利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271

doi:10.3724/SP.J.1006.2022.11039

作物学报 ›› 2022, Vol. 48 ›› Issue (3): 553-564.doi: 10.3724/SP.J.1006.2022.11039

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271

刘丹^1**(), 周彩娥^1**, 王晓婷¹, 吴启蒙¹, 张旭¹, 王琪琳¹, 曾庆东², 康振生², 韩德俊¹^,^*(), 吴建辉¹^,^*()

¹西北农林科技大学农学院/旱区作物逆境生物学国家重点实验室, 陕西杨凌 712100
²西北农林科技大学植物保护学院/旱区作物逆境生物学国家重点实验室, 陕西杨凌 712100

收稿日期:2021-04-07 接受日期:2021-06-16 出版日期:2022-03-12 网络出版日期:2021-07-19
通讯作者: 韩德俊,吴建辉
作者简介:刘丹, E-mail: 17734508020@163.com第一联系人：^**同等贡献
基金资助:
国家自然科学基金项目(31901494);国家自然科学基金项目(31901869);国家自然科学基金项目(31971890)

Rapid identification of adult plant wheat stripe rust resistance gene YrC271 using high-throughput SNP array-based bulked segregant analysis

LIU Dan^1**(), ZHOU Cai-E^1**, WANG Xiao-Ting¹, WU Qi-Meng¹, ZHANG Xu¹, WANG Qi-Lin¹, ZENG Qing-Dong², KANG Zhen-Sheng², HAN De-Jun¹^,^*(), WU Jian-Hui¹^,^*()

¹State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
²State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China

Received:2021-04-07 Accepted:2021-06-16 Published:2022-03-12 Published online:2021-07-19
Contact: HAN De-Jun,WU Jian-Hui
About author:First author contact:^**Contributed equally to this work
Supported by:
National Natural Science Foundation of China(31901494);National Natural Science Foundation of China(31901869);National Natural Science Foundation of China(31971890)

摘要/Abstract

摘要：

由国际玉米小麦改良中心(CIMMYT)培育的春小麦高代选系C271对小麦条锈病保持抗性近40年。为明确C271的抗条锈病遗传组分, 利用感病品种晋麦79与C271杂交构建含有229个F_2:3家系的遗传群体, 并于2019年在陕西杨凌和四川江油进行成株期病害调查。运用集群分离分析(BSA)结合高密度660K芯片策略在3B染色体短臂上快速挖掘出大量的与抗病关联的SNP, 利用等位基因特异的定量PCR标记(AQP)进行验证并作图, 成功检测到一个效应值较大的QTL, 可解释表型变异为22.7%~30.8%, 暂命名为YrC271, 位于标记AX-109001377和AX-111087256之间, 约1.9 cM, 对应的物理距离1.9 Mb。利用已公布的小麦基因组信息对该区间进行比较基因组分析, 结果表明, 与中国春基因组相比, 不同材料间存在小片段的插入以及倒位现象, 但总体共线性良好。同时利用1484份小麦660K分型数据对该区间进行单倍型分析, 总体可分为5种区间单倍型, 其中C271所在的单倍型组的抗性优于其他组。虽然C271不含有Yr30和Yr58连锁标记的阳性片段, 但从相对遗传位置、条锈病抗性表现以及育种系谱看, YrC271与Yr30和Yr58都很类似, 其关系需要进一步确认。对主效QTL定位来讲, 芯片结合BSA策略可快速锁定目标QTL区域, 再应用AQP技术既提高了作图效率, 也降低了标记分析的成本, 为高通量基因/QTL定位工作提供了借鉴。

关键词: 条锈病成株抗性, YrC271, SNP标记, 比较基因组分析, 单倍型分析

Abstract:

Wheat cultivar C271 registered as PI 210904 in the USDA National Small Grains Collection was developed from Punjab Pakistan in 1953 and it confers adult plant resistance (APR) to stripe rust both in the United States and China for many years. In the present study, we dissected the genetic basis of stripe rust resistance on 229 F_2:3 populations produced by crossing Jinmai 79 and C271 in the fields of Yangling and Jiangyou. Bulked segregant analysis coupled with wheat 660K SNP array placed the majority of SNPs differences on chromosome arm 3BS. After using allele-specific quantitative PCR based genotyping assay (AQP) to confirm the SNPs, a linkage map was constructed and a major locus was detected across all environments based on IciMapping v4.1 software. The QTL, designated as YrC271, was flanked by SNP markers AX-109001377 and AX-111087256 with a genetic interval of 1.9 cM corresponding to a physical distance of 1.9 Mb in RefSeq v.1.0 (positions 6.1-8.0 Mb). Comparative genomics analysis was performed to detect the collinear genomic regions of different hexaploid wheat accessions (Triticum aestivum), T. dicoccoides, and T. turgidum. More than 340 SNPs in the physical region were extracted for haplotype analysis in a panel of over 1484 worldwide common wheat accessions, and five major haplotypes (Hap1, Hap2, Hap3, Hap4, and Hap5) were identified. And the favorable haplotype Hap1 was highly associated with stripe rust resistance. YrC271 appeared to be similar to YrC271 based on comparison of relative distance, stripe rust responses, and pedigree analyses, but allelism tests, cloning or precise phenotypic comparisons would be needed for confirmation. The YrC271 region provided the opportunity for further map-based cloning and haplotypes analysis enabled pyramiding favorable alleles into commercial cultivars by marker-assisted selection.

Key words: adult plant resistance to stripe rust, YrC271, SNP markers, comparative genomics analysis, haplotype analysis

刘丹, 周彩娥, 王晓婷, 吴启蒙, 张旭, 王琪琳, 曾庆东, 康振生, 韩德俊, 吴建辉. 利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271[J]. 作物学报, 2022, 48(3): 553-564.

LIU Dan, ZHOU Cai-E, WANG Xiao-Ting, WU Qi-Meng, ZHANG Xu, WANG Qi-Lin, ZENG Qing-Dong, KANG Zhen-Sheng, HAN De-Jun, WU Jian-Hui. Rapid identification of adult plant wheat stripe rust resistance gene YrC271 using high-throughput SNP array-based bulked segregant analysis[J]. Acta Agronomica Sinica, 2022, 48(3): 553-564.

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环境 Environment	IT杨凌 2019 IT Yangling in 2019	IT江油 2019 IT Jiangyou in 2019	MDS杨凌 2019 MDS Yangling in 2019	MDS江油 2019 MDS Jiangyou in 2019
IT杨凌2019 IT Yangling in 2019	1
IT江油2019 IT Jiangyou in 2019	0.89^**	1
MDS杨凌2019 MDS Yangling in 2019	0.86^**		1
MDS江油2019MDS Jiangyou in 2019		0.85^**	0.90^**	1

变异来源 Source of variations	反应型IT		严重度MDS
变异来源 Source of variations	自由度 DF	均方 Mean square	自由度 DF	均方 Mean square
基因型 Lines (L)	228	15.22^**	228	1952.66^**
重复 Replicates/environments	2	14.07	2	21,443.81
环境 Environments (E)	1	1.54	1	1360.89
基因型×环境 L × E	228	0.87	228	100.30
误差 Error	456	1.99	456	272.18
基因型方差 σ²_g	3.31		420.12
广义遗传力 h²_b	0.87		0.86

标记名称 Marker ID	引物序列 Primer sequence (5′-3′)
AX-110965644	A_FAM	GAAGGTGACCAAGTTCATGCTGGGAGGCATAAAAAATTGCAGGCTG
	B_HEX	GAAGGTCGGAGTCAACGGATTGGGAGGCATAAAAAATTGCAGGCTA
	C_reverse	ATCGCTCCAGTTCTTGATGTGTCCA
AX-108828571	A_FAM	GAAGGTGACCAAGTTCATGCTGCTTGTAGCAGACAGAATTACCA
	B_HEX	GAAGGTCGGAGTCAACGGATTGCTTGTAGCAGACAGAATTACCG
	C_reverse	CAGAACTCCAGTGCCCTTCT
AX-109001377	A_FAM	GAAGGTGACCAAGTTCATGCTGGATACCATCCGCCCAAGT
	B_HEX	GAAGGTCGGAGTCAACGGATTGGATACCATCCGCCCAAGC
	C_reverse	TCGGGGTTCAGCCACACC
AX-109828842	A_FAM	GAAGGTGACCAAGTTCATGCTGCATTCCCTGCCATCACG
	B_HEX	GAAGGTCGGAGTCAACGGATTGCATTCCCTGCCATCACA
	C_reverse	GCTTTTATGTGGCACCGGTG
AX-109925313	A_FAM	GAAGGTGACCAAGTTCATGCTTTGCAGCGAAGAGTTTGGTT
	B_HEX	GAAGGTCGGAGTCAACGGATTTTGCAGCGAAGAGTTTGGTG
	C_reverse	CCGGCTGATCTGACCATCAT
AX-111087256	A_FAM	GAAGGTGACCAAGTTCATGCTGAGAAATCAACTCACACAAATTT
	B_HEX	GAAGGTCGGAGTCAACGGATTGAGAAATCAACTCACACAAATTC
	C_reverse	TGTTTGATGTATGCGTGAGCTATT
AX-109966241	A_FAM	GAAGGTGACCAAGTTCATGCTAGCATAAAAGGTGGCCCAAGCCATG
	B_HEX	GAAGGTCGGAGTCAACGGATTAGCATAAAAGGTGGCCCAAGCCATA
	C_reverse	TGTTGACTCGCAGATGTACTTTGCCTTTGCACAGTAATTTTTACC
AX-89750431	A_FAM	GAAGGTGACCAAGTTCATGCTCTTTGCACAGTAATTTTTACC
	B_HEX	GAAGGTCGGAGTCAACGGATTCTTTGCACAGTAATTTTTACA
	C_reverse	CAGAAATCAGAGAGGAGAGTTC
AX-109997090	A_FAM	GAAGGTGACCAAGTTCATGCTATGCTGAGGTTTCCGGTCAGAT
	B_HEX	GAAGGTCGGAGTCAACGGATTATGCTGAGGTTTCCGGTCAGAC
	C_reverse	TGACAAACCCGGGTCAAACA

环境 Environment	标记区间 Marker interval	最大似然值 LOD	加性效应 Add	表型变异率 PVE (%)
反应型Infection type (IT)
杨凌2019 Yangling in 2019	AX-109001377-AX-111087256	15.9	-1.5	28.6
江油2019 Jiangyou in 2019	AX-109001377-AX-111087256	16.4	-1.5	29.9
平均 Mean	AX-109001377-AX-111087256	17.2	-1.5	30.8
最大严重度Maximum disease severtiy (MDS)
杨凌2019 Yangling in 2019	AX-109001377-AX-111087256	12.2	-14.2	22.7
江油2019 Jiangyou in 2019	AX-109001377-AX-111087256	13.6	-15.5	25.0
平均Mean	AX-109001377-AX-111087256	13.5	-14.8	24.8

利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271

Rapid identification of adult plant wheat stripe rust resistance gene YrC271 using high-throughput SNP array-based bulked segregant analysis

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