Genotype-by-sequencing disclosed genetic diversity and revealed unexpected synonymy in a representative collection of the Italian olive germplasm

We used genotyping-by-sequencing (GBS) to perform a genome-wide diversity study on a collection of 94 olive cultivars representative of the Italian germplasm. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively.Such SNP datasets were used to investigate genetic variation and establish relationships among the individuals across the population as independently assessed by a parametric and a non-parametric population structure analysis software. Even if the two pipelines generated a 3-fold difference in the number of SNPs, both unveiled wide genetic variability within Italian cultivars and allowed genotypes to be clustered based on the geographical area of cultivation as well as on traits related to morphology and fruit size.本研究采用测序分型（genotyping-by-sequencing, GBS）技术，对代表意大利种质资源的94份橄榄品种集合开展全基因组多样性分析。分别通过基于参考基因组与不依赖参考基因组的单核苷酸多态性（single nucleotide polymorphism, SNP）检测流程，得到22088个与8088个高质量SNP位点。利用上述SNP数据集探究该群体内个体间的遗传变异并构建亲缘关系，相关分析由参数化及非参数化群体结构分析软件独立完成。尽管两种流程得到的SNP数量存在3倍差异，但二者均揭示了意大利橄榄品种内广泛存在的遗传变异，且均可依据栽培地理区域以及形态与果实大小相关性状对基因型进行聚类。