Genome-wide clonal variability in European pear Rocha using high-throughput sequencing

Pears (Pyrus) are one of the most economically important fruits worldwide. The Pyrus genus is characterized by a high degree of genetic variability between species and interspecific hybrids, and several studies have been performed to assess this variability for both cultivated and wild accessions. These studies have mostly been limited by the resolving power of traditional molecular markers, although in the recent past the availability of reference genome sequences or SNP arrays for pear have enhanced the capability of high-resolution genomics studies. These tools can also be applied to better understand the intra-varietal (or clonal) variability in pear. Here we report the first high resolution genomics analysis of a pear clonal population using whole genome sequencing (WGS). Results showed unique signatures for the accumulation of mutations and transposable element insertions in each clone, which are likely related to their history of propagation and cultivation. The nucleotide diversity remained low in the clonal collection with the exception of few genomic windows, suggesting that balancing selection may be occurring. These windows included mainly genes related to plant fertility. Regions with higher mutational load were partially associated with transcription factors, probably reflecting the distinctive phenotypes in the collection. The annotation of variants also revealed the theoretical disruption of relevant genes in pear. Taken together, the results from this study show that pear clones accumulate mutations differently, and that those mutations can play a role on pear phenotypes, meaning that the study of pear clonal populations can be relevant in genetic studies, mainly when comparing with traditional association studies.

Automated summary

This study conducted a high-resolution genomic analysis of a pear clonal population, revealing unique signatures of mutations and transposable element insertions in different clones, which are likely related to their propagation and cultivation history. The nucleotide diversity of the clonal population remained low, except for a few genomic windows, suggesting the occurrence of balancing selection. Genes related to plant fertility were found in these windows. Regions with higher mutational load were associated with transcription factors, reflecting distinct phenotypes in the collection. The annotation of variants also indicated the theoretical disruption of relevant genes in pear. These findings highlight the importance of studying pear clonal populations in genetic research, particularly in comparison to traditional association studies.