Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (8): 1429-1443.doi: 10.3864/j.issn.0578-1752.2023.08.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification of Adult Plant Stripe Rust Resistance Candidate Genes of YrZ501-2BL by Gene Association and Transciptome Analysis in Wheat (Triticum aestivum L.)

ZHANG Xu1(), HAN JinYu1(), LI ChenChen1, ZHANG DanDan1, WU QiMeng1, LIU ShengJie1, JIAO HanXuan1, HUANG Shuo1, LI ChunLian1, WANG ChangFa1, ZENG QingDong2, KANG ZhenSheng2, HAN DeJun1(), WU JianHui1()   

  1. 1 College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, Shaanxi
    2 College of Plant Protection, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, Shaanxi
  • Received:2022-12-08 Accepted:2023-01-19 Online:2023-04-16 Published:2023-04-23

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Abstract:

【Objective】Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), significantly reduced wheat production worldwide. Identification of stripe rust resistance genes is the foundation of improving wheat resistance breeding and revealing its genetic mechanism.【Method】A multi-omics approach combined with genome-wide association study (GWAS) was used for dissecting adult plant stripe rust resistance for wheat advanced breeding lines collected from International Maize and Wheat Improvement Center (CIMMYT) and International Centre for Agricultural Research in the Dry Areas (ICARDA) bread-wheat breeding programs. In the present study, a diversity panel of 411 wheat lines from CIMMYT and ICARDA was used for genome-wide association study and a major locus on chromosome arm 2BL was identified. In order to verify the stability of the locus, the resistant line Z501 with the resistance allele of the locus was crossed by the susceptible line Jinmai 79, and the locus tentatively named YrZ501 was successfully confirmed using linkage mapping based on F2:3 genetic population of Jinmai 79×Z501. Then we performed candidate gene analysis based on gene annotation, comparative genome, transcriptome and gene-based association analysis. 【Result】Combining GWAS and linkage mapping results, the YrZ501-2BL was located in the physical interval of 0.26 Mb (575.706-576.587 Mb) on chromosome 2B. According to the annotation information of Chinese Spring reference genome IWGSC v1.1, there were six high confidence genes of 12 genes in this region. Using online website, the target interval in the Chinese spring reference genome was compared with other published different ploidy wheat genomes. The six high-confidence genes within this interval can basically be found homologous in other wheat lines, and the genes arranged in the same order, indicating that the interval may not have large fragment insertions, deletions and inversions. The above results showed that we can perform candidate gene prediction analysis based on the reference genome information. After analysis of their transcriptomic data between the resistant parent Z501 and susceptible parent Jimai 79, only three genes, TraesCS2B02G406400, TraesCS2B02G406500 and TraesCS2B02G406600 showed variable expression levels and were induced by stripe rust infection. Further, they encode GATA transcription factor, SH3 domain-containing protein 2 and zinc finger protein, respectively. Gene-based association analysis revealed that there was a significant SNP (G1369A) in TraesCS2B02G406500 that was associated with stripe rust responses. Although this SNP (G1369A) did not cause amino acid coding changes (both TCG and TCA encode serine), it may be associated with alternative splicing. Moreover, it showed significant differences of the stripe rust responses between the different haplotypes (G1369A). Further analysis revealed two other variants G1377A and G1431A, that caused amino acid changes, i. e. valine (GTT) to isoleucine (ATT) and valine (GTG) to methionine (ATG), respectively. However, the two SNPs were rare variants as they accounting for only 0.87% of the 455 re-sequencing wheat accessions and they were not tested for significance. In summary, TraesCS2B02G406500 was preliminarily considered as an important candidate gene of YrZ501-2BL. In addition, the corresponding AQP markers were developed based on the SNPs among the YrZ501 candidate regions, which can be used to marker-assisted selection in molecular breeding application of wheat stripe rust resistance.【Conclusion】A candidate causal gene TraesCS2B02G406500 associated with stripe rust resistance was successfully identified on wheat chromosome 2B using an integrated method of multi-omics and association analysis, which laid a solid foundation for further gene cloning and functional verification.

Key words: Triticum aestivum, stripe rust resistance, YrZ501, integrative analysis of multiple omics, SH3P2

Fig. 1

Genome-wide association and linkage mapping of QYr.nwafu-2BL.1 (YrZ501) and its reference physical map a: GWAS analysis of stripe rust responses using 411 spring wheat lines. The horizontal line shows the genome-wide significance threshold -log10 (P) value of 3.4 (same for c); b, c: Local Manhattan plot of SNPs associated with stripe-rust resistance surrounding the chromosome 2B peak. The region enclosed in gray dotted lines represents the potential candidate region; d: Polymorphic SNPs distributions on each chromosome identified by the 660K SNP array; e: The physical location density of polymorphic SNPs on chromosome 2B; f: Genetic linkage map of QYr.nwafu-2BL.1 (YrZ501) on wheat chromosome 2B based on genotype data from RILs. The red bar indicates the candidate interval for QYr.nwafu-2BL.1 (YrZ501); g: Predicted genes in the QYr.nwafu-2BL.1 (YrZ501) candidate region"

Fig. 2

Stripe rust responses of Z501 and Jinmai 79 in the field"

Table 1

Stripe rust responses of F2 and F2:3 populations of Jinmai79×Z501 and genetic analysis"

亲本/群体
Parents/Populations		 反应型Infection type 理论比率
Theoretical ratio		 χ2值
χ2 value		 P值
P-value
1—3
（抗病Resistant）		 1—9
（抗感分离Segregate）		 7—9
（感病Susceptible）
Z501 30
晋麦79 Jinmai 79 30
F2 67 239 1﹕3 1.57 0.20
F2:3 67 162 77 1﹕2﹕1 1.71 0.42

Fig. 3

Collinearity analysis of YrZ501 physical interval and its genomes with different ploidy wheat varieties"

Fig. 4

Transcriptome analysis of candidate genes in the of YrZ501 physical interval a: The functional annotation information of the gene in the candidate interval; b: The corresponding transcriptome expression of parent Z501 and Jinmai 79"

Fig. 5

Gene-based association analysis The candidate gene associations of 3 candidate genes in 2.5 were analyzed using 455 wheat resequencing materials. The grey horizontal dotted line indicated that the significant threshold -log10(P) was 3. a: The LD-map of TraesCS2B02G406600; b: The LD-map of TraesCS2B02G406600; c: The LD-map of TraesCS2B02G406600; d: Exon-intron structure and DNA polymorphism of TraesCS2B02G406500; e: Phenotypic severity of different haplotypes of TraesCS2B02G406500 in different environments (Hap3 is incorporated into Hap1 that it is rare and has the same phenotype as Hap1). Asterisk indicates the extremely significant difference between different haplotypes at P<0.01 (Student’s t-test)"

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