Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population

Bruna Mendes,António Marcos Ramos,Marta A Antunes,Ana Usié,Teresa Sampaio,Carla Borges,Fernanda Simões,Filipe Costa E Silva,Hugo Magalhães,Maria Helena Almeida

doi:10.3390/f13020226

Abstract

Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak.

Highlights

The application of different filtering parameters in the initial SNP output resulted in four sets of SNPs used for identity by descent (IBD) estimation, each containing different numbers of SNPs
The results showed that PRIMUS predicted more relationships than previously anticipated in Table 1, with filtering of the IBD matrices using expected mean of IBD portions for familial relationship categories, using the approach described by Blouin and colleagues [28] (Table 2)
Pedigree information can be a valuable tool for future management strategies of cork oak populations, including future cork oak breeding schemes

Summary

Introduction

Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean. Cork oak covers 23% of the national forest area in Portugal, being the dominant species of the “montado” agroforestry system (“dehesa” in Spain). In addition to its important ecological value, “montado” combines cork production with extensive agriculture or pasture and livestock. Portugal and Spain are the main cork producers worldwide

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