Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam (Dioscorea alata L.) tubers.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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.
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. wuzhigang177@126.com.
Zhi-Gang
ZG
Wu
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. jiangwu8888@163.com.
Wu
W
Jiang
School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, VIC, Australia. nitin.mantri@rmit.edu.au.
Nitin
N
Mantri
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. 850254737@qq.com.|School of pharmacy, Wenzhou Medical University, Wenzhou, 325035, P.R. China. 850254737@qq.com.
Xiao-Qing
XQ
Bao
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. 623816984@qq.com.|School of pharmacy, Wenzhou Medical University, Wenzhou, 325035, P.R. China. 623816984@qq.com.
Song-Lin
SL
Chen
Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. yzswzg@gmail.com.
Zheng-Ming
ZM
Tao
D000429:Alcohol Oxidoreductases / Q000235:genetics / Q000378:metabolism; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D027742:Dioscorea / Q000235:genetics*; D005419:Flavonoids / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D005964:Glucosyltransferases / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D019753:Intramolecular Lyases / Q000235:genetics / Q000378:metabolism; D018895:Microsatellite Repeats / Q000235:genetics*; D006899:Mixed Function Oxygenases / Q000235:genetics / Q000378:metabolism; D010105:Oxygenases / Q000235:genetics / Q000378:metabolism; D010858:Pigmentation / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
D005419:Flavonoids; D010940:Plant Proteins; D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; D000429:Alcohol Oxidoreductases; C056570:dihydroflavanol 4-reductase; D010105:Oxygenases; C105763:leucoanthocyanidin dioxygenase; C048797:flavanone 3-dioxygenase; C038888:flavonoid 3'-hydroxylase; D005964:Glucosyltransferases; C023249:flavonol 3-O-glucosyltransferase; D019753:Intramolecular Lyases; C019865:chalcone isomerase