Exome Sequencing from Bulked Segregant Analysis Identifies a Gene for All Stage Resistance to Stripe Rust on Chromosome 1AL in Chinese Wheat Landrace Xiaohemai

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive diseases of wheat. Identifying novel resistance genes applicable for developing disease resistant cultivars is important for the sustainable control of wheat stripe rust. Chinese wheat landrace Xiaohemai (XHM) is an elite germplasm line with all-stage resistance (ASR) effective against predominant Chinese Pst races. In this study, we performed a bulked segregant analysis coupled with exome capture sequencing (BSE-seq) to identify a candidate genomic region strongly associated with stripe rust resistance on chromosome 1AL in 173 F2:3 lines derived from cross XHM × Avocet S. The gene, designated as YrXH-1AL, was validated by a conventional quantitative trait locus analysis using newly developed Kompetitive allele-specific PCR (KASP) markers, explaining up to 48.50% of the phenotypic variance. By testing a secondary mapping population comprising 144 lines from the same cross at the seedling stage with prevalent Pst race CYR34, YrXH-1AL was identified as a single Mendelian factor in a 1.5 cM interval flanked by KASP markers KP1A_484.33 and KP1A_490.09. This region corresponded to a 5.76 Mb genomic interval on Chinese Spring chromosome 1AL. Furthermore, two co-segregating KASP markers showed high polymorphisms among 130 Chinese wheat cultivars and could be used for marker-assisted selection. Because no other Yr genes for ASR that originated from common wheat have been detected on chromosome 1AL, YrXH-1AL is likely a novel gene that can be incorporated into modern breeding materials to develop wheat cultivars with enhanced stripe rust resistance.

Molecular Mapping and Analysis of an Excellent Quantitative Trait Loci Conferring Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landrace Gaoxianguangtoumai

The Chinese wheat landrace “Gaoxianguangtoumai” (GX) has exhibited a high level of adult-plant resistance (APR) to stripe rust in the field for more than a decade. To reveal the genetic background for APR to stripe rust in GX, a set of 249 F6:8 (F6, F7, and F8) recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar “Taichung 29.” The parents and RILs were evaluated for disease severity at the adult-plant stage in the field by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers finally. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS in GX, were detected on chromosomes 2AS and 7DS, which explained 15.5–27.0% and 11.5–13.5% of the total phenotypic variation, respectively. Compared with published Yr genes and QTL, QYr.GX-7DS and Yr18 may be the same, whereas QYr.GX-2AS is likely to be novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which presents in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a heterogeneous inbred family (HIF) population from a residual heterozygous plant in an F8 generation of RIL, QYr.GX-2AS was further flanked by KP2A_36.85 and KP2A_38.22 with a physical distance of about 1.37Mb and co-segregated with the KP2A_37.09. Furthermore, three tightly linked Kompetitive allele-specific PCR (KASP) markers were highly polymorphic among 109 Chinese wheat cultivars. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

Mendelization and Molecular Mapping of a Large-effect QTL Conferring Durable Adult-plant Resistance to Stripe Rust in a Chinese Wheat Landrace ‘Gaoxianguangtoumai’

The Chinese wheat landrace ‘Gaoxianguangtoumai’ (GX) has exhibited a high degree of adult-plant resistance (APR) to stripe rust in field environments for more than a decade. To reveal the genetic basis for APR to stripe rust in GX, a set of 249 F6:8 recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar ‘Taichung 29’. The parents and RILs were evaluated for disease severity at the adult-plant stage in field environments by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons, and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS from GX, were detected on chromosomes 2AS and 7DS, which explained 15.5–27.0% and 9.6–15.6% of the total phenotypic variation, respectively. Compared with published genes and QTL, QYr.GX-7DS is likely Yr18, whereas QYr.GX-2AS is probably novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which present in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a near-isogenic line population, QYr.GX-2AS was further mapped to an interval with a physical distance of about 1.37 Mb and co-segregated with a Kompetitive allele-specific PCR (KASP) marker. Furthermore, three tightly linked KASP markers were highly polymorphic among 109 Chinese wheat cultivars. The short physical interval and tightly linked KASP markers developed in this study will facilitate marker-assisted selection and map-based cloning of QYr.GX-2AS.

Characterization of PmDGM conferring powdery mildew resistance in Chinese wheat landrace Duanganmang

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating disease threatening yield and quality. Host resistance is considered the most effective and preferred means to control this disease. Wheat landrace Duanganmang (DGM) showed high resistance or near immunity to Bgt mixture from Henan province, China. DGM was crossed with highly susceptible Chinese wheat landrace Huixianhong (HXH) and cultivar Shimai 15 (SM15) to produce genetic populations. The resistance of DGM to Bgt isolate E09 was shown to be controlled by a single dominant Mendelian factor, tentatively designated PmDGM. Marker analysis and 55K SNP (single nucleotide polymorphism) array scanning showed that this gene was positioned in the Pm5 interval (2.4 cM or 1.61 Mb) flanked by Xhenu099 and Xmp1158 in the Chinese Spring reference genome. Homology-based cloning and sequence analysis demonstrated that DGM has the identical NLR gene (Pm5e) and RXL gene reported in Fuzhuang 30 (FZ30) conferring and modifying the powdery mildew resistance, respectively. However, based on the different reaction patterns to the Bgt isolate B15 between DGM and FZ30, we speculate that DGM may have two tightly linked genes that could not be separated in the current mapping population, one is PmDGM and the other is Pm5e. Hence, this study provides a valuable resistance resource for improvement of powdery mildew resistance.

A stable QTL on Chromosome 5BL Combined with Yr18 Conferring High-level Adult-plant Resistance to Stripe Rust in Chinese Wheat Landrace Anyuehong

Chinese wheat landrace Anyuehong (AYH) has displayed high levels of stable adult-plant resistance (APR) to stripe rust for more than 15 years. To identify QTL for stripe rust resistance in AYH, a set of 110 recombinant inbred lines (RILs) was developed from a cross between AYH and susceptible cultivar Taichung 29. The parents and RILs were evaluated for final disease severity (FDS) in six field tests with a mixture of predominant Pst races at the adult-plant stage and genotyped using the wheat 55K SNP array to construct a genetic map with 1,143 SNP markers. Three QTL, designated as QYr.AYH-1AS, QYr.AYH-5BL and QYr.AYH-7DS, were mapped on chromosome 1AS, 5BL and 7DS, respectively. RILs combining three QTL showed significantly reduced FDS compared with the lines in other combinations. Of them, QYr.AYH-5BL and QYr.AYH-7DS were stably detected in all environments, explaining 13.6–21.4% and 17.6–33.6% of phenotypic variation, respectively. Compared with previous studies, QYr.AYH-5BL may be a new QTL, while QYr.AYH-7DS may be Yr18. Haplotype analysis revealed that QYr.AYH-5BL is likely present in 6.2% of the 323 surveyed Chinese wheat landraces. The Kompetitive allele specific PCR (KASP) markers for QYr.AYH-5BL were developed by the linked SNP markers to successfully confirm the effects of the QTL in a validation population derived from a residual heterozygous line, and were further assessed in 38 Chinese wheat landraces and 92 cultivars. Our results indicated that QYr.AYH-5BL with linked KASP markers should have potential value for marker-assisted selection to improve stripe rust resistance in breeding programs.