Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations.

Aleksandra Skalska,Jiwan Han,Rafał K Wóycicki,John H Doonan,Anne C Roulin,Karolina Susek,Fiona Corke,Luis A J Mur,Martin Vickers,Metin Tuna,Michele Wyler,Saurabh Chaudhary,Martin Swain,Robert Hasterok,Hefin W Williams,Christoph Stritt,Gulsemin Savas Tuna

doi:10.3390/ijms21186700

Abstract

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.

Highlights

IntroductionBrachypodium distachyon (hereafter Brachypodium) is a well-established grass model species, to be found mostly in countries bordering the Mediterranean
Brachypodium distachyon is a well-established grass model species, to be found mostly in countries bordering the Mediterranean
The populations could be split between Extremely Delayed Flowering (EDF+) phenotype, which was most common in the T+ populations, and those where flowering was more rapid [10]

Summary

Introduction

Brachypodium distachyon (hereafter Brachypodium) is a well-established grass model species, to be found mostly in countries bordering the Mediterranean. Genotyping by sequencing of >1400 accessions allowed the definition of a geographical split between the Western and Eastern Mediterranean populations but within each population there existed the same A and B subspecies. This study focused on existing inbred Turkish (T+) and Spanish (S+) accessions and identified 3,933,264 high-confidence SNPs. Phenotypically, the populations could be split between Extremely Delayed Flowering (EDF+) phenotype, which was most common in the T+ populations, and those where flowering was more rapid [10]. The populations could be split between Extremely Delayed Flowering (EDF+) phenotype, which was most common in the T+ populations, and those where flowering was more rapid [10]

Methods

Results

Discussion

Conclusion