S01 - Session O2 - How to explain QTL imbalance between ohnologous chromosomes?

Authors: Tanguy Lallemand *, Sébastien Aubourg, Jean-Marc Celton, Claudine Landès

Polyploidy is a driver of genetic innovation in eukaryotic organisms, especially in plants. In 2011, a high quality genome sequence was published for the domesticated apple ( Malus domestica Borkh), which confirmed a Whole Genome Duplication (WGD) event that occured 50 million years ago. Following the projection of 589 QTLs covering several phenotypic traits onto a single physical map, we identified significant QTL imbalance between ohnologous chromosome fragments. To understand this imbalance, we studied the rate of gene sequence evolution between syntenic blocks and investigated whether expression differences between ohnologous pairs of genes could be associated with the observed imbalance. A turnkey snakemake pipeline was written to compute Ka/Ks between triplets composed by Malus ohnologous gene pairs and their orthologs in Prunus persica as its closest related species without a WGD. To investigate a potential transcription imbalance a mapping pipeline was written and used on all publicly available RNA-seq runs meeting our quality criteria. Rather than testing two conditions against each other, we tested differential expression between pairs of ohnologous genes for each experimental condition. Results derived from the Ka/Ks analysis on the apple gene sequences indicate that QTL imbalances cannot be associated with particular sequence divergence between ohnologous pairs of genes. Using data from 149 RNA-seq experiments, our results show that of the 16,376 ohnologous gene pairs, 10,376 are differentially expressed. Statistical analysis demonstrated that this transcriptional imbalance was significant for 6 chromosome pairs, which is consistent with the observed QTL imbalance. We expect to enrich our analysis by comparing the evolution of transposable element content located within syntenic blocks for which both QTL and transcriptional imbalance were identified.