d)
h2AE (%)
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
*表示P<0.05;**表示P<0.01。A：加性效应值为正,表示增效等位变异来自亲本南农1138-2。h2A：由加性效应解释的表型变异。h2AE：由加性QTL与环境互作效应解释的表型变异。报道位点：在SoyBase数据库中与本文报道QTL位置相邻或者重叠的位点。下同 *indicates P<0. 05; ** indicates P<0. 01. The positive value indicates that NN1138-2 contributed the allele to an increase in FT. h2A: Phenotypic variation explained by additive effects. h2AE: Phenotypic variation explained by additive QTL and environmental interaction effects. The reported locus indicates the QTLs name for flowering time in the SoyBase database. The same as below
方条的长度代表QTL置信区间。空白长条代表使用CIM方法在不同环境中定位到的QTL;黑色长条代表使用MCIM在联合环境中定位到的QTL;虚线代表相连的QTL间具有上位性互作 Fig. 3Locations of QTL for flowering time in soybean linkage map in NJK3N-RIL population
The length of the bar represents the confidence interval of the QTL. The blank bars represent the QTL detected by CIM method in different environment. The solid black bars represent the QTL detected by MCIM method in joint environment. Dotted lines represent epistatic interactions between connected QTLs
Table 5 表5 表5NJK3N-RIL群体不同环境中开花期QTL分析 Table 5Detection of QTL associated with flowering time in the NJK3N-RIL population grown in different environments
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
R 2：QTL在单个环境中的表型解释率 R 2: Phenotypic variation explained by QTL in single environment
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新窗口打开|下载原图ZIP|生成PPT
新窗口打开|下载原图ZIP|生成PPT
新窗口打开|下载原图ZIP|生成PPT
