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

本研究采用基于测序的基因分型（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研究。分别采用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个和8088个高质量SNP。利用上述SNP数据集，本研究解析了群体遗传变异并构建了该种质群体内个体间的遗传关系，分析过程分别通过参数化与非参数化群体结构分析软件进行独立评估。尽管两种检测流程得到的SNP数量存在三倍差异，但二者均揭示了意大利橄榄品种间存在丰富的遗传变异，且均可基于种植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。