Cytogenetic identification and molecular marker development for the novel stripe rust-resistant wheat- Thinopyrum intermedium translocation line WTT11

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. Xiaoyan 78829, a partial amphidiploid developed by crossing common wheat with Thinopyrum intermedium, is immune to wheat stripe rust. To transfer the resistance gene of this excellent germplasm resource to wheat, the translocation line WTT11 was produced by pollen irradiation and assessed for immunity to stripe rust races CYR32, CYR33 and CYR34. A novel stripe rust-resistance locus derived from Th. intermedium was confirmed by linkage and diagnostic marker analyses. Molecular cytogenetic analyses revealed that WTT11 carries a TTh·2DL translocation. The breakpoint of 1B was located at 95.5 MB, and the alien segments were found to be homoeologous to wheat-group chromosomes 6 and 7 according to a wheat660K single-nucleotide polymorphism (SNP) array analysis. Ten previously developed PCR-based markers were confirmed to rapidly trace the alien segments of WTT11, and 20 kompetitive allele-specific PCR (KASP) markers were developed to enable genotyping of Th. intermedium and common wheat. Evaluation of agronomic traits in two consecutive crop seasons uncovered some favorable agronomic traits in WTT11, such as lower plant height and longer main panicles, that may be applicable to wheat improvement. As a novel genetic resource, the new resistance locus may be useful for wheat disease-resistance breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s42994-021-00060-3.

Keywords: CYR34; Cytogenetic analyses; KASP markers; PCR-based markers; Wheat660k SNP array; Wheat–Thinopyrum intermedium translocation line.

Fig. 1

Procedure for producing wheat–Th. intermedium translocation line WTT11

Fig. 2

Genomic in situ hybridization (GISH), multi-color fluorescence in situ hybridization (mc-FISH) and multi-color GISH (mc-GISH) analyses of WTT11. GISH showed wheat chromosomes (blue) and Th. intermedium chromosome segments (green) (A). The mc-FISH showed the signal patterns of pAs1 (red) and pSc119.2 (green) in WTT11 (B). The mc-GISH showed the detection of chromosomes of the A-, B-, D- and Th. intermedium genomes based on yellow, blown, red and green fluorescence, respectively (C). The arrows note a pair of translocated chromosomes, and triangles note one pair of chromosomes 4A carrying B-genome chromosome segments. Bar = 20 μm

Fig. 3

The seedling testing responses of WTT11 and its parents. Stripe rust responses of WTT11 and Xiaoyan 81 inoculated with Pst races CYR32, CYR33 and CYR34 (A). Stripe rust responses of WTT11 and its parents (B) and two individuals from Y11 (2) population (C) inoculated with Pst race CYR34. The seedling resistance evaluation results are shown: WTT11 (IT = 0;), Xiaoyan 78829 (IT = 0;), Xiaoyan 343 (IT = 0;), Lumai 21 (IT = 1), Xiaoyan 81 (IT = 3), Y11 (2)-1 (IT = 0), Y11 (2)-2 (IT = 3), Yannong 19 (IT = 3). Infection types 0–2 were resistance and 3–4 were susceptibility

Fig. 4

The deletion analysis in WTT11 genome. The deleted ratio for chromosome 1B (A). The red line indicated an average deleted value in chromosome 1B. The deleted ratio was calculated in 3-MB sliding windows, with 1-MB steps. The breakpoint of 1B was detected at 95.5 MB. The percentage of deleted SNPs distributed in two physical regions of chromosome 1B (B). Counting the percentage of the missing SNPs in each physical region of 1B, 86.37% of the missing SNPs on chromosome 1B were within the region 0–95.5 MB

Fig. 5

The homoeologous analysis of alien chromosomal segments from WTT11. The heterozygous ratio was heterozygous SNPs in WTT11, in accordance with both Th. intermedium and Xiaoyan 81’s genotypes, to all SNPs in each chromosome. It was counted in 50-MB sliding windows at 1-MB intervals, and plotted along the chromosome. The alien segments were homoeologous to wheat chromosome fragment with the highest ratio

Fig. 6

The amplification result of M-XNXY68-151 in 121 individuals from Y11 (2) population and its parents. M: Marker II, 1–121: Y11 (2) 1–121, 122: WTT11, 123: Th. intermedium, 124: Xiaoyan 78829, 125: Xiaoyan 343, 126: Lumai 21, 127: Xiaoyan 81, 128: Yannong 19, 129: Chinese Spring

Fig. 7

KASP marker amplification result of Kasp-AX-109538133. Using the KASP marker Kasp-AX-109538133, the genotyping result of 19 Th. intermedium accessions and 6 wheat cultivars was displayed. Red rotund shapes represent the homozygous 19 Th. intermedium accessions and Chinese Spring special SNPs, blue rotund shapes represent the homozygous common wheat special SNPs and green rotund shape represents the heterozygous Jimai 22 special SNP