Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.

Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China. Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage. The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars.

Stripe rust (also called yellow rust) is a common and serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici. The narrow genetic basis of modern wheat cultivars and rapid evolution of the rust pathogen have been responsible for periodic and devastating epidemics of wheat rust diseases. In this study, we conducted a genome-wide association study with 44,059 single nucleotide polymorphism markers to identify loci associated with resistance to stripe rust in 244 Sichuan wheat accessions, including 79 landraces and 165 cultivars, in six environments. In all the field assessments, 24 accessions displayed stable high resistance to stripe rust. Significant correlations among environments were observed for both infection (IT) and disease severity (DS), and high heritability levels were found for both IT and DS. Using mixed linear models, 12 quantitative trait loci (QTLs) significantly associated with IT and/or DS were identified. Two QTLs were mapped on chromosomes 5AS and 5AL and were distant from previously identified stripe rust resistance genes or QTL regions, indicating that they may be novel resistance loci. Our results revealed that resistance alleles to stripe rust were accumulated in Sichuan wheat germplasm, implying direct or indirect selection for improved stripe rust resistance in elite wheat breeding programs. The identified stable QTLs or favorable alleles could be important chromosome regions in Sichuan wheat that controlled the resistance to stripe rust. These markers can be used molecular marker-assisted breeding of Sichuan wheat cultivars, and will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.

Chinese endemic wheat, comprising Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum), Yunnan hulled wheat (T. aestivum ssp. yunnanense), and Xinjiang rice wheat (T. petropavlovskyi), are genetically and morphologically unique. To examine the adult plant resistance to stripe rust among Chinese endemic wheat germplasms, a panel of 213 accessions was inoculated with mixed virulent races of wheat stripe rust (Puccinia striiformis f. sp. tritici) in four different field environments. Four traits associated with stripe rust resistance, infection type, final disease severity, disease index, and area under the disease progress curve, were used to evaluate the accessions. The phenotypic datasets were used for 55K single-nucleotide polymorphism (SNP) array-based genome-wide association studies to identify effective resistance loci. Eighty-nine accessions with stable resistance were identified in at least three of the four environments by phenotypic evaluation. Eleven markers located on chromosomes 1A, 2B, 5A, 5D, 7B, and 7D by the genome-wide association studies analysis showed significant associations with at least two resistance-associated traits in two of the environments. These loci, corresponding to seven genomic regions based on linkage disequilibrium decay distance, explained 9.3 to 26.0% of the total phenotypic variation. Five quantitative trait loci (QTLs) on chromosomes 1A, 2B, 7B, and 7D overlapped or were in close proximity to previously reported QTLs based on the consensus and physical maps using the reference sequence of bread wheat (IWGSC RefSeq v1.0). The other two QTLs were potential novel QTLs given their physical positions. Haplotype variants of QTL QYr.sicau-2BS showed subspecies-specific inheritance of the stripe rust resistance locus. Resistant loci among Chinese endemic wheat germplasms could be introduced into common wheat cultivars, and the high-confidence SNP markers will aid in marker-assisted selection in breeding for stripe rust disease resistance.

Wheat is a major staple food crop worldwide, due to its total yield and unique processing quality. Its grain yield and quality are threatened by Fusarium head blight (FHB), which is mainly caused by Fusarium graminearum. Salicylic acid (SA) has a strong and toxic effect on F. graminearum and is a hopeful target for sustainable control of FHB. F. graminearum is capable of efficientdealing with SA stress. However, the underlying mechanisms remain unclear. Here, we characterized FgMFS1 (FGSG_03725), a major facilitator superfamily (MFS) transporter gene in F. graminearum. FgMFS1 was highly expressed during infection and was upregulated by SA. The predicted three-dimensional structure of the FgMFS1 protein was consistent with the schematic for the antiporter. The subcellular localization experiment indicated that FgMFS1 was usually expressed in the vacuole of hyphae, but was alternatively distributed in the cell membrane under SA treatment, indicating an element of F. graminearum in response to SA. ΔFgMFS1 (loss of function mutant of FgMFS1) showed enhanced sensitivity to SA, less pathogenicity towards wheat, and reduced DON production under SA stress. Re-introduction of a functional FgMFS1 gene into ∆FgMFS1 recovered the mutant phenotypes. Wheat spikes inoculated with ΔFgMFS1 accumulated more SA when compared to those inoculated with the wild-type strain. Ecotopic expression of FgMFS1 in yeast enhanced its tolerance to SA as expected, further demonstrating that FgMFS1 functions as an SA exporter. In conclusion, FgMFS1 encodes an SA exporter in F. graminearum, which is critical for its response to wheat endogenous SA and pathogenicity towards wheat.

As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44,059 polymorphic markers from the 55 K single nucleotide polymorphism (SNP) chip. A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, 21 candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport. QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.