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Genetic diversity, Population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers

机译：基于SSR标记的法国苹果种质资源的遗传多样性，种群结构，亲子关系分析和核心种质的构建

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In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P(ID) over the 21 retained SSR loci close to 10-28. Pairwise comparisons revealed 34% redundancy and 18.5% putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity He of 0.82 and observed heterozygosity Ho of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider and Moderncultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as ‘King of Pippin’ and ‘Calville Rouge d’Hiver’ as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90% of the total dessert allelic diversity, whereas a dessert sub-core collection of 48 cultivars contained 71% of diversity. For cider apples, a 48-cultivars core collection contained 83% of the total cider allelic diversity.
机译：苹果遗传资源的深入表征是遗传改良和种质管理的前提。在这项研究中，我们用24个SSR标记物对2163个法国种的非常大的集合进行了指纹鉴定，以评估其遗传多样性，种群结构和遗传关系，并将这些特征与品种的选择日期或用途（旧的或现代的，甜品或苹果酒）联系起来。品种），并构建核心馆藏。大多数标记具有很高的判别力和强大的品种识别能力，在21个保留的SSR位点接近10-28的情况下，身份P（ID）的可能性较高。成对比较显示34％的冗余和18.5％的假定三倍体。结果表明，种质多样性很高，预期杂合度He为0.82，观察到杂合度Ho为0.83。基于贝叶斯模型的聚类方法揭示了三个亚组（FST = 0.014-0.048）中的一个弱但显着的结构，尽管大约相当于预先定义的三个亚群（Old Dessert，Old Cider和Moderncultivars）。亲子关系分析建立了已知的和未知的关系，尤其是在旧品种之间，并且频繁出现“ Pippin国王”和“ Calville Rouge d'Hiver”等品种。最后，构建了基于等位基因多样性的核心集合。 278个栽培品种的大型甜点核心收藏品占甜点等位基因总多样性的90％，而48个栽培品种的甜点次核心收藏品包含71％的多样性。苹果酒的48个品种的核心品种占苹果酒等位基因多样性的83％。

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