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Browsing by Subject "Genome-Wide Association"

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    Genome-wide association mapping of fusarium head blight resistance and agromorphological traits in barley landraces from Ethiopia and Eritrea
    (Crop Science, 2015-06-12) Steffenson, Brian; Mamo, Bullo Erena
    Fusarium head blight (FHB), caused primarily by Fusarium graminearum, is an important disease of barley (Hordeum vulgare L.), and other cereals. In barley, the genetic basis of FHB resistance has been intensively studied through linkage mapping that identified several quantitative trait loci (QTL). However, our understanding and application of these QTL in breeding is still limited due to the complex nature and low-to-moderate heritability of FHB resistance. Previous studies used either breeding lines, unimproved varieties, or germplasm selections. Here, we used association mapping in barley landraces to identify QTL associated with FHB severity, deoxynivalenol (DON) concentration and correlated agromorphological traits. Diverse barley landraces (n = 298) from Ethiopia and Eritrea were evaluated for the traits under field conditions for 2 yr (2011–2012) in Crookston, MN, and genotyped with 7842 single nucleotide polymorphism (SNP) markers. Association mapping analysis using a mixed model corrected for pairwise relatedness between individuals identified one common resistance QTL on barley chromosome 2HL significantly associated with both FHB severity and DON concentration and another one on 4HL associated with DON concentration. The QTL identified on 2HL is associated with the row-type locus Vrs1. Both of these QTL were not significantly associated with heading date or plant height unlike other QTL reported in previous studies. Thus, the resistant accessions carrying these QTL may be used in breeding programs without the confounding effects from these agromorphological traits. Importantly, these QTL could be new alleles preserved in this unique germplasm, and the linked SNP markers found may be useful in marker-assisted introgression of resistance.
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    A genome-wide association study for culm cellulose content in barley reveals candidate genes co-expressed with members of the cellulose synthase a gene family
    (PLoS ONE, 2015-07-08) Steffenson, Brian; Houston, Kelly; Burton, Rachel A; Sznajder, Beata; Rafalski, Antoni J; Dhugga, Kanwarpal S; Mather, Diane E; Taylor, Jillian; Waugh, Robbie; Fincher, Geoffrey B
    Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two – rowed and 288 six – rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with CELLULOSE SYNTHASE A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.