新疆冬小麦品种资源主要产量性状全基因组关联分析

doi:10.3864/j.issn.0578-1752.2023.18.001

中国农业科学 ›› 2023, Vol. 56 ›› Issue (18): 3487-3499.doi: 10.3864/j.issn.0578-1752.2023.18.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

新疆冬小麦品种资源主要产量性状全基因组关联分析

马艳明¹^,²(), 娄鸿耀³, 张胜军⁴, 王威¹, 郭营⁵, 倪中福², 刘杰²()

¹ 新疆农业科学院农作物品种资源研究所，乌鲁木齐 830091
² 中国农业大学农学院，北京 100193
³ 北京市农林科学院杂交小麦研究所，北京 100097
⁴ 新疆伊犁哈萨克自治州农业科学研究所，新疆伊宁 835011
⁵ 山东农业大学农学院，山东泰安 271018

收稿日期:2023-03-27 接受日期:2023-05-25 出版日期:2023-09-16 发布日期:2023-09-21
通信作者:
刘杰，Tel：010-62734072；E-mail：jieliu@cau.edu.cn
联系方式: 马艳明，Tel：13999260539；E-mail：ymma213@sina.com。
基金资助:
国家科技资源共享服务平台-国家作物种质资源库项目(NCGRC-2021-029)

Genome-Wide Association Analysis of Yield Traits in Xinjiang Winter Wheat Germplasm

MA YanMing¹^,²(), LOU HongYao³, ZHANG ShengJun⁴, WANG Wei¹, GUO Ying⁵, NI ZhongFu², LIU Jie²()

¹ Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi 830091
² College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193
³ Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097
⁴ Institute of Agricultural Sciences of Ili Prefecture, Yining 835011, Xinjiang
⁵ College of Agronomy, Shandong Agricultural University, Tai’an 271018, Shandong

Received:2023-03-27 Accepted:2023-05-25 Published:2023-09-16 Online:2023-09-21

摘要/Abstract

摘要：

【目的】高产是小麦育种的永恒主题，利用全基因组关联分析发掘控制小麦产量性状的QTL区段及优异基因，为小麦分子标记辅助选择育种提供理论依据和标记信息。【方法】以新疆本地188个冬小麦品种资源为材料，利用小麦55K SNP芯片进行全基因组扫描，通过对6个不同环境下的株高、穗长、小穗数、可育小穗数、穗粒数、千粒重、粒长、粒宽、籽粒长/宽比9个产量相关性状进行表型鉴定，利用6个环境下各性状数据及最佳线性无偏预测（BLUP）数据，基于混合线性模型（MLM）对表型和基因型进行全基因组关联分析。【结果】经主成分分析，将188个材料分为地方品种和育成品种2个亚群；利用6个环境下各性状数据，9个性状共检测到1 309个显著性SNP标记，其中，每个显著性SNP位点可解释7.259%—70.792%的表型变异。利用BLUP数据，9个性状共检测到66个显著性位点，同时与2个性状关联的共有SNP位点有5个，贡献率波动范围为8.498%—21.877%。将同时与2个性状或2个以上环境关联到的重复位点作为稳定的显著性关联位点，9个性状共检测到38个稳定关联位点，包括株高重复位点5个，穗长重复位点10个，小穗数重复位点10个，结实小穗数重复位点6个，穗粒数重复位点6个，千粒重重复位点1个，可解释9.10%—23.81%的表型变异。将这38个位点与已发布小麦基因组位点比对，仅找到3个与本研究关联重复位点位置相近、且有注释基因功能的基因，分别是：2A染色体上与株高关联位点AX-108794050距离相近的TraesCS2A01G448800，与转录因子bHLH71的代谢合成有关；1A染色体上与穗长关联位点AX-110689765距离相近的TraesCS2A01G448800，与蛋白质编码有关；4B染色体上与千粒重关联位点AX-110399975距离相近的TraesCS4B01G031100，与编码丝氨酸/苏氨酸蛋白激酶SD1-8有关，参与对细胞增殖与分化的调控。【结论】检测到38个与小麦产量性状关联的QTL位点，关联的优良等位基因具有降低株高、增加穗长、小穗数、可育小穗数、穗粒数和千粒重的作用。

关键词: 小麦, 产量性状, SNP标记, 关联分析, 候选基因

Abstract:

【Objective】To discover new high yield genes in wheat by association analysis, which can provide technical supports for the innovation and genetic improvement of high yield germplasm resources in wheat.【Method】Totally 188 bread wheat cultivars in Xinjiang were genotyped using the wheat 55K genotyping assay. GWAS was carried out to identify the signifcant single nucleotide polymorphisms (SNPs) which were associated with 9 wheat yield traits in 6 environments. The MLM algorithm in TASSEL5.0 was used to analyze the nine traits related to wheat yield traits.【Result】Totally 1309 SNPs explained 7.259%-70.792% of the phenotypic variation. 38 SNP loci were identifed, which were significantly correlated with 5 plant height weight SNP loci, 10 spike length weight SNP loci, 10 spikelet number SNP loci, 6 fertile spikelet number SNP loci, 6 spike grain number SNP loci, and 1 thousand grain weight SNP loci. These loci can explain 9.10%-23.81% of phenotypic variations. Comparing these 38 loci with the published wheat genome loci, only 3 functional genes were found, which annotated with gene function. There genes are: TraesCS2A01G448800 on chromosome 2A, which is close to the plant height associated site AX-108794050 and is related to the metabolic synthesis of transcription factor bHLH71; TraesCS2A01G448800, located on chromosome 1A at a distance similar to the spike length associated site AX-110689765, is related to protein coding; TraesCS4B01G031100, located on the 4B chromosome at a distance similar to the 1000 grain weight associated site AX-110399975, is associated with the encoding serine/threonine protein kinase SD1-8 and is involved in regulating cell proliferation and differentiation. 【Conclusion】38 QTL loci associated with wheat yield traits were detected. After verification, it was found that the associated excellent alleles have the effect of reducing plant height, increasing spike length, spikelet number, fertile spikelet number, grain number per spike, and thousand grain weight.

Key words: wheat, yield traits, SNP, association analysis, candidate genes

马艳明, 娄鸿耀, 张胜军, 王威, 郭营, 倪中福, 刘杰. 新疆冬小麦品种资源主要产量性状全基因组关联分析[J]. 中国农业科学, 2023, 56(18): 3487-3499.

MA YanMing, LOU HongYao, ZHANG ShengJun, WANG Wei, GUO Ying, NI ZhongFu, LIU Jie. Genome-Wide Association Analysis of Yield Traits in Xinjiang Winter Wheat Germplasm[J]. Scientia Agricultura Sinica, 2023, 56(18): 3487-3499.

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图/表 4

图1

图2

表1

38个重复位点的物理位置、P值及解释的表型变异率"

性状 Trait	标记 SNP	染色体 Chr.	物理位置 Position (bp)	P							PVE (%)
性状 Trait	标记 SNP	染色体 Chr.	物理位置 Position (bp)	E1	E2	E3	E4	E5	E6	BLUP	E1	E2	E3	E4	E5	E6	BLUP
PH	AX-108794050	2A	698175277	3.76E-06	1.08E-05					1.06E-05	11.60	11.60					10.10
	AX-108838330	4B	465981233		6.31E-05					4.80E-06		9.00					12.90
	AX-109467555	6A	417439944		3.11E-05					4.28E-05		9.60					11.40
	AX-109857508	2A	19661854	1.41E-05	8.26E-05					2.20E-05	12.40	9.50					11.40
	AX-110969164	7B	53530940	1.37E-05	5.65E-05					1.84E-05	13.80	11.30					12.80
SL	AX-111524633	1A	229272328		6.67E-08					1.67E-05		26.90					12.70
	AX-110359663	2A	555501466		1.81E-08					3.06E-05		24.50					14.80
	AX-110956005	5A	384438157		1.19E-10					1.987-08		28.80					21.90
	AX-108852957	6A	611194075		1.61E-08					6.62E-05		26.40					12.10
	AX-110689765	6A	12313027		1.63E-05					9.13E-05		11.40					9.10
	AX-109282231	3B	138504166		8.79E-05					1.02E-05		11.60					14.90
	AX-108758415	7B	687068740		7.82E-13					5.99E-05		36.60					11.10
	AX-111722527	2D	527923732		7.31E-10					1.54E-05		26.70					12.80
	AX-110568577	4D	200403065		1.64E-09					9.80E-05		27.40					11.10
	AX-109822039	5D	154563929		1.78E-07					1.14E-06		22.80					16.10
SN	AX-108825815	3A	526860477						2.49E-05	7.23E-05						12.60	10.80
	AX-108977066	3A	526923011				8.55E-05		1.43E-05	1.40E-05		10.80				13.30	12.70
	AX-109365068	5A	69079172	5.43E-06						5.21E-05	11.80						9.20
	AX-110105180	4A	549802334						4.76E-05	7.71E-05						14.20	12.80
	AX-110123746	4D	469869704	2.33E-06						6.47E-05	15.10						11.10
	AX-110419722	3A	514225494						2.29E-05	1.61E-05						13.80	16.10
	AX-111073226	7A	383199757	8.41E-05						8.90E-05	10.80						10.80
SN	AX-111074553	6B	610906100	3.16E-07						1.19E-05	16.60						12.50
	AX-111523929	1A	516381475	3.15E-07						1.18E-05	18.70						13.50
	AX-111700650	7B	548781811	3.21E-07						4.72E-06	18.10						13.40
FSN	AX-110123746	4D	469869704	3.52E-07		9.72E-05				1.08E-05	17.60		10.80				13.50
	AX-111073226	7A	383199757	4.54E-05		7.21E-05				3.44E-05	11.50		9.30				12.00
	AX-111523929	1A	516381475	4.63E-08		5.66E-05				1.81E-06	22.50		12.60				16.60
	AX-111074553	6B	610906100	2.84E-07						7.44E-06	16.60						13.00
	AX-111700650	7B	548781811	1.11E-06						2.58E-06	15.90						11.70
	AX-109545508	2A	324629159	7.76E-07						1.92E-05	16.70						12.90
GNPS	AX-108745367	1A	554125804	4.45E-05	2.18E-08					3.82E-05	11.60	25.70					12.92
	AX-110509054	6A	71539737	7.04E-05	2.27E-08					1.91E-05	11.00	22.70					12.35
	AX-112290916	4B	241185348	1.65E-06						1.24E-05	16.70						12.87
	AX-110270363	4D	200804203	3.53E-08						3.69E-05	21.60						11.77
	AX-111523929	1A	516381475		2.92E-08					1.35E-09		22.53					23.81
	AX-110123746	4D	469869704		3.69E-05					8.14E-09		11.77					22.73
TKW	AX-110399975	3B	23344933	4.66E-06						9.81E-05	11.60						10.30

表1

图3

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新疆冬小麦品种资源主要产量性状全基因组关联分析

Genome-Wide Association Analysis of Yield Traits in Xinjiang Winter Wheat Germplasm

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