Tree Genetics & Genomes ( IF 2.4 ) Pub Date : 2020-05-13 , DOI: 10.1007/s11295-020-01439-x Helena Everaert , Jocelyn De Wever , Thi Kim Hong Tang , Thi Lam An Vu , Kevin Maebe , Hayley Rottiers , Steve Lefever , Guy Smagghe , Koen Dewettinck , Kathy Messens
Vietnam has the potential to become a larger cocoa producer as the country experiences climatic conditions favorable to the growth of the crop. However, to enable a high cacao quality, genetic methods are required to identify and conserve promising cacao cultivars. Previous research as discussed by Everaert et al. (2017), using 14 microsatellite (SSR) markers, showed a genetic characterization of Vietnamese cacao, but additional research is required to further clarify the genetic background of the different Vietnamese cacao cultivars. Therefore, in this study, the Vietnamese dataset was enlarged, and a classification model was developed. Firstly, we compared the classification strength of the 14 previously applied SSR markers and 42 additional single nucleotide polymorphism (SNP) markers, either separately or combined, using 53 international reference cacao cultivars. Secondly, the most classifying marker set was used to examine the genetic associations of the Vietnamese cultivars to the reference cultivars, using Bayesian clustering and principal coordinate analysis (PCoA). The classification method based on the combined marker set performed best and could subdivide the Vietnamese cultivars in three clusters. The first cluster was strongly related to Nanay, the second to Criollo/Trinitario, and the third predominantly to Amelonado and Criollo/Trinitario. For all marker sets, an apparent high genetic diversity could be observed for the total Vietnam collection. The obtained knowledge provides a strong genetic basis for the Vietnamese cacao industry. In addition, the proposed marker set and the analysis workflow could be applied worldwide for future breeding programs and further production of origin chocolate.
中文翻译:
利用SNP和SSR标记评估越南可可品种的遗传分类。
随着越南经历有利于作物生长的气候条件,越南有可能成为更大的可可豆生产国。然而,为了获得高可可品质,需要遗传方法来鉴定和保存有希望的可可品种。Everaert等人讨论的先前研究。(2017)使用14个微卫星(SSR)标记显示了越南可可的遗传特征,但需要进一步研究以进一步阐明越南可可不同品种的遗传背景。因此,在这项研究中,越南数据集被扩大,并建立了分类模型。首先,我们比较了先前使用的14种SSR标记和42种其他单核苷酸多态性(SNP)标记的分类强度,无论是单独使用还是组合使用,使用了53个国际参考可可品种。其次,使用贝叶斯聚类和主坐标分析(PCoA),使用分类最多的标记集来检查越南品种与参考品种的遗传关联。基于组合标记集的分类方法效果最好,可以将越南品种分为三个类。第一个集群与Nanay密切相关,第二个集群与Criollo / Trinitario关联,第三个主要与Amelonado和Criollo / Trinitario关联。对于所有标记集,在整个越南收集物中都可以观察到明显的高遗传多样性。所获得的知识为越南可可产业提供了强大的遗传基础。此外,