Biology subjects

Tinker, N. A.

Publications and source records attributed to Tinker, N. A..

3 recordsLinked to original sources

bioRxiv2024

Genetic mapping of the powdery mildew resistance gene Pm13 on oat chromosome 1D

Powdery mildew, caused by the biotrophic fungus Blumeria graminis DC. f. sp. avenae, is a widespread disease of oats, especially in the temperate regions of Western and Central Europe, and the use of resistant varieties is the most sustainable way to ensure stable yields. Therefore, the identification of robust and effective resistance to powdery mildew is of great interest for oat breeding. In contrast to race-specific resistance genes, adult plant resistance (APR) is generally considered to be more durable. The oat variety Firth, as well as related varieties such as Husky or Flamingstip, contains an unknown APR gene, which was previously located on chromosome 1D using DArT markers. The aim of this study was to confirm and refine the chromosomal location of this resistance gene, tentatively named Pm13. To this end, two independent experiments were carried out using different genetic material under natural infection conditions in the field: genome-wide association mapping (GWAS) in a diverse set of 250 oat lines grown in ten environments and QTL mapping in a HuskyxAVE1284 bi-parental population grown in three environments. Both approaches identified a QTL for powdery mildew resistance on the distal end of chromosome 1D in the hexaploid Sang oat genome. The locus explained up to 15 % of the phenotypic variance in GWAS and 64 % of the phenotypic variance in QTL mapping. Comparison of field data with results from laboratory leaf segment tests confirmed that Pm13 does indeed confer APR. The sequence information of the identified linked markers may allow the development of molecular markers useful for early selection of oat lines with high levels of APR.

plant biology↗

bioRxiv2019

Multivariate Genome-wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (Avena sativa L.)

Oat (Avena sativa L.) has a high concentration of oils, comprised primarily of healthful unsaturated oleic and linoleic fatty acids. To accelerate oat plant breeding efforts, we sought to identify loci associated with variation in fatty acid composition, defined as the types and quantities of fatty acids. We genotyped a panel of 500 oat cultivars with genotyping-by-sequencing and measured the concentrations of ten fatty acids in these oat cultivars grown in two environments. Measurements of individual fatty acids were highly correlated across samples, consistent with fatty acids participating in shared biosynthetic pathways. We leveraged these phenotypic correlations in two multivariate genome-wide association study (GWAS) approaches. In the first analysis, we fitted a multivariate linear mixed model for all ten fatty acids simultaneously while accounting for population structure and relatedness among cultivars. In the second, we performed a univariate association test for each principal component (PC) derived from a singular value decomposition of the phenotypic data matrix. To aid interpretation of results from the multivariate analyses, we also conducted univariate association tests for each trait. The multivariate mixed model approach yielded 148 genome-wide significant single-nucleotide polymorphisms (SNPs) at a 10% false-discovery rate, compared to 129 and 73 significant SNPs in the PC and univariate analyses, respectively. Thus, explicit modeling of the correlation structure between fatty acids in a multivariate framework enabled identification of loci associated with variation in seed fatty acid concentration that were not detected in the univariate analyses. Ultimately, a detailed characterization of the loci underlying fatty acid variation can be used to enhance the nutritional profile of oats through breeding.

genetics↗

bioRxiv2018

Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene

The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene(pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of thepgK1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. marrocana and A. murphyi, but did not show a close relationship with any extant diploid species.

evolutionary biology↗