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

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.

Quercus suber L. Genetic Resources: Variability and Strategies for Its Conservation

“…The recent developments of high-throughput sequencing technologies have facilitated the sequencing of entire genomes, supporting the development of new genomic resources and identifying single-nucleotide polymorphism (SNP). Mendes et al [46] investigated the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping in a natural regenerated cork oak population. Kinships were successfully identified, and some families' pedigrees were established, which support that pedigree information can be a valuable tool for future management strategies of cork oak populations, including future cork oak breeding schemes [46].…”

“…Mendes et al [46] investigated the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping in a natural regenerated cork oak population. Kinships were successfully identified, and some families' pedigrees were established, which support that pedigree information can be a valuable tool for future management strategies of cork oak populations, including future cork oak breeding schemes [46].…”

“…Quercus suber shows genetic variation among populations in adaptive traits, possibly because of adaptation to climate and environmental changes along its geographical distribution [33]. It is of utmost importance to conserve this diversity as a base resource for the improvement and management of genetic resources and stands, as well as for breeding strategies and conservation [46]. In this context, conservation strategies should ideally include populations from all the different abiotic and biotic conditions.…”

Detailed kinship estimation for detecting bias among breeding families in a reintroduced population of the endangered bagrid catfish Tachysurus ichikawai

“…Although some studies have shown that using more SNPs can increase the number of identified kinships (Mendes et al, 2022), we chose to prioritize the creation of an SNP dataset with minimal errors by applying filtering conditions, even if it meant a reduction in the number of SNPs. This is because when a large number of SNPs were used under loose filtering conditions, the estimation of kinships did not yield satisfactory results when the assumed error rate was high in COLONY 2.0.…”