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Identification of quantitative trait loci (QTL) associated with important traits is one of the first steps towards deploying marker-assisted selection, but the lack of stability and consistency in identifying QTL across environments and populations remains a limitation. We conducted this study to identify QTL associated with agronomic traits in wheat (Triticum aestivum L.) across management-specific environments. A total of 204 wheat lines derived from the 'Peace' × 'Carberry' cross were evaluated in 2016 and 2017 under conventional and organic managements in Edmonton, Canada, and genotyped with diversity arrays technology markers. Using the leastsquares means for each management system, 53 QTL were identified for nine agronomic traits, 14 of which were consistently identified in both managements. The largest QTL we identified was associated with plant height (QPht.dms-4B), which might be the plant height-reducing gene Rht-B1b from 'Carberry'. It explained 54 and 49% of the phenotypic variation in conventional and organic management, respectively. The second largest QTL was associated with gluten strength (QSds.dms-1A) in both managements. We identified consistent QTL across both organic and conventional managements, even though they were generally minor-effect QTL. Twelve organic management-specific QTL were found for grain yield, days to heading and maturity, plant height, test weight, and thousand-kernel weight, but most explained relatively low amount of phenotypic variation. The QTL identified across managements, especially the gluten strength QTL (QSds.dms-1A), may serve as useful markers in selection. The QSds.dms-1A region needs to be investigated further to confirm whether it is the Gli-1 storage protein gene.

Stripe rust, leaf rust, and the leaf spot complex are economically important diseases of wheat (Triticum aestivum L.) in western Canada, and genetic host resistance is the most successful management strategy. This study was conducted to identify quantitative trait loci (QTL) associated with these diseases and to provide wheat breeders with sources of potential disease resistance genes. A total of 208 recombinant inbred lines derived from a cross between Canadian spring wheat cultivars ‘Peace’ and ‘Carberry’ were evaluated from 2014 to 2017 in stripe rust, leaf rust, and leaf spot nurseries in Alberta and British Columbia. All lines were genotyped with sequencing‐based Diversity Arrays Technology (DArTseq) markers. Using the least square means of the combined environments, two stripe rust resistance QTL, two leaf rust resistance QTL, and three leaf spot resistance QTL were identified. The stripe rust QTL were located on chromosomes 3A and 4B, the leaf rust QTL were located on chromosomes 4A and 3D, and the leaf spot QTL were located on 2A, 4B and 7D. The stripe rust resistance QTL on 4B, contributed by ‘Carberry’, was previously identified in other studies using a population derived from ‘Carberry’. Results from this study suggest that ‘Carberry’ may be an attractive parental source for breeders to enhance resistance against stripe rust and leaf spot with minor resistance alleles.

In previous studies, we reported quantitative trait loci (QTL) associated with the heading, flowering, and maturity time in four hard red spring wheat recombinant inbred line (RIL) populations but the results are scattered in population-specific genetic maps, which is challenging to exploit efficiently in breeding. Here, we mapped and characterized QTL associated with these three earliness traits using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. Our data consisted of (i) 6526 single nucleotide polymorphisms (SNPs) and two traits evaluated at five conventionally managed environments in the ‘Cutler’ × ‘AC Barrie’ population; (ii) 3158 SNPs and two traits evaluated across three organic and seven conventional managements in the ‘Attila’ × ‘CDC Go’ population; (iii) 5731 SilicoDArT and SNP markers and the three traits evaluated at four conventional and organic management systems in the ‘Peace’ × ‘Carberry’ population; and (iv) 1058 SNPs and two traits evaluated across two conventionally and organically managed environments in the ‘Peace’ × ‘CDC Stanley’ population. Using composite interval mapping, the phenotypic data across all environments, and the IWGSC RefSeq v2.0 physical maps, we identified a total of 44 QTL associated with days to heading (11), flowering (10), and maturity (23). Fifteen of the 44 QTL were common to both conventional and organic management systems, and the remaining QTL were specific to either the conventional (21) or organic (8) management systems. Some QTL harbor known genes, including the Vrn-A1, Vrn-B1, Rht-A1, and Rht-B1 that regulate photoperiodism, flowering time, and plant height in wheat, which lays a solid basis for cloning and further characterization.

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