The Coffea genus includes about 124 species, of which Coffea arabica L. and Coffea canephora Pierre ex A. Froehner are the most commercially important, supplying 63 and 37% of the world coffee production, respectively. C. arabica L. is associated with better cup quality, but presents serious problems with pests and diseases, potentiated by climate change. The development of new varieties of C. arabica L. requires the inclusion of genetic diversity, looking for incorporating new genes to tolerate or resist the most important pests and diseases, maintaining or improving yield and cup quality of the new materials. The technology of diversity arrays based on sequencing (DArTseq™) allows the rapid identification of the single nucleotide polymorphism (SNP) for a genomic approach of genetic diversity. The objectives of the present study were: (1) to evaluate the diversity and genetic structure of a central coffee collection of the Mexican National Bank of Coffee Germplasm; (2) assess the reproducibility and error rates of the markers and their broad representation in the genome and (3) to propose a new collection with representative and divergent promising genotypes for stablishing a coffee breeding program in Mexico. 87 coffee accessions of three different species of the Coffea genus were sequenced and 16,995 SNP markers were derived from 34,000 unique sequences obtained by the DArTseq™ method. After removing the markers with more than 10% of missing data and the MAF < 5%, we end up with 1739 polymorphic SNP markers for the analysis. A dendrogram was generated which divided the accessions into five divergent groups where promising genotypes were identified. In conclusion, there is genetic diversity among the accessions of Coffea spp. for use in future breeding programs.

该咖啡树属包括约124种，其中的阿拉伯咖啡L.和果咖啡皮埃尔前A. Froehner是最重要的商业，提供世界咖啡产量的63和37％，分别。C. arabica L.与更好的杯子质量有关，但由于气候变化而加剧了病虫害的严重问题。阿拉伯茶新品种的开发L.要求包括遗传多样性，寻求纳入新的基因以耐受或抵抗最重要的病虫害，保持或提高新材料的产量和杯子品质。基于测序的多样性阵列技术（DArTseq™）可以快速鉴定单核苷酸多态性（SNP），从而实现遗传多样性的基因组方法。本研究的目标是：（1）评价墨西哥国家咖啡种质银行中央咖啡集合的多样性和遗传结构；（2）评估标记的可再现性和错误率及其在基因组中的广泛代表，（3）提出一个具有代表性和不同前途基因型的新品种，以在墨西哥建立咖啡育种计划。对咖啡属进行测序，并从通过DArTseq™方法获得的34,000个独特序列中获得16,995个SNP标记。在删除丢失数据超过10％且MAF <5％的标记后，我们最终得到了1739个多态性SNP标记用于分析。生成树状图，将种质分为五个不同的组，在其中鉴定出有希望的基因型。总之，咖啡种的种间存在遗传多样性。供将来的育种程序使用。