Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici ( Pst ), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats. Electronic supplementary material The online version of this article (10.1186/s12915-019-0684-y) contains supplementary material, which is available to authorized users.

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Disease resistance is critical in soft red winter wheat (Triticum aestivum L.) cultivars. Leaf rust caused by Puccinia triticina Eriks and stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Eriks. are destructive pathogens of wheat. Phenotypic data were collected at diverse locations for resistance to leaf rust (North Carolina, Texas, and Virginia) and stripe rust (Arkansas, North Carolina, Georgia, Texas, and Virginia) in a Pioneer ‘25R47’ /‘Jamestown’ (P47/JT) population composed of 186 F5:9 recombinant inbred lines (RILs). The P47/JT RILs were genotyped with a public 90K iSelect single‐nucleotide polymorphism array. Analysis of the P47/JT population identified two quantitative trait loci (QTL) for leaf rust resistance on chromosome 5B and two QTL for stripe rust resistance on chromosomes 3B and 6A. These QTL were associated with both infection type and disease severity. Phenotypic variation (%) explained by the putative leaf rust resistance QTL of Jamestown on 5B was as high as 22.1%. Variation explained by the putative stripe rust resistance QTL of Jamestown on 3B and 6A was as high as 11.1 and 14.3%, respectively. Introgression and pyramiding of these QTL with other genes conferring resistance to leaf and stripe rusts via marker‐assisted selection will facilitate development of soft red winter wheat cultivars having more durable resistance.

Net blotch (Pyrenophora teres) is one of the most devastating diseases of barley (Hordeum vulgare L.) worldwide. Identification of diagnostic molecular markers associated with genes and quantitative trait loci (QTL) for net blotch resistance will facilitate pyramiding of independent genes. Linkage mapping was used to identify chromosomal locations of the independent, dominant genes conditioning net blotch resistance in the winter barley ‘Nomini’ (PI 566929) and spring barley CIho 2291. The F2 populations of 238 and 193 individuals, derived from crosses between the susceptible spring barley parent ‘Hector’ (CIho 15514) and the resistant parents Nomini and CIho 2291, respectively, were used to map the genes governing resistance in the resistant parents. The dominant gene governing resistance in Nomini, temporarily designated Rpt‐Nomini, was mapped to a 9.2‐cM region of barley chromosome 6H between the flanking microsatellite markers Bmag0344a (r2 = 0.7) and Bmag0103a (r2 = 0.9), which were 6.8 and 2.4 cM away from Rpt‐Nomini, respectively. The dominant gene governing resistance in CIho 2291, temporarily designated Rpt‐CIho2291, was mapped to a 34.3‐cM interval on the distal region of barley chromosome 6H between the flanking microsatellite markers Bmag0173 (r2 = 0.65) and Bmag0500 (r2 = 0.26), which were 9.9 and 24.4 cM away from Rpt‐CIho2291, respectively. Identification of the chromosomal location of Rpt‐Nomini and Rpt‐CIho2291 will facilitate efforts in pyramiding multiple genes for net blotch resistance.