Journal Article

Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla

Tissue, David T., Ahrens, Collin W., Murray, Kevin, Rymer, Paul D., Borevitz, Justin O., Ferguson, Scott, Mazanec, Richard A., Jones, Ashley, Byrne, Margaret

2024

Overview

Background Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla . Results We found 273 genomic variants determining traits with moderate heritability ( h 2 SNP  = 0.26–0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. Conclusions Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Adaptation / Animal Genetics and Genomics / Australia / Biomedical and Life Sciences / Chromosomes / Climate change / Climate models / Climate prediction / Climatic changes / Constraints / Corymbia calophylla / Drought / Droughts / Environmental aspects / Epistasis / Epistasis, Genetic / Eucalyptus / Forest management / Genes / Genetic aspects / Genome wide association study (GWAS) / Genome, Plant / Genomes / Genomics / Genotype & phenotype / Growth / Haplotypes / Heritability / Influence / Life Sciences / Microarrays / Microbial Genetics and Genomics / Myrtaceae / Phenotype / Physiology / Plant Genetics and Genomics / Plant species / Pleiotropy / Polymorphism, Single Nucleotide / Proteomics / Quantitative genetics / Quantitative Trait Loci / Regulatory sequences / Trees / Water use efficiency / Wildlife conservation