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Predicting the geographic origin of Spanish Cedar ( Cedrela odorata L.) based on DNA variation
Conservation Genetics ( IF 2.0 ) Pub Date : 2020-06-03 , DOI: 10.1007/s10592-020-01282-6
Kristen N. Finch , Richard C. Cronn , Marianella C. Ayala Richter , Céline Blanc-Jolivet , Mónica C. Correa Guerrero , Luis De Stefano Beltrán , Carmen R. García-Dávila , Eurídice N. Honorio Coronado , Sonia Palacios-Ramos , Kathelyn Paredes-Villanueva , F. Andrew Jones

The legality of wood products often depends on their origin, creating a need for forensic tools that verify claims of provenance for wood products. The neotropical tree species Cedrela odorata (Spanish cedar) is economically valuable for its wood and faces threats of overexploitation. We developed a 140 SNP assay for geographic localization of C. odorata specimens. Target capture and short-read sequencing of 46 C. odorata specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. We assessed the broad applicability of these SNPs on 356 specimens from eight Cedrela species, three tissue types, and a range of DNA mass inputs. Origin prediction error was evaluated with discrete and continuous spatial assignment methods focusing on C. odorata specimens. Discrete classification with random forests readily differentiated specimens originating in Central America versus South America (5.8% error), while uncertainty increased as specimens were divided into smaller regions. Continuous spatial prediction with SPASIBA showed a median prediction error of 188.7 km. Our results demonstrate that array SNPs and resulting genotypes accurately validate C. odorata geographic origin at the continental scale and show promise for country-level verification, but that finer-scale assignment likely requires denser spatial sampling. Our study underscores the important role of herbaria for developing genomic resources, and joins a growing list of studies that highlight the role of genomic tools for conservation of threatened species.



中文翻译:

基于DNA变异预测西班牙雪松(Cedrela odorata L.)的地理起源

木制品的合法性通常取决于其来源,因此需要一种法证工具来验证木制品的来源要求。新热带树种Cedrela odorata(西班牙雪松)因其木材而在经济上具有价值,并面临过度开发的威胁。我们开发了140个SNP检测方法来用于香茅标本的地理定位。目标捕获和短读序列的46个臭椿样品使我们能够鉴定140个可提供信息的SNP,这些SNP通过纬度,温度和降水来区分臭椿样品。我们评估了这些SNP在来自八个Cedrela的356个样本中的广泛适用性物种,三种组织类型以及一系列DNA质量输入。用离散和连续空间分配方法评估了原产地预测误差,该方法着重于香茅标本。用随机森林进行的离散分类可以轻松地区分源自中美洲和南美的标本(误差为5.8%),而随着标本分为较小区域的不确定性增加。用SPASIBA进行的连续空间预测显示中位预测误差为188.7 km。我们的结果表明,阵列SNP和所产生的基因型可准确验证香茅大陆规模的地理起源,显示出对国家级验证的希望,但是更精细的分配可能需要更密集的空间采样。我们的研究强调了草本植物在开发基因组资源方面的重要作用,并加入了越来越多的研究,这些研究突出了基因组工具在保护濒危物种中的作用。

更新日期:2020-06-03
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