Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence

A genome-wide association study for culm cellulose content in barley reveals candidate genes co-expressed with members of the <i>Cellulose Synthase A </i>gene family

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.Kelly Houston, Rachel A. Burton, Beata Sznajder, Antoni J. Rafalski, Kanwarpal S. Dhugga, Diane E. Mather, Jillian Taylor, Brian J. Steffenson, Robbie Waugh, Geoffrey B. Finche

Control of foliar diseases in barley:towards an integrated approach

Barley is one of the world's most important crops providing food and related products for millions of people. Diseases continue to pose a serious threat to barley production, despite the use of fungicides and resistant varieties, highlighting the impact of fungicide resistance and the breakdown of host plant resistance on the efficacy of control measures. This paper reviews progress towards an integrated approach for disease management in barley in which new methods may be combined with existing measures to improve the efficacy of control in the long-term. Advances have been made in genetic mapping of resistance (R) genes and in identifying novel sources of genes in wild barley populations and land races. Marker assisted selection techniques are being used to pyramid R genes to increase the durability of resistance. Elicitors to induce host resistance used in combination with fungicides can provide effective disease control in the field and could delay the evolution of fungicide insensitivity. Traits that may contribute to disease tolerance and escape have been identified and the extent of genetic variation within barley germplasm is being determined. Tools are being developed to integrate the above methods via an assessment of the risk of economic injury occurring from disease to guide decisions on the requirement for fungicide treatment. Barriers exist to the adoption of integrated management approaches from growers and end-users further down the supply chain (e. g. acceptance of variety mixtures) and policy incentives from government may be required for it to be taken up in practice. © 2012 KNPV