Wu Zhi-Gang, Jiang Wu, Mantri Nitin, Bao Xiao-Qing, Chen Song-Lin, Tao Zheng-Ming
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China.
School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, VIC, Australia.
BMC Genomics. 2015 Apr 30;16(1):346. doi: 10.1186/s12864-015-1547-8.
Yam (Dioscorea alata L.) is an important tuber crop and purple pigmented elite cultivar has recently become popular because of associated health benefits. Identifying candidate genes responsible for flavonoid biosynthesis pathway (FBP) will facilitate understanding the molecular mechanism of controlling pigment formation in yam tubers. Here, we used Illumina sequencing to characterize the transcriptome of tubers from elite purple-flesh cultivar (DP) and conventional white-flesh cultivar (DW) of yam. In this process, we also designed high quality molecular markers to assist molecular breeding for tuber trait improvement.
A total of 125,123 unigenes were identified from the DP and DW cDNA libraries, of which about 49.5% (60,020 unigenes) were annotated by BLASTX analysis using the publicly available protein database. These unigenes were further annotated functionally and subject to biochemical pathway analysis. 511 genes were identified to be more than 2-fold (FDR < 0.05) differentially expressed between the two yam cultivars, of which 288 genes were up-regulated and 223 genes were down-regulated in the DP tubers. Transcriptome analysis detected 61 unigenes encoding multiple well-known enzymes in the FBP. Furthermore, the unigenes encoding chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3'-monooxygenase (F3'H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and flavonol 3-O-glucosyltransferase (UF3GT) were found to be significantly up-regulated in the DP, implying that these genes were potentially associated with tuber color formation in this elite cultivar. The expression of these genes was further confirmed by qRT-PCR. Finally, 11,793 SSRs were successfully identified with these unigenes and 6,082 SSR markers were developed using Primer 3.
This study provides the first comprehensive transcriptomic dataset for yam tubers, which will significantly contribute to genomic research of this and other related species. Some key genes associated with purple-flesh trait were successfully identified, thus providing valuable information about molecular process of regulating pigment accumulation in elite yam tubers. In the future, this information might be directly used to genetically manipulate the conventional white-fleshed tuber cultivars to enable them to produce purple flesh. In addition, our SSR marker sets will facilitate identification of QTLs for various tuber traits in yam breeding programs.
山药（薯蓣属植物）是一种重要的块茎作物，紫色素优良品种因具有相关健康益处最近受到欢迎。鉴定参与类黄酮生物合成途径（FBP）的候选基因将有助于理解山药块茎中色素形成的分子机制。在此，我们使用Illumina测序对山药优良紫肉品种（DP）和传统白肉品种（DW）的块茎转录组进行表征。在此过程中，我们还设计了高质量分子标记以辅助块茎性状改良的分子育种。
从DP和DW cDNA文库中共鉴定出125,123个单基因，其中约49.5%（60,020个单基因）通过使用公开可用蛋白质数据库的BLASTX分析进行了注释。这些单基因进一步进行了功能注释并进行了生化途径分析。鉴定出511个基因在两个山药品种之间差异表达超过2倍（FDR < 0.05），其中288个基因在DP块茎中上调，223个基因下调。转录组分析检测到61个编码FBP中多种知名酶的单基因。此外，发现编码查尔酮异构酶（CHS）、黄烷酮3 - 羟化酶（F3H）、类黄酮3'-单加氧酶（F3'H）、二氢黄酮醇4 - 还原酶（DFR）、无色花青素双加氧酶（LDOX）和黄酮醇3 - O - 葡萄糖基转移酶（UF3GT）的单基因在DP中显著上调，这意味着这些基因可能与该优良品种的块茎颜色形成有关。这些基因的表达通过qRT - PCR进一步得到证实。最后，利用这些单基因成功鉴定出11,793个SSR，并使用Primer 3开发了6,082个SSR标记。
本研究为山药块茎提供了首个全面的转录组数据集，这将对该物种及其他相关物种的基因组研究做出重大贡献。成功鉴定出一些与紫肉性状相关的关键基因，从而提供了关于优良山药块茎中调节色素积累分子过程的有价值信息。未来，这些信息可能直接用于对传统白肉块茎品种进行基因操作，使其能够产生紫肉。此外，我们的SSR标记集将有助于在山药育种计划中鉴定各种块茎性状的QTL。
