RTM-GWAS方法应用于大豆RIL群体百粒重QTL检测的功效

doi:10.3864/j.issn.0578-1752.2020.09.004

中国农业科学 ›› 2020, Vol. 53 ›› Issue (9): 1730-1742.doi: 10.3864/j.issn.0578-1752.2020.09.004

• 专题：限制性两阶段多位点全基因组关联分析法的应用 • 上一篇下一篇

RTM-GWAS方法应用于大豆RIL群体百粒重QTL检测的功效

潘丽媛¹,贺建波¹(),赵晋铭¹,王吴彬¹,邢光南¹,喻德跃¹,张小燕³,李春燕³,陈受宜²,盖钧镒¹()

¹ 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/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;
² 中国科学院遗传发育研究所/植物基因组学国家重点实验室,北京 100101;
³ 山东圣丰种业科技有限公司,山东嘉祥 272400

收稿日期:2019-08-24 接受日期:2020-01-02 出版日期:2020-05-01 发布日期:2020-05-13
通讯作者: 贺建波,盖钧镒
作者简介:潘丽媛,E-mail：panly89@126.com。
基金资助:
国家自然科学基金(31701447);国家作物育种重点研发计划(2017YFD0101500);国家作物育种重点研发计划(2017YFD0102002);长江学者和创新团队发展计划(PCSIRT_17R55);教育部111项目(B08025);中央高校基本科研业务费项目(KYT201801);农业部国家大豆产业技术体系CARS-04;江苏省优势学科建设工程专项;江苏省JCIC-MCP项目

Detection Power of RTM-GWAS Applied to 100-Seed Weight QTL Identification in a Recombinant Inbred Lines Population of Soybean

LiYuan PAN¹,JianBo HE¹(),JinMing ZHAO¹,WuBin WANG¹,GuangNan XING¹,DeYue YU¹,XiaoYan ZHANG³,ChunYan LI³,ShouYi CHEN²,JunYi GAI¹()

¹ Soybean Research Institute, Nanjing Agricultural University /National Center for Soybean Improvement /Key Laboratory of Biology and Genetic Improvement of Soybean (General), Ministry of Agriculture/State Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095;
² Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Genomics, Beijing 100101;
³ Shandong Shofine Seed Technology Co. Ltd., Jiaxiang 272400, Shandong

Received:2019-08-24 Accepted:2020-01-02 Online:2020-05-01 Published:2020-05-13
Contact: JianBo HE,JunYi GAI

摘要/Abstract

摘要：

【目的】为全面解析大豆重组自交系群体中调控百粒重性状的QTL体系,将限制性两阶段多位点全基因组关联分析方法（RTM-GWAS）和不同定位方法进行比较、优选,为后续候选基因体系探索及分子标记辅助育种设计提供依据。【方法】利用以科丰1号和南农1138-2为亲本衍生的重组自交系群体NJRIKY的427个家系,通过由全基因组39 353个SNP构建的3 683个SNPLDB标记及3个环境下的百粒重表型数据,选用复合区间作图法（CIM）、基于混合线性模型的全基因组关联分析方法（MLM-GWAS）和RTM-GWAS3种方法检测百粒重QTL,通过QTL数目和总的表型变异解释率比较检测功效,挑选最佳定位结果进行NJRIKY群体中的百粒重遗传体系解析。通过候选基因体系的功能注释,挖掘调控大豆百粒重的生物学途径。【结果】科丰1号与南农1138-2的百粒重差异较大,多环境平均数分别为9.0和17.9 g,遗传变异系数为12.4%,遗传率为85.4%,适用于百粒重性状的遗传解析。比较3种方法定位结果表明RTM-GWAS方法表现最佳,检测QTL数目最多（57个）,解释表型变异最多（70.78%）。而CIM仅检测到14个QTL,解释了56.47%的表型变异,MLM-GWAS仅定位到6个QTL,解释了18.47%的表型变异。RTM-GWAS共检测到57个QTL,分布在19条染色体上,表型变异解释率为0.03%—7.57%,其中41个QTL覆盖了已报道的来自30个双亲群体的81个百粒重QTL,16个QTL为新发现位点,包含一个表型变异解释率大于3%的大效应位点Sw-09-2。此外,检测的57个QTL中有20个位点与环境存在互作效应。这57个QTL构成了影响NJRIKY群体百粒重性状的遗传体系。通过SNPLDB标记与预测基因内的SNP进行χ²检验,共筛选到36个候选基因,其中4个候选基因来自大效应QTL,剩余32个候选基因来自小效应QTL。通过GO注释发现这些候选基因功能注释丰富,其中13个候选基因与籽粒发育直接相关,剩余的候选基因功能丰富,包含转运、转录调节因子等,表明不同生物学途径的基因共同调控NJRIKY群体中百粒重性状的表达。【结论】3种定位方法中,高效的RTM-GWAS方法检测到较为全面的NJRIKY群体的百粒重QTL,更适用于双亲RIL群体的QTL定位。不同功能的候选基因共同调控了复杂的百粒重性状的表达。

关键词: 大豆, 百粒重, QTL, 重组自交家系, 限制性两阶段多位点全基因组关联分析

Abstract:

【Objective】To thoroughly dissect the QTL system conferring 100-seed weight in a recombinant inbred lines population, the restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS) method was compared with other mapping methods for method optimization, which will provides basis for further exploration of candidate gene system and molecular marker-assisted design breeding. 【Method】A recombinant inbred line population consisting of 427 lines derived from a cross between Kefeng-1 and NN1138-2 was tested for its 100-seed weight under three environments. A total of 3 683 SNPLDBs (SNP linkage disequilibrium blocks) composed of 39 353 SNPs were applied to QTL mapping using three different mapping procedures, including the composite interval mapping (CIM) method, the mixed linear model (MLM-GWAS) method and the RTM-GWAS method, and the best mapping procedure was selected for the analysis of the 100-seed weight genetic system in NJRIKY population through comparing their detection power, including the detected number of QTLs and total phenotypic variation explained. 【Result】The 100-seed weight of Kefeng-1 and NN1138-2 were 9.0 g and 17.9 g, respectively, showing significant difference. The genotypic coefficient of variation and heritability of the trait were 12.4% and 85.4%, respectively. These results indicated that the population was suitable for genetic analysis of 100-seed weight trait. The RTM-GWAS procedure performed the best with the largest number of QTLs (57) explaining the most phenotypic variation (PVE=70.78%), while a total of 14 and 6 QTLs contributing 56.47% and 18.47% phenotypic variation were detected using CIM and MLM-GWAS, respectively. The 57 QTLs detected from the RTM-GWAS distributed on 19 chromosomes, of which 41 QTLs overlapped with 81 QTLs identified from 30 bi-parental populations in the literature. Furthermore, the PVE of 57 QTLs ranged from 0.03% to 7.57%, of which 16 QTLs were novel ones, including one large contribution major QTL Sw-09-2 (PVE>3%). Furthermore, 20 QTLs had significant interaction effect with environment. A total of 36 candidate genes were annotated from 37 QTLs through χ² test between SNPLDB markers and SNPs harboring in the predicted genes, of which 4 candidate genes were from the large contribution QTLs and other 32 candidate genes were from the small contribution QTLs. These candidate genes were included in different biological processes, of which 13 candidate genes were grouped in seed development directly, and the remaining candidate genes were grouped into different functions, such as transport, transcriptional regulators, etc., indicating that these genes from different biological pathways regulate the expression of 100-seed weight trait in NJRIKY together. 【Conclusion】Among the three different mapping procedures, RTM-GWAS procedure is the most powerful one which can provide a relatively thorough detection of 100-seed weight QTLs in NJRIKY population, therefore, it is more suitable for QTL mapping in bi-parental population such as RIL population. The candidate genes with various functions jointly regulated the complex expression of 100-seed weight trait.

Key words: soybean [Glycine max (L.) Merr.], 100-seed weight, QTL (quantitative trait locus), recombinant inbred lines population, restricted two-stage multi-locus genome-wide association analysis

潘丽媛,贺建波,赵晋铭,王吴彬,邢光南,喻德跃,张小燕,李春燕,陈受宜,盖钧镒. RTM-GWAS方法应用于大豆RIL群体百粒重QTL检测的功效[J]. 中国农业科学, 2020, 53(9): 1730-1742.

LiYuan PAN,JianBo HE,JinMing ZHAO,WuBin WANG,GuangNan XING,DeYue YU,XiaoYan ZHANG,ChunYan LI,ShouYi CHEN,JunYi GAI. Detection Power of RTM-GWAS Applied to 100-Seed Weight QTL Identification in a Recombinant Inbred Lines Population of Soybean[J]. Scientia Agricultura Sinica, 2020, 53(9): 1730-1742.

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图/表 9

图1

表1

表2

表3

图2

表4

表5

NJRIKY群体中与百粒重性状关联的QTL位点"

QTL	标记 Marker	-lgP	贡献率 R² (%)	QTL	标记 Marker	-lgP	贡献率 R² (%)
Sw-11-2	Gm11_BLOCK_5228756_5269867	56.22	7.57*	Sw-05-1	Gm05_BLOCK_28628661_28825701	7.42	0.82*
Sw-09-2	Gm09_BLOCK_34358756_34538440	39.72	5.12*	Sw-04-1	Gm04_BLOCK_10110270_10257050	6.78	0.74
Sw-04-7	Gm04_BLOCK_39928569_39957258	29.72	3.72*	Sw-06-1	Gm06_BLOCK_5723355_5918489	6.58	0.71
Sw-08-1	Gm08_16468204	28.90	3.61	Sw-06-3	Gm06_30304358	6.52	0.71*
Sw-10-1	Gm10_BLOCK_41285429_41285653	26.41	3.27	Sw-15-2	Gm15_25471398	6.31	0.68
Sw-18-5	Gm18_59805347	24.23	2.98*	Sw-16-5	Gm16_BLOCK_23266112_23462965	5.98	0.64
Sw-13-1	Gm13_31358574	23.33	2.86*	Sw-02-1	Gm02_BLOCK_2190737_2384686	5.72	0.61*
Sw-17-1	Gm17_BLOCK_2938402_3123352	20.28	2.45	Sw-04-4	Gm04_BLOCK_19626939_19826251	5.51	0.59
Sw-04-9	Gm04_BLOCK_40868266_40917625	19.75	2.38	Sw-03-2	Gm03_BLOCK_41020781_41042956	5.12	0.54
Sw-16-1	Gm16_BLOCK_12959169_13153966	16.33	1.94	Sw-03-1	Gm03_3970385	4.52	0.47
Sw-01-2	Gm01_BLOCK_55629182_55799927	15.79	1.87*	Sw-15-3	Gm15_36895087	4.48	0.46
Sw-18-1	Gm18_BLOCK_1922631_2035120	15.72	1.86*	Sw-06-2	Gm06_20892550	4.34	0.45*
Sw-14-4	Gm14_BLOCK_44088379_44288183	15.18	1.79*	Sw-04-2	Gm04_BLOCK_10815779_11015107	3.97	0.40
Sw-14-1	Gm14_1033115	14.10	1.65	Sw-10-3	Gm10_BLOCK_41542940_41691982	3.68	0.37
Sw-07-1	Gm07_BLOCK_1944869_1966911	12.09	1.40	Sw-01-1	Gm01_BLOCK_12639088_12838656	3.65	0.36
Sw-09-1	Gm09_BLOCK_264001_463636	11.95	1.38*	Sw-12-2	Gm12_BLOCK_37972975_37975786	3.46	0.34*
Sw-15-1	Gm15_BLOCK_9079223_9250661	11.21	1.29*	Sw-14-2	Gm14_BLOCK_13649138_13846641	3.19	0.31
Sw-04-8	Gm04_BLOCK_40184350_40334324	10.84	1.24	Sw-14-3	Gm14_BLOCK_42062012_42261888	2.98	0.29
Sw-18-2	Gm18_36907653	10.77	1.23	Sw-04-11	Gm04_BLOCK_47626591_47646641	2.94	0.28
Sw-10-2	Gm10_41392627	10.09	1.15	Sw-16-2	Gm16_15575581	2.92	0.28
Sw-08-2	Gm08_BLOCK_19121233_19314940	9.71	1.10	Sw-04-10	Gm04_41805915	2.65	0.25
Sw-09-3	Gm09_BLOCK_39036252_39210642	9.27	1.04	Sw-16-4	Gm16_BLOCK_21928405_22126811	2.54	0.24
Sw-11-1	Gm11_BLOCK_767896_842085	8.80	0.99	Sw-04-6	Gm04_BLOCK_26906733_27091677	2.54	0.24*
Sw-12-1	Gm12_BLOCK_35239969_35240158	8.77	0.98	Sw-18-4	Gm18_56862453	2.13	0.19
Sw-17-2	Gm17_BLOCK_7387475_7572446	8.11	0.90*	Sw-04-3	Gm04_BLOCK_17249185_17373282	2.03	0.18
Sw-16-3	Gm16_BLOCK_17551378_17602014	8.03	0.89	Sw-05-2	Gm05_30058805	1.83	0.16*
Sw-18-3	Gm18_BLOCK_56236139_56414021	8.00	0.89	Sw-12-3	Gm12_BLOCK_38208501_38296133	1.61	0.13*
Sw-02-2	Gm02_BLOCK_48637411_48823121	7.59	0.84	Sw-20-1	Gm20_236372	1.52	0.13
Sw-04-5	Gm04_BLOCK_23431433_23626782	7.59	0.84*	共计Total	57		70.78

表5

图3

表6

RTM-GWAS方法中检测到的与百粒重相关的候选基因体系"

QTL	解释率 R² (%)	候选基因 Candidate gene	SNP数目 No. of SNPs	GO注释 GO description
Sw-01-2	1.87	Glyma01g45220	6	胚胎发育Embryo Development
Sw-02-1	0.61	Glyma02g02860	1	PSII相关的光收集复合物II过程PSII associated light-harvesting complex II process
Sw-02-2	0.84	Glyma02g43960	2	种子休眠时胚胎发育终止Embryo development ending in seed dormancy
Sw-03-1	0.47	Glyma03g04020	1	多糖分解过程Polysaccharide catabolic process
Sw-03-2	0.54	Glyma03g33360	1	麦芽糖代谢过程Maltose metabolic process
Sw-04-1	0.74	Glyma04g11582	1	转运Transport
Sw-04-7	3.72	Glyma04g34070	1	响应镉离子Response to cadmium- ion
Sw-04-9	2.38	Glyma04g34660	1	脂肪酸代谢过程Fatty acid catabolic process
Sw-04-10	0.25	Glyma04g35511	1	转录的调节,依赖DNA Regulation of transcription, DNA-dependent
Sw-04-11	0.28	Glyma04g41810	2	蛋白质糖基化Protein glycosylation
Sw-05-1	0.82	Glyma05g23100	1
Sw-06-1	0.71	Glyma06g07880	2	种子休眠时胚胎发育终止Embryo development ending in seed dormancy
Sw-07-1	1.40	Glyma07g02940	3	ATP分解过程ATP catabolic process
Sw-08-1	3.61	Glyma08g21620	3	分生组织生长调节Regulation of meristem growth
Sw-08-2	1.10	Glyma08g24950	1	细胞生长Cell growth
Sw-09-1	1.38	Glyma09g00430	4	响应脱落酸Response to abscisic acid stimulus
Sw-09-3	1.04	Glyma09g32540	2	毒素分解过程Toxin catabolic process
Sw-10-1,	3.27	Glyma10g32920	2	种子发育Seed development
Sw-10-2	1.15		2
Sw-10-3	0.37	Glyma10g33160	1	花器官的形成Floral organ formation
Sw-11-1	0.99	Glyma11g01405	4	鸟苷四磷酸代谢过程Guanosine tetraphosphate metabolic process
Sw-11-2	7.57	Glyma11g07430	1	葡糖醛酸木聚糖代谢过程Glucuronoxylan metabolic process
Sw-12-1	0.98	Glyma12g31670	2	细胞过程规则Abaxial cell fate specification
Sw-12-3	0.13	Glyma12g35020	4	转录正调控Positive regulation of transcription
Sw-13-1	2.86	Glyma13g28260	1
Sw-14-1	1.65	Glyma14g01790	1	多糖生物合成过程Polysaccharide biosynthetic process
Sw-14-3	0.29	Glyma14g33820	1	花发育调节作用Regulation of flower development
Sw-14-4	1.79	Glyma14g35260	1	核转录mRNA分解代谢过程Nuclear-transcribed mRNA catabolic process
Sw-15-1	1.29	Glyma15g12410	4	蛋白质糖基化Protein glycosylation
Sw-16-5	0.64	Glyma16g20730	1	过渡金属离子转运Transition metal ion transport
Sw-17-1	2.45	Glyma17g04360	1
Sw-17-2	0.90	Glyma17g09961	3
Sw-18-1	1.86	Glyma18g02940	1	转录调控Regulation of transcription
Sw-18-3	0.89	Glyma18g46517	2
Sw-18-4	0.19	Glyma18g47240	1	表皮细胞分裂调节Regulation of epidermal cell division
Sw-18-5	2.98	Glyma18g50760	3	多糖生物合成过程Polysaccharide biosynthetic process
Sw-20-1	0.13	Glyma20g00565	4
共计Total	54.12	36

表6

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环境 Environment	亲本 Parent (g)			重组自交系群体 RIL
环境 Environment	科丰1号 Kefeng-1	南农1138-2 NN1138-2	平均值 Mean	最小值 Min.	最大值 Max.	遗传变异系数GCV(%)	遗传率 h²(%)
12JP	8.5	15.7	11.4	7.5	16.0	13.5	93.3
13JP	8.8	14.9	11.6	7.6	20.6	15.5	92.5
13SF	9.8	23.2	13.9	9.2	19.5	15.1	93.9
平均 Mean	9.0	17.9	12.3	8.6	17.1	12.4	85.4

变异来源 Source of variation	自由度 DF	均方 MS	F值 F value	P值 P value
环境 Environment	2	2308.47	101.66	<0.0001
重复（环境）Replication(Environment)	6	20.08	12.59	<0.0001
区组（环境×重复）Block(Environment×Replication)	180	1.34	1.78	<0.0001
家系 Line	426	23.66	6.81	<0.0001
家系×环境 Line×Environment	851	3.50	4.67	<0.0001
误差 Error	2245	0.75
合计 Total	3710

定位方法 Method	检测的QTL Detected QTLs	表型变异解释率 PVE (%)	已报道的QTL Reported QTLs
RTM-GWAS
Mapped QTL	57(19)	70.78	41(84)
LC major QTL	5(5)	23.30
SC major QTL	52(19)	47.48
QTL×Env.	20(13)	4.20
Unmapped QTL		14.52
CIM
Mapped QTL	14(8)	56.47	13(16)
MLM-GWAS
Mapped QTL	6(3)	18.47	6(18)

标记Marker	LOD/-lgP	表型变异解释率PVE (%)	SoyBase QTL
CIM
Gm04_BLOCK_15191938_15271503	3.67	2.94	5-2
Gm04_BLOCK_36700318_36900222	3.08	2.55	36-15
Gm04_BLOCK_39069193_39185415	2.93	2.37	36-15
Gm04_BLOCK_38868989_39068925	2.45	2.01	36-15
Gm04_BLOCK_29674388_29831299	1.96	1.59	20-2
Gm08_BLOCK_19121233_19314940	4.11	3.41	7-1,34-1,34-13,36-1,37-8
Gm09_BLOCK_35812609_35851884	6.81	5.76	40-4
Gm09_36859571	6.97	5.86	40-4
Gm10_BLOCK_49435374_49524464	4.44	3.69
Gm11_3955010	7.78	6.91	37-9
Gm11_BLOCK_5228756_5269867	12.39	11.03	21-1
Gm14_BLOCK_29877119_30044908	2.36	1.90	23-1,13-2
Gm15_BLOCK_29781764_29980832	3.69	2.95	6-1,36-12
Gm18_54211355	4.12	3.50	3-3
总计Total		56.47
MLM-GWAS
Gm04_BLOCK_23431433_23626782	3.72	3.36	20-2,5-2,36-15,45-3
Gm11_BLOCK_4611160_4662697	3.27	2.88	37-9
Gm11_BLOCK_5228756_5269867	4.03	3.69	37-9,21-1,22-2,49-2
Gm11_20972740	3.12	2.73	21-1,20-4,20-3,11-1,32-1,4-1,10-3,36-11
Gm18_BLOCK_16884478_16885174	3.40	3.03	2-5
Gm18_45987500	3.17	2.78	27-1
总计Total		18.47

RTM-GWAS方法应用于大豆RIL群体百粒重QTL检测的功效

Detection Power of RTM-GWAS Applied to 100-Seed Weight QTL Identification in a Recombinant Inbred Lines Population of Soybean

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