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Article|17 May 2022|OPEN
Genome-wide clonal variability in European pear “Rocha” using high-throughput sequencing
Octávio Serra1 , , Rui Maia de Sousa2 , Joana Bagoin Guimarães3 , José Matos3,4 , Patricia Vicente2 and Miguel Leão de Sousa2 , Fernanda Simões,3
1Instituto Nacional de Investigação Agrária e Veterinária, I.P., Banco Português de Germoplasma Vegetal (BPGV), Quinta de S. José, S. Pedro de Merelim 4700-859 Braga, Portugal
2Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
3Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
4Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
*Corresponding author. E-mail: octavio.serra@iniav.pt

Horticulture Research 9,
Article number: uhac111 (2022)
doi: https://doi.org/10.1093/hr/uhac111
Views: 41

Received: 16 Nov 2021
Accepted: 27 Apr 2022
Published online: 17 May 2022

Abstract

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.