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

Abstract

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

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.

Figures/Tables 7

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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

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

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