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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (3): 553-564.doi: 10.3724/SP.J.1006.2022.11039

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

LIU Dan1**(), ZHOU Cai-E1**, WANG Xiao-Ting1, WU Qi-Meng1, ZHANG Xu1, WANG Qi-Lin1, ZENG Qing-Dong2, KANG Zhen-Sheng2, HAN De-Jun1,*(), WU Jian-Hui1,*()   

  1. 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 Online:2022-03-12 Published:2021-07-19
  • Contact: HAN De-Jun,WU Jian-Hui E-mail:17734508020@163.com;handj@nwafu.edu.cn;wujh@nwafu.edu.cn
  • 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)

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 F2:3 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

Fig. 1

Population construction and data processing and analysis process A: phenotypes of Jinmai 79, C271, and their progenies across all environments and data collected at heading-flowering stage. B: frequency distribution of IT and MDS for 229 F2:3 lines grown at Yangling (YL) and Jiangyou (JY) in 2019. Black arrows indicate the parental line means. C: distributions of the polymorphic SNPs in each chromosome by 660K SNP arrays and (D) positions of SNPs in chromosome 3B and (F) 5A. Selected SNPs in the red dotted boxes were analyzed in AQP assays. G: genetic linkage maps of YrC271; H: deletion bin map of 3BS."

Table 1

Correlation analysis of IT (infection type) and MDS (maximum disease severities) for F2:3 population across two environments"

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

Table 2

Variance components of IT (infection type) and MDS (maximum disease severities) scores for F2:3 population"

变异来源
Source of variations
反应型IT 严重度MDS
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 σ2g 3.31 420.12
广义遗传力 h2b 0.87 0.86

Table 3

AQP primers for mapping YrC271"

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

Table 4

Summary of stripe rust resistance QTL detected by ICIM in the Jinmai 79 × C271 F2:3 population across two environments"

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

Fig. 2

Collinearity analysis of YrC271 physical interval and its genomes with different ploidy wheat varieties"

Fig. 3

Haplotype performance of YrC271 interval (A) and its resistance to stripe rust (B) YL, TS, and JY means Yangling, Tianshui, and Jiangyou."

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