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Genomic Diversity and Climate Adaptation in Brachypodium

Pip Wilson, Jared Streich, Justin Borevitz
doi: https://doi.org/10.1101/015495
Pip Wilson
1Centre of Excellence in Plant Energy Biology, 134 Linnaeus Way, Australian National University, Canberra, ACT 2601
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  • For correspondence: Justin.Borevitz@anu.edu.au
Jared Streich
1Centre of Excellence in Plant Energy Biology, 134 Linnaeus Way, Australian National University, Canberra, ACT 2601
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  • For correspondence: Justin.Borevitz@anu.edu.au
Justin Borevitz
1Centre of Excellence in Plant Energy Biology, 134 Linnaeus Way, Australian National University, Canberra, ACT 2601
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  • For correspondence: Justin.Borevitz@anu.edu.au
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Abstract

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.

  • Abbreviations

    GBS
    genotyping by sequencing
    GWAS
    genome wide association studies
    QTL
    quantitative trait loci
    MaxEnt
    Maximum Entropy
    SNPs
    single nucleotide polymorphisms
  • Glossary

    Accession
    A collection of seeds from one location. This includes bulk collections and maternal descent lines
    Ecotype
    An individual or group whose genetic distinction is strongly associated to an environment or type
    Genotype
    This 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 plants
    Population
    Non-random mating between groups within a specified geographic space
    Subspecies
    In 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
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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    Posted February 23, 2015.
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    Genomic Diversity and Climate Adaptation in Brachypodium
    Pip Wilson, Jared Streich, Justin Borevitz
    bioRxiv 015495; doi: https://doi.org/10.1101/015495
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    Genomic Diversity and Climate Adaptation in Brachypodium
    Pip Wilson, Jared Streich, Justin Borevitz
    bioRxiv 015495; doi: https://doi.org/10.1101/015495

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