TY - JOUR T1 - Genomic Diversity and Climate Adaptation in Brachypodium JF - bioRxiv DO - 10.1101/015495 SP - 015495 AU - Pip Wilson AU - Jared Streich AU - Justin Borevitz Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/02/23/015495.abstract N2 - The Brachypodium genus contains the model grasses B. distachyon, B. stacei and B. hybridum, that are useful for molecular and physiological studies relevant to grain, pasture and bioenergy crops, as well as ecology. In this chapter we discuss the natural variation in climate/geography, genotypic and phenotypic diversity that exists within these species. We describe utilisation of this diversity via two methods, Genome Wide Association Studies and Landscape Genomics, to examine the interaction between specific genetic variants, phenotype, and environment. The aim is to identify adaptive loci that control specific traits in specific environments and understand the contribution of background polygenetic variation shaped by demographic processes. With recent developments in high throughput phenotyping, cheaper genotyping by sequencing and higher spatial/temporal resolution of climate data, these approaches can exploit the diversity of the Brachypodium. Experiments using this toolkit will reveal alleles, genes and pathways underlying agriculturally important and environmentally sensitive traits for use in grass breeding.GBSgenotyping by sequencingGWASgenome wide association studiesQTLquantitative trait lociMaxEntMaximum EntropySNPssingle nucleotide polymorphismsAccessionA collection of seeds from one location. This includes bulk collections and maternal descent linesEcotypeAn individual or group whose genetic distinction is strongly associated to an environment or typeGenotypeThis general term is used either to describe the genotype at a locus such as a SNP (AA, Aa, aa) or a background whole genome genotype which can have levels of species, subspecies, population genetic structure group, family, individual maternal line)Phenotype (qualitative and quantitative)Measurable traits expressed by plantsPopulationNon-random mating between groups within a specified geographic spaceSubspeciesIn this paper, subspecies is a major hierarchical cluster of genotype groups and their respective families and/or genotypes. Subspecies could interbreed but don’t in natural environment due to some sort of natural barrier ER -