Chromosomal dominance in apple after whole genome duplication

T. Lallemand, S. Aubourg, J.-M. Celton, C. Landès
Whole genome duplication (WGD) is a massive mechanism consisting of the duplication of the entire genome. By increasing the size of the genome and removing the selective constraint, WGD is an important driver of genetic innovation. The Rosaceae family has experienced at least 3 WGDs in its evolutionary history. For apple (Malus domestica), which belongs to this family, an additional WGD occurred recently (50 mYA). This WGD is well conserved and not found outside the Maloideae subfamily. Apple is therefore an organism of choice to study the fate of duplicated genes after WGD. In a previous analysis, a QTL disequilibrium was observed between ohnologous chromosome pairs. The aim of this project is to identify the molecular mechanism driving this observed disequilibrium. Using a turnkey Snakemake pipeline, our first step was to compute the Ka/Ks ratio to estimate the selective pressure on ohnologous gene pairs. Secondly, we compared the expression levels between ohnologous genes using a large number of biological samples. Primary analyses indicate that while Ka/Ks ratio does not differ between ohnologous genes, significant transcriptional differences were identified at the chromosome level. This subgenome dominance could explain in part the observed disequilibrium in the number of QTLs carried by the ohnologous chromosome pairs.
Lallemand, T., Aubourg, S., Celton, J.-M. and Landès, C. (2023). Chromosomal dominance in apple after whole genome duplication. Acta Hortic. 1362, 57-64
DOI: 10.17660/ActaHortic.2023.1362.9
whole genome duplication, apple, bioinformatics, RNA-Seq, Ka/Ks, genome evolution

Acta Horticulturae