小麦条锈菌SNP分子标记的开发与应用

doi:10.6048/j.issn.1001-4330.2025.05.019

新疆农业科学 ›› 2025, Vol. 62 ›› Issue (5): 1219-1225.DOI: 10.6048/j.issn.1001-4330.2025.05.019

小麦条锈菌SNP分子标记的开发与应用

来汉林¹(), 李进², 沈煜洋², 邓菲菲², 杨红³, 李广阔², 李月¹(), 高海峰²()

1.新疆农业大学生命科学学院/新疆极端环境生物生态适应与进化重点实验室,乌鲁木齐 830052
2.新疆维吾尔自治区农业科学院植物保护研究所/农业部西北荒漠绿洲作物有害生物综合治理重点实验室,乌鲁木齐 830091
3.新疆农业大学农学院,乌鲁木齐 830052

收稿日期:2024-10-05 出版日期:2025-05-20 发布日期:2025-07-09
通信作者: 高海峰(1983-),男,河南人,研究员,硕士生导师,研究方向为粮食作物病虫草害防治,(E-mail) ghf20044666@163.com;
李月(1984-),女,河南人,副教授,硕士生导师,研究方向为作物逆境分子生物学,(E-mail)liyue6905@126.com.
作者简介:来汉林(1996-),男,湖北人,硕士研究生,研究方向为植物保护、生物化学与分子生物学,(E-mail)930062867@qq.com
基金资助:
新疆维吾尔自治区重点研发专项(2022B02015-3);新疆小麦产业技术体系(XJARS-01);现代农业产业技术体系(CARS-03-88);上海合作组织科技伙伴计划及国际科技合作计划项目(2023E01015);新疆农业科学院农业科技创新稳定支持专项(xjnkywdzc-2023004-1);新疆维吾尔自治区自然科学基金项目(2022D01A270)

Development of SNP molecular markers applied to genetic structure analysis of wheat stripe rust fungus

LAI Hailin¹(), LI Jin², SHEN Yuyang², DE Feifei², YANG Hong³, LI Guangkuo², LI Yue¹(), GAO Haifeng²()

1. Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University,Urumqi 830052,China
2. Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs / Institute of Plant Protection,Xinjiang Academy of Agricultural Sciences,Urumqi 830091, China
3. College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China

Received:2024-10-05 Published:2025-05-20 Online:2025-07-09
Supported by:
Major Scientific R & D Program Special Project of Xinjiang Uygur Autonomous Region(2022B02015-3);Earmarked Fund for(XJARS-01);Earmarked Fund for CARS(CARS-03-88);Regional Coordinated Innovation Project (Shanghai Cooperation Organization S & T Partnership Program)(2023E01015);Agricultural S & T Innovation Stability Support Special Project of Xinjiang Academy of Agricultural Sciences(xjnkywdzc-2023004-1);Project of Natural Science Foundation of Xinjiang Uygur Autonomous Region(2022D01A270)

摘要/Abstract

摘要：

【目的】开发出新的KASP-SNP引物,揭示不同流行区域条锈菌群体之间的遗传结构差异。【方法】在已有的SNP位点基础上,筛选出次等位基因频率>0.4的SNP位点,并设计成KASP-SNP引物,分析伊犁河谷春小麦、冬小麦条锈菌菌株进行遗传结构和引物多态性。【结果】筛选出18对扩增稳定、基因分型效果明显的KASP-SNP引物,伊犁河谷春小麦条锈菌群体与冬小麦条锈菌群体之间存在一定的遗传差异,18对引物的多态性信息含量指数平均为0.273 5,基因多样性指数平均为0.332 5,高于SSR的平均多样性指数。【结论】开发了18对KASP-SNP引物具有丰富的多态性,可用于小麦条锈菌的群体遗传结构分析。

关键词: 小麦条锈菌; KASP-SNP引物开发; 遗传结构; 分子标记

Abstract:

【Objective】 This project aims to develop new KASP-SNP primers to reveal the differences in genetic structure among Puccinia striiformis f. sp. trititc populations in different endemic regions. 【Methods】 On the basis of existing SNP loci, we screened SNP loci with suballele frequency > 0.4 and designed KASP-SNP primers to analyze the genetic structure and primer polymorphisms of spring and winter wheat Puccinia striiformis f. sp. trititc in the Ili River Valley. 【Results】 Eighteen pairs of KASP-SNP primers with stable amplification and obvious genotyping effect were finally selected, there were certain genetic differences between the spring and winter wheat stripe rust populations in the Ili River Valley, and the polymorphic information content index of the 18 pairs of primers averaged 0.273,5, and the gene diversity index averaged 0.332,5, which was higher than the SSR average diversity index. 【Conclusion】 The 18 pairs of KASP-SNP primers developed in this study are rich in polymorphism and can be used to analyze the population genetic structure of Puccinia striiformis f. sp. trititc.

Key words: wheat stripe rust; SNP molecular marker; genetic structure; KASP technique

中图分类号:

S435、123

来汉林, 李进, 沈煜洋, 邓菲菲, 杨红, 李广阔, 李月, 高海峰. 小麦条锈菌SNP分子标记的开发与应用[J]. 新疆农业科学, 2025, 62(5): 1219-1225.

LAI Hailin, LI Jin, SHEN Yuyang, DE Feifei, YANG Hong, LI Guangkuo, LI Yue, GAO Haifeng. Development of SNP molecular markers applied to genetic structure analysis of wheat stripe rust fungus[J]. Xinjiang Agricultural Sciences, 2025, 62(5): 1219-1225.

图/表 5

参考文献 20

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采样点 Location	分离菌株 No.of isolates	北纬(N) North Latitude	东经(E) East Longitude
巩留县春小麦采样点 Spring wheat Sampling point in Gongliu County	2	43°14'49″	82°48'49″
	2	43°15'34″	82°44'8″
	6	43°14'57″	82°49'21″
昭苏先春小麦采样点 Spring wheat Sampling point in Zhaosu County	4	43°6'54″	81°3'7″
	4	43°8'42″	81°21'23″
	7	43°9'10″	81°10'38″
新源县春小麦采样点 Spring wheat Sampling point in Xinyuan County	3	43°15'43″	82°51'46″
新源县春小麦采样点 Spring wheat Sampling point in Xinyuan County	2	43°27'9″	83°55'15″
特克斯县春小麦采样点 Spring wheat Sampling point in Tekes County	2	43°2'58″	81°47'55″
	6	43°4'51″	81°47'26″
	9	43°12'7″	81°39'47″
尼勒克县春小麦采样点 Spring wheat Sampling point in Nilka County	6	43°50'55″	82°34'10″
尼勒克县春小麦采样点 Spring wheat Sampling point in Nilka County	6	43°46'54″	83°12'58″
巩留县冬小麦采样点 Winter wheat Sampling point in Gongliu County	3	43°28'3.88″	82°07'4.48″
	4	43°31'8.99″	82°03'4.39″
	4	43°34'7.44″	81°58'6.58″
新源县冬小麦采样点 Winter wheat Sampling point in Xinyuan County	3	43°32'8.05″	83°10'3.73″
	5	43°26'1.64″	83°26'6.50″
	4	43°29'0.71″	83°38'2.30″
察布查尔锡伯自治县冬小麦采样点 Winter wheat Sampling point in Chabuchar Xibe Autonomous County	4	43°48'6.15″	80°48'8.30″
	4	43°43'7.64″	81°23'2.44″

采样点 Location	分离菌株 No.of isolates	北纬(N) North Latitude	东经(E) East Longitude
巩留县春小麦采样点 Spring wheat Sampling point in Gongliu County	2	43°14'49″	82°48'49″
	2	43°15'34″	82°44'8″
	6	43°14'57″	82°49'21″
昭苏先春小麦采样点 Spring wheat Sampling point in Zhaosu County	4	43°6'54″	81°3'7″
	4	43°8'42″	81°21'23″
	7	43°9'10″	81°10'38″
新源县春小麦采样点 Spring wheat Sampling point in Xinyuan County	3	43°15'43″	82°51'46″
新源县春小麦采样点 Spring wheat Sampling point in Xinyuan County	2	43°27'9″	83°55'15″
特克斯县春小麦采样点 Spring wheat Sampling point in Tekes County	2	43°2'58″	81°47'55″
	6	43°4'51″	81°47'26″
	9	43°12'7″	81°39'47″
尼勒克县春小麦采样点 Spring wheat Sampling point in Nilka County	6	43°50'55″	82°34'10″
尼勒克县春小麦采样点 Spring wheat Sampling point in Nilka County	6	43°46'54″	83°12'58″
巩留县冬小麦采样点 Winter wheat Sampling point in Gongliu County	3	43°28'3.88″	82°07'4.48″
	4	43°31'8.99″	82°03'4.39″
	4	43°34'7.44″	81°58'6.58″
新源县冬小麦采样点 Winter wheat Sampling point in Xinyuan County	3	43°32'8.05″	83°10'3.73″
	5	43°26'1.64″	83°26'6.50″
	4	43°29'0.71″	83°38'2.30″
察布查尔锡伯自治县冬小麦采样点 Winter wheat Sampling point in Chabuchar Xibe Autonomous County	4	43°48'6.15″	80°48'8.30″
	4	43°43'7.64″	81°23'2.44″

引物 Primer	SNP位置 SNP sequencing loci	引物序列 Sequence
PS1	Supercont2.93648	F: CCCAGTATGCATTTCTCAAAATCGATCA
		H: CCCAGTATGCATTTCTCAAAATCGATCG
		R: CCTTGTCGTAATCGTCGTTCCCATT
PS2	Supercont3.442202	F: TCTTGATGCCGGATGTGGTGGT
		H: CTTGATGCCGGATGTGGTGGC
		R: CAATCAATCCTTCTTCTTCTTTGCCTCCAT
PS3	Supercont14.389177	F: GAGACTTGATGAGTTTTTCTTTCTTTCCC
		H: TGAGACTTGATGAGTTTTTCTTTCTTTCCT
		R: AGATTCTTCCCGGATTCGACAAATTCA
PS4	Supercont1.298417	F: CAAAGCTCACAGGGCTGATTTTTACT
		H: AAAGCTCACAGGGCTGATTTTTACC
		R: TCATGCCAGCTCAATTCCTGCGTAGT
PS5	Supercont12.777518	F: GCCATTCGCAGTAGCATCGGTA
		H: GCCATTCGCAGTAGCATCGGTG
		R: GGTAAGCATGATCTTCTATGACCTACAGT
PS6	Supercont16.108630	F: CTGGTTCTGTTTGATACAACAATGTGAC
		H: CCTGGTTCTGTTTGATACAACAATGTGAT
		R: CACCTATGATTACCTACGGATGCTGAT
PS7	Supercont23.73782	F: CTCTCCACTTTTCGGATTCGCTAATAATC
		H: CTCTCCACTTTTCGGATTCGCTAATAATT
		R: GGACCGACTGAATTAGCCTTAACAACTA
PS8	Supercont109.152246	F: CGTCTGACACCTCGTCGTGAAG
		H: CGTCTGACACCTCGTCGTGAAC
		R: GCAGCACTACCTCGGGCTAGTA
PS9	Supercont116.239091	F: CCGTGGAACTCCAGTGTTTTGTCTA
		H: CGTGGAACTCCAGTGTTTTGTCTG
		R: CAAAACGTAGCCGCAGGGATGAAA
PS10	Supercont117.206340	F: CCCGAACCACAGCCTAGACTG
		H: TCCCGAACCACAGCCTAGACTA
		R: GCAAGGAATTGTTGTCCAGTTCTCTT
PS11	Supercont131.292765	F: GTTAGAATCCTGAGGTCCACTAATGAT
		H: GTTAGAATCCTGAGGTCCACTAATGAC
		R: ACATCGGTCGAAGGCTGTTCAA
PS12	Supercont113.62255	F: TCATGTGATTCGAACTCTCGGATGC
		H: AATCATGTGATTCGAACTCTCGGATGT
		R:GAAAACCACCCCGAAAAACTAAGATCAAT
PS13	Supercont120.53959	F: GAAGAAGGTGCAGGTAGAGTAATCTTA
		H: AAGAAGGTGCAGGTAGAGTAATCTTG
		R: CCAGCATGTTCAGCTTCTTCCAAA
PS14	Supercont136.207251	F: GAGCCTAAAGAAATGAACGATCAGC
		H: TGAGCCTAAAGAAATGAACGATCAGT
		R: CTCTTCACCCAAATCCCTGTCCAT
PS15	Supercont137.24508	F: CACACATCAAATCAACGTTCATACTCCA
		H: ACACATCAAATCAACGTTCATACTCCG
		R: CCAGAAACGTGGTGTGCCAACTT
PS16	Supercont24.180282	F: AGACGACTTGGCAAGGGGAACTA
		H: GACGACTTGGCAAGGGGAACTG
		R: GTCCATTGGATTTGTGCTGCTGAGTAT
PS17	Supercont15.804248	F: CACTGCAAATACTGTTGACATCCTCAT
		H: CACTGCAAATACTGTTGACATCCTCAA
		R: AAGGAGGGCCAGTGCTCTTACTT
PS18	Supercont121.147828	F: CAAGAAGCCCACTTTTGACTACCTT
		H: AAGAAGCCCACTTTTGACTACCTG
		R: GGCCGACCAGACGTGCAAA

引物 Primer	SNP位置 SNP sequencing loci	引物序列 Sequence
PS1	Supercont2.93648	F: CCCAGTATGCATTTCTCAAAATCGATCA
		H: CCCAGTATGCATTTCTCAAAATCGATCG
		R: CCTTGTCGTAATCGTCGTTCCCATT
PS2	Supercont3.442202	F: TCTTGATGCCGGATGTGGTGGT
		H: CTTGATGCCGGATGTGGTGGC
		R: CAATCAATCCTTCTTCTTCTTTGCCTCCAT
PS3	Supercont14.389177	F: GAGACTTGATGAGTTTTTCTTTCTTTCCC
		H: TGAGACTTGATGAGTTTTTCTTTCTTTCCT
		R: AGATTCTTCCCGGATTCGACAAATTCA
PS4	Supercont1.298417	F: CAAAGCTCACAGGGCTGATTTTTACT
		H: AAAGCTCACAGGGCTGATTTTTACC
		R: TCATGCCAGCTCAATTCCTGCGTAGT
PS5	Supercont12.777518	F: GCCATTCGCAGTAGCATCGGTA
		H: GCCATTCGCAGTAGCATCGGTG
		R: GGTAAGCATGATCTTCTATGACCTACAGT
PS6	Supercont16.108630	F: CTGGTTCTGTTTGATACAACAATGTGAC
		H: CCTGGTTCTGTTTGATACAACAATGTGAT
		R: CACCTATGATTACCTACGGATGCTGAT
PS7	Supercont23.73782	F: CTCTCCACTTTTCGGATTCGCTAATAATC
		H: CTCTCCACTTTTCGGATTCGCTAATAATT
		R: GGACCGACTGAATTAGCCTTAACAACTA
PS8	Supercont109.152246	F: CGTCTGACACCTCGTCGTGAAG
		H: CGTCTGACACCTCGTCGTGAAC
		R: GCAGCACTACCTCGGGCTAGTA
PS9	Supercont116.239091	F: CCGTGGAACTCCAGTGTTTTGTCTA
		H: CGTGGAACTCCAGTGTTTTGTCTG
		R: CAAAACGTAGCCGCAGGGATGAAA
PS10	Supercont117.206340	F: CCCGAACCACAGCCTAGACTG
		H: TCCCGAACCACAGCCTAGACTA
		R: GCAAGGAATTGTTGTCCAGTTCTCTT
PS11	Supercont131.292765	F: GTTAGAATCCTGAGGTCCACTAATGAT
		H: GTTAGAATCCTGAGGTCCACTAATGAC
		R: ACATCGGTCGAAGGCTGTTCAA
PS12	Supercont113.62255	F: TCATGTGATTCGAACTCTCGGATGC
		H: AATCATGTGATTCGAACTCTCGGATGT
		R:GAAAACCACCCCGAAAAACTAAGATCAAT
PS13	Supercont120.53959	F: GAAGAAGGTGCAGGTAGAGTAATCTTA
		H: AAGAAGGTGCAGGTAGAGTAATCTTG
		R: CCAGCATGTTCAGCTTCTTCCAAA
PS14	Supercont136.207251	F: GAGCCTAAAGAAATGAACGATCAGC
		H: TGAGCCTAAAGAAATGAACGATCAGT
		R: CTCTTCACCCAAATCCCTGTCCAT
PS15	Supercont137.24508	F: CACACATCAAATCAACGTTCATACTCCA
		H: ACACATCAAATCAACGTTCATACTCCG
		R: CCAGAAACGTGGTGTGCCAACTT
PS16	Supercont24.180282	F: AGACGACTTGGCAAGGGGAACTA
		H: GACGACTTGGCAAGGGGAACTG
		R: GTCCATTGGATTTGTGCTGCTGAGTAT
PS17	Supercont15.804248	F: CACTGCAAATACTGTTGACATCCTCAT
		H: CACTGCAAATACTGTTGACATCCTCAA
		R: AAGGAGGGCCAGTGCTCTTACTT
PS18	Supercont121.147828	F: CAAGAAGCCCACTTTTGACTACCTT
		H: AAGAAGCCCACTTTTGACTACCTG
		R: GGCCGACCAGACGTGCAAA

引物 Primer	基因多样性指数 Gene diversity	多态性含量指数 Polymorphic information content
PS1	0.442 4	0.344 6
PS2	0.257 3	0.224 2
PS3	0.298 4	0.253 9
PS4	0.271 4	0.234 6
PS5	0.338 6	0.281 3
PS6	0.369 1	0.301 0
PS7	0.268 0	0.232 1
PS8	0.384 5	0.310 6
PS9	0.253 7	0.221 5
PS10	0.266 2	0.230 8
PS11	0.317 0	0.268 3
PS12	0.469 5	0.359 3
PS13	0.446 7	0.346 9
PS14	0.286 8	0.245 7
PS15	0.411 3	0.316 4
PS16	0.178 4	0.162 4
PS17	0.270 5	0.235 3
PS18	0.454 2	0.353 4
平均	0.332 5	0.273 5

小麦条锈菌SNP分子标记的开发与应用

Development of SNP molecular markers applied to genetic structure analysis of wheat stripe rust fungus

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