CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France.
DNA Res. 2012;19(1):23-35. doi: 10.1093/dnares/dsr039. Epub 2011 Dec 30.
Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.
可可树是几个热带国家具有重要经济价值的树种。对其进行遗传改良对于提供对重大疾病的保护和提高巧克力质量至关重要。我们发现并绘制了新的表达序列标签-单核苷酸多态性（EST-SNP）和简单重复序列（SSR）标记，并构建了高密度遗传图谱。通过筛选 149650 个 EST，在计算机中检测到 5246 个 SNP，其中 1536 个对应于具有推定功能的基因，而 851 个在遗传资源的集合中具有明显的多态模式。此外，在克里奥罗基因组上检测到 409 个新的 SSR 标记。最后，在现有的 418 个共显性标记上添加了 681 个新的 EST-SNPs 和 163 个新的 SSRs，以构建一个大型共识遗传图谱。该高密度图谱和本研究中鉴定的一系列新遗传标记是可可基因组学和标记辅助育种的一个里程碑。该数据可在 http://tropgenedb.cirad.fr 上获得。
