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Genomic Diversity and Climate Adaptation in Brachypodium

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Genetics and Genomics of Brachypodium

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 18))

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 of invasive species and environmental adaptation. In this chapter we discuss the natural variation in climate/geography, genotypic and phenotypic diversity that exists within these species. We describe the utilisation of this diversity via two methods, Genome Wide Association Studies and Landscape Genomics, to examine the interaction between genetic variation, 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, sequencing, and population samples with higher spatial/temporal resolution of climate data, these approaches can exploit the diversity of these Brachypodium spp. Experiments using this toolkit will reveal alleles, genes and pathways underlying agriculturally important and environmentally sensitive traits.

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Abbreviations

GBS:

Genotyping by sequencing

GWAS:

Genome wide association studies

MaxEnt:

Maximum entropy

QTL:

Quantitative trait loci

SNPs:

Single nucleotide polymorphisms

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Acknowledgments

We would like to acknowledge our collaborators: Location data and seed—Shuangshuang Liu of the Kent Bradford lab at UC Davis United states, Pilar Catalan from the University of Zaragoza in Huesca Spain, Luis Mur at Aberystwyth University at Aberystwyth Wales, Dave Garvin from University of Minnesota/USDA United States and John Vogel from JGI/UC Berkeley.

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Authors and Affiliations

  1. Centre of Excellence in Plant Energy Biology, Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia

    Pip Wilson, Jared Streich & Justin Borevitz

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  1. Pip Wilson
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  2. Jared Streich
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  3. Justin Borevitz
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Corresponding author

Correspondence to Justin Borevitz .

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Editors and Affiliations

  1. DOE Joint Genome Institute, Walnut Creek, California, USA

    John P. Vogel

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, subgroup, 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.

Subgroup

In this paper, subgroup is a major hierarchical cluster of genotype groups and their respective families and/or genotypes. Subgroups could interbreed but don’t in natural environments due to some sort of natural barrier.

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Wilson, P., Streich, J., Borevitz, J. (2015). Genomic Diversity and Climate Adaptation in Brachypodium . In: Vogel, J. (eds) Genetics and Genomics of Brachypodium. Plant Genetics and Genomics: Crops and Models, vol 18. Springer, Cham. https://doi.org/10.1007/7397_2015_18

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