冠层活性相关性状全基因组关联分析及其对产量性状遗传效应的解析

doi:10.3864/j.issn.0578-1752.2024.04.001

中国农业科学 ›› 2024, Vol. 57 ›› Issue (4): 627-637.doi: 10.3864/j.issn.0578-1752.2024.04.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

冠层活性相关性状全基因组关联分析及其对产量性状遗传效应的解析

李法计¹(), 程敦公¹, 余晓丛², 闻伟锷³, 刘金栋⁴, 翟胜男¹, 刘爱峰¹, 郭军¹, 曹新有¹, 刘成¹, 宋健民¹, 刘建军¹, 李豪圣¹()

¹ 山东省农业科学院作物研究所/小麦玉米国家工程研究中心/农业农村部黄淮北部小麦生物学与遗传育种重点实验室/山东省小麦技术创新中心/济南市小麦遗传改良重点实验室，济南 250100
² 菏泽学院农业与生物工程学院（牡丹学院），山东菏泽 274015
³ 遵义医科大学细胞生物学教研室，贵州遵义 563099
⁴ 中国农业科学院作物科学研究所，北京 100081

收稿日期:2023-07-17 接受日期:2023-09-12 出版日期:2024-02-16 发布日期:2024-02-20
通信作者:
李豪圣，E-mail：lihaosheng810@163.com。
联系方式: 李法计，E-mail：lifajily@163.com。
基金资助:
山东省重点研发计划（重大科技创新工程）(2021LZGC009); 泰山产业领军人才工程(LJNY202006); 国家现代农业产业技术体系(CARS-03-6); 2023年山东省农业科学院科技创新工程(CXGC2023A01); 济南市“新高校20条”资助项目(202228067)

Genome-Wide Association Studies for Canopy Activity Related Traits and Its Genetic Effects on Yield-Related Traits

LI FaJi¹(), CHENG DunGong¹, YU XiaoCong², WEN WeiE³, LIU JinDong⁴, ZHAI ShengNan¹, LIU AiFeng¹, GUO Jun¹, CAO XinYou¹, LIU Cheng¹, SONG JianMin¹, LIU JianJun¹, LI HaoSheng¹()

¹ Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Key Laboratory of Wheat Biology and Genetics and Breeding in Northern Huang-Huai River Plain, Ministry of Agriculture and Rural Affairs/Shandong Technology Innovation Center of Wheat/Jinan Key Laboratory of Wheat Genetic Improvement, Jinan 250100
² College of Agricultral and Biological Engineering (College of Tree Peony), Heze University, Heze 274015, Shandong
³ Department of Cell Biology, Zunyi Medical University, Zunyi 563099, Guizhou
⁴ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081

Received:2023-07-17 Accepted:2023-09-12 Published:2024-02-16 Online:2024-02-20

摘要/Abstract

摘要：

【目的】冠层活性是反映作物生长发育的重要指标，发掘小麦冠层活性相关基因并分析其与产量性状的关系，为解析产量遗传结构和辅助育种提供理论支撑。【方法】以166份国内外小麦品种为材料，将其种植于河南安阳和安徽濉溪，结合已构建的包含326 570个来源于小麦90K和660K SNP芯片标记的高密度整合物理图谱，对苗期和花后10 d归一化植被指数（NDVI-S和NDVI-10）及花后10 d旗叶叶绿素含量（Chl-10）进行关联分析，并与前期利用相同材料得到的产量相关性状结果进行比较。【结果】NDVI-S、NDVI-10和Chl-10在基因型、环境及基因型×环境互作间变异方差均达极显著（P<0.01）差异，广义遗传力（h2 b）分别为0.81、0.81和0.91。分别检测到13、12和15个与NDVI-S、NDVI-10和Chl-10显著相关的位点，其中，有12、11和12个为新位点，5个位点与2个以上性状有关。166份小麦品种含有NDVI-S、NDVI-10和Chl-10优异等位基因数变幅分别为4-11、3-11和4-12，且随着优异等位基因数目增加其对应表型值呈递增趋势。NDVI-S与千粒重、粒长和粒宽显著正相关（P<0.01）;Chl-10与产量和旗叶宽显著正相关（P<0.01），与单位面积穗数、株高和穗下节长显著负相关（P<0.01）。检测到7个同时与产量和冠层活性相关的多效性位点。【结论】NDVI-S可用于品种产量性状的选择，检测到的稳定位点和多效性位点可在开发标记后用于育种材料的检测。

关键词: 小麦, 冠层活性, 产量, 归一化植被指数, 叶绿素含量, 关联分析

Abstract:

【Objective】Canopy activity is an important indicator of wheat growth and development. Identification the loci for canopy activity related traits and their relationships with grain yield (GY) related traits can provide theoretical support for the dissection of genetic structure of yield trait and assisted wheat breeding.【Method】A total of 166 wheat varieties originating from both domestic and international sources were planted in Anyang of Henan province and Suixi of Anhui province in cropping seasons. With the integrated physical map containing 326 570 SNP markers from the wheat 90K and 660K chips, genome-wide association studies for normalized difference vegetation index at seedling stage (NDVI-S) and 10 days after flowering (NDVI-10), and chlorophyll content in flag leaf at 10 days after flowering (Chl-10) were carried out. The results were compared with the previous study for GY related traits using the same material. 【Result】Analysis of variance (ANOVA) showed highly significant effects (P<0.01) of genotypes, environments and genotype×environment interactions on NDVI-S, NDVI-10 and Chl-10, with broad-sense heritabilities (h2 b) of 0.81, 0.81 and 0.91, respectively. Thirteen, 12 and 15 loci were detected to be significantly correlated with NDVI-S, NDVI-10 and Chl-10, respectively, among which 12, 11 and 12 were new, and five loci were associated with two or more traits. The number of favorable alleles for NDVI-S, NDVI-10 and Chl-10 ranged from 4 to 11, 3 to 11 and 4 to 12, respectively, in the 166 wheat varieties, and the phenotypic values increased with the accumulation of favorable alleles. NDVI-S showed significant (P<0.01) and positive correlations with thousand-kernel weight, kernel length and kernel width. Chl-10 was significant positively correlated with GY and flag leaf width (P<0.01), whereas significant negatively correlated with spike number per unit area, plant height and uppermost internode length (P<0.01). Seven pleiotropic loci were detected co-related with both GY and canopy activity related traits.【Conclusion】NDVI-S can be directly used for selection of yield traits. The stable and pleiotropic loci detected in this study can be used for marker-assisted selection.

Key words: Triticum aestivum, canopy activity, grain yield, normalized difference vegetation index, chlorophyll content, genome- wide association studies

李法计, 程敦公, 余晓丛, 闻伟锷, 刘金栋, 翟胜男, 刘爱峰, 郭军, 曹新有, 刘成, 宋健民, 刘建军, 李豪圣. 冠层活性相关性状全基因组关联分析及其对产量性状遗传效应的解析[J]. 中国农业科学, 2024, 57(4): 627-637.

LI FaJi, CHENG DunGong, YU XiaoCong, WEN WeiE, LIU JinDong, ZHAI ShengNan, LIU AiFeng, GUO Jun, CAO XinYou, LIU Cheng, SONG JianMin, LIU JianJun, LI HaoSheng. Genome-Wide Association Studies for Canopy Activity Related Traits and Its Genetic Effects on Yield-Related Traits[J]. Scientia Agricultura Sinica, 2024, 57(4): 627-637.

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图/表 8

表1

图1

表2

图2

表3

冠层活性相关性状显著性位点及与前人研究比较"

性状 Trait	标记^a Marker	染色体 Chr.	物理位置^b Physical position (bp)	环境 Environment	SNP^c	P	贡献率 R² (%)	QTL/标记/基因^d QTL/marker/gene
苗期归一化植被指数 NDVI-S	AX-109973814	1A	553879787-556989408	E1/E4/E5	A/G	3.76E^-04-9.45E^-04	7.2-8.8
	AX-89581383	2A	31905918-31954704	E1/E5	C/T	1.92E^-04-9.38E^-04	7.3-8.9
	AX-95099338	2B	794345863-794501909	E2/E3/E5	C/T	2.30E^-05-9.94E^-04	6.9-12.5
	AX-108780837	3B	800187839-803762562	E2/E3/E4/E5	G/T	2.37E^-04-9.92E^-04	6.9-9.8
	AX-111488372	4A	688477376-692653638	E1/E4/E5	C/T	4.42E^-04-9.97E^-04	7.0-8.5
	AX-108817291	4B	32178420-42912748	E1/E3/E4/E5	A/G	4.67E^-05-9.70E^-04	7.0-11.1
	AX-109416328	5A	511336844-516799817	E3/E4/E5	C/T	7.41E^-05-9.99E^-04	7.0-10.5
	AX-108827844	5B	584820626-587603152	E1/E2/E5	C/T	2.25E^-05-9.21E^-04	7.0-11.7
	AX-95010007	5D	479879394-483521914	E2/E4/E5	C/T	1.02E^-04-7.72E^-04	7.7-10.0
	AX-108871828	6B	705307814-705307884	E1/E5	A/G	2.65E^-04-6.98E^-04	7.6-8.8	QNDVI-S.caas-6BL^[24]
	AX-110399902	7A	511044701-514432331	E2/E4/E5	A/C	1.14E^-04-9.79E^-04	6.9-10.0
	AX-109353477	7B	53647905-59320644	E1/E4/E5	C/T	9.49E^-06-9.99E^-04	6.8-13.5
	AX-111483621	7B	700393032-704402945	E2/E3/E5	G/T	1.81E^-04-9.82E^-04	7.1-9.2
花后10 d归一化植被指数NDVI-10	AX-89581383	2A	31905918-31958182	E2/E3/E5	C/T	5.03E^-06-9.14E^-04	7.9-11.4
	AX-110065934	3A	20031674-24754209	E1/E2/E4/E5	C/T	1.28E^-05-9.82E^-04	7.3-13.7
	AX-111066255	4A	3156028-4485378	E3/E4/E5	G/T	3.83E^-05-9.39E^-04	7.1-12.1
	IWB9838	5A	444529778-444893234	E1/E4/E5	A/G	1.26E^-04-7.27E^-04	7.7-9.4	QNDVI-10.caas-5AL ^[24]
	AX-111085648	5A	509652100-509992242	E2/E3/E4	A/G	6.29E^-04-9.85E^-04	7.5-8.6
	AX-110413050	5A	538001880-540914319	E2/E3/E4/E5	G/T	3.99E^-05-9.99E^-04	7.0-11.5
	AX-110910427	5B	416212499-420974307	E1/E2/E5	A/G	3.33E^-05-9.95E^-04	7.2-11.7
	AX-108831704	5B	571816645-572547249	E2/E4/E5	A/G	8.35E^-05-6.95E^-04	8.0-10.4
	AX-110458337	5D	512761945-515042348	E2/E3/E5	C/T	8.47E^-05-5.92E^-04	8.1-11.3
	IWA497	7A	515006880-517518517	E1/E4/E5	A/G	2.26E^-05-9.29E^-04	7.1-11.7
	IWA5912	7A	674272175-674276806	E1/E2/E5	A/G	3.94E^-05-7.05E^-04	7.4-10.8
	AX-111094331	7B	720812571-725728459	E2/E4/E5	A/G	2.86E^-07-9.10E^-04	6.7-18.5
花后10 d旗叶叶绿素含量 Chl-10	AX-89478051	1A	10746438-11665198	E1/E3/E4/E5	C/T	1.15E^-04-8.89E^-04	7.3-9.8
	AX-110019816	1A	572240419-574819040	E2/E3/E4/E5	A/G	2.21E^-04-6.48E^-04	7.7-8.8
	AX-109271027	1B	14147203-14149354	E1/E3/E4/E5	C/T	3.72E^-05-9.09E^-04	7.4-10.5
	IWB34618	1B	39590913-41642839	E1/E2/E3/E4/E5	C/T	1.49E^-05-9.73E^-04	6.9-11.7
	AX-110906318	1B	464709853-465687627	E3/E4/E5	A/G	2.36E^-05-9.71E^-04	6.6-9.3
	AX-111696227	1B	562234252-563750279	E3/E4/E5	G/T	6.29E^-06-9.62E^-04	6.8-13.9
	AX-111592648	2B	670837387-674035196	E1/E2/E3/E4/E5	C/T	5.71E^-05-8.91E^-04	6.8-10.1
	AX-108767341	2D	79064947-79552104	E1/E2/E3/E4/E5	A/C	4.79E^-05-8.80E^-04	6.9-11.0	QChl-A.caas-2DS^[11]
	AX-111709018	4A	3126102-3126172	E1/E2/E5	C/T	5.19E^-04-9.10E^-04	6.8-7.7
	AX-109356891	4A	688401664-690885158	E1/E2/E3/E5	C/G	3.89E^-04-9.72E^-04	6.4-8.4
	AX-110921829	4A	726314392-729886306	E1/E2/E3/E4/E5	C/T	1.74E^-04-9.42E^-04	6.8-9.7
	IWB31092	5A	510096358-514153660	E1/E2/E3/E4/E5	A/G	1.33E^-05-9.76E^-04	6.5-12.1	IWB21197^[21]
	AX-111078602	5B	576574518-576574588	E3/E4/E5	C/T	4.38E^-04-4.82E^-04	7.7-8.1
	AX-110462661	6A	26782691-26782761	E1/E2/E4/E5	C/T	2.28E^-04-9.14E^-04	7.1-9.8	QChl-10.caas-6AS^[11]; QChl-6A^[20]; Qchl-saw-6A^[22]
	AX-110587099	7A	6330314-12989016	E1/E2/E3/E4/E5	C/T	8.19E^-05-9.97E^-04	6.7-10.3

表3

图3

表4

表5

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性状 Trait	均方值Mean square					遗传力 h2 b
性状 Trait	基因型 Genotype (G)	环境 Environment (E)	重复 Replicate	基因型×环境 G×E	误差 Error	遗传力 h2 b
NDVI-S	0.003**	0.047**	0.003**	0.001**	0.001	0.81
NDVI-10	0.009**	0.048**	0.001	0.002**	0.001	0.81
Chl-10	74.25**	1212.76**	26.24**	7.47**	1.64	0.91

性状 Trait	环境 Environment	平均值 Mean	标准差 SD	范围 Range	变异系数 CV
NDVI-S	E1	0.20	0.013	0.17-0.24	0.056
	E2	0.18	0.018	0.15-0.25	0.072
	E3	0.21	0.021	0.14-0.27	0.079
	E4	0.20	0.023	0.11-0.26	0.087
	E5	0.20	0.015	0.15-0.24	0.063
NDVI-10	E1	0.75	0.028	0.66-0.80	0.035
	E2	0.76	0.027	0.66-0.84	0.032
	E3	0.75	0.046	0.63-0.87	0.053
	E4	0.74	0.040	0.58-0.83	0.048
	E5	0.75	0.026	0.68-0.82	0.032
Chl-10	E1	54	2.6	46-61	0.043
	E2	53	2.8	45-59	0.047
	E3	53	2.8	45-60	0.047
	E4	50	3.1	43-57	0.055
	E5	53	2.5	46-59	0.042

性状Trait	NDVI-S	NDVI-10	Chl-10
产量GY	-0.001	0.170*	0.405**
每平方米穗数SN	-0.052	0.154*	-0.367**
穗粒数KNS	-0.034	-0.190*	0.220**
千粒重TKW	0.370**	0.082	0.290**
粒长KL	0.293**	0.148	0.037
粒宽KW	0.321**	0.035	0.245**
穗长SL	-0.002	-0.211**	0.071
穗干重SDW	0.312**	-0.179*	0.346**
抽穗期HD	-0.237**	0.142	0.159*
株高PH	0.243**	-0.287**	-0.381**
穗下节长UIL	0.209**	-0.249**	-0.362**
旗叶长FLL	0.231**	-0.034	-0.291**
旗叶宽FLW	-0.092	0.091	0.514**

染色体 Chr.	物理位置 Physical interval (bp)	冠层活性相关性状显著性位点 Significant loci for canopy activity related traits	产量相关性状显著性位点 Significant loci for grain yield related traits
1A	8291180-11950637	AX-89478051 (Chl-10)	IWB6999 (KW); AX-109621606 (FLL)
2A	27328522-31954704	AX-89581383 (NDVI-S; NDVI-10)	AX-94546135 (GY); AX-111037158 (KW; HD); AX-110988136 (PH)
5A	509652100-516799817	AX-109416328 (NDVI-S); AX-111085648 (NDVI-10); IWB31092 (Chl-10)	AX-109367907 (SL)
5A	538001880-547648338	AX-110413050 (NDVI-10)	AX-110919697 (SL); AX-110675353 (PH)
5B	571816645-587603152	AX-108827844 (NDVI-S); AX-108831704 (NDVI-10); AX-111078602 (Chl-10)	AX-110995303 (GY); AX-110971192 (SL); AX-108921249 (PH)
6B	696641914-709221403	AX-108871828 (NDVI-S)	AX-95260682 (SN); AX-109820966 (KW); AX-109459603 (FLL)
7A	511044701-517518517	AX-110399902 (NDVI-S); IWA497 (NDVI-10)	AX-110127979 (GY); AX-109921812 (HD)

冠层活性相关性状全基因组关联分析及其对产量性状遗传效应的解析

Genome-Wide Association Studies for Canopy Activity Related Traits and Its Genetic Effects on Yield-Related Traits

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