Gene discovery and microarray analysis of cacao (Theobroma cacao L.) varieties
Gene discovery and microarray analysis of cacao (Theobroma cacao L.) varieties
复制标题
DOI：
10.1007/s00425-002-0882-6
复制
发表时间：
2002-12-01
期刊：
影响因子：
4.3
通讯作者：
Jones, CA
中科院分区：
文献类型：
--
作者：
Jones, PG;Allaway, D;Jones, CA
可可豆采自发育相对落后的热带树可可（Theobroma cacao L.）由于虫害和疾病，潜在产量受到很大损失。为了发现和理解这种商品作物中假定的天然抗性机制的稳定性，对巧克力生产至关重要，我们进行了一项基因发现计划，并证明了其在基因表达阵列中的应用。测序和组装豆和叶cDNA文库插入物产生了1，380个成员的独特重叠群集。使用Blast和MetaFam对该基因集进行高质量注释，为75%的重叠群产生注释，并使我们能够识别可可豆和叶子中表达的基因类型。微阵列构建使用扩增插入的单基因集和挑战与豆和叶RNA从五个可可品种。微阵列在五个随机选择的可可基因型中表现良好，并且没有显示出对叶或豆组织的偏倚。这表明基因序列可用于跨可可基因型和组织类型的微阵列分析。与所选基因的实时PCR结果相比，阵列结果显示与差异基因表达模式相关。我们希望得到的DNA序列和分子微阵列平台将有助于可可社区了解候选可可植物的基础，可能的稳定性和致病型抗性范围。
The cacao bean harvest from the relatively under developed tropical tree cacao (Theobroma cacao L.) is subject to high losses in potential production due to pests and diseases. To discover and understand the stability of putative natural resistance mechanisms in this commodity crop, essential for chocolate production, we undertook a gene-discovery program and demonstrated its use in gene-expression arrays. Sequencing and assembling bean and leaf cDNA library inserts produced a unique contig set of 1,380 members. High-quality annotation of this gene set using Blast and MetaFam produced annotation for 75% of the contigs and allowed us to identify the types of gene expressed in cacao beans and leaves. Microarrays were constructed using amplified inserts of the uni-gene set and challenged with bean and leaf RNA from five cacao varieties. The microarray performed well across the five randomly chosen cacao genotypes and did not show a bias towards either leaf or bean tissues. This demonstrates that the gene sequences are useful for microarray analysis across cacao genotypes and tissue types. The array results, when compared with real-time PCR results for selected genes, showed a correlation with differential gene-expression patterns. We intend that the resultant DNA sequences and molecular microarray platform will help the cacao community to understand the basis, likely stability and pathotype resistance range of candidate cacao plants.