Abstract
Chinese yam (Dioscorea opposita) is an important tuberous crop used for both food and medicine. Despite a long history of cultivation, the understanding of D. opposita genetics and molecular biology remains scant, which has limited its genetic improvement. This work presents a de novo transcriptome sequencing analysis of microtuber formation in D. opposita. We assembled cDNA libraries from different stages during the process of microtuber formation, designated as initial explants (EXP), axillary bud proliferation after three weeks (BUD), and microtuber visible after four weeks (MTV). More differentially expressed genes (DEGs) and pathways were identified between BUD vs. EXP than in MTV vs. BUD, indicating that proliferation of the axillary bud is the key stage of microtuber induction. Gene classification and pathway enrichment analysis showed that microtuber formation is tightly coordinated with primary metabolism, such as amino acid biosynthesis, ribosomal component biosynthesis, and starch and sucrose metabolism. The formation of the microtuber is regulated by a variety of plant hormones, including ABA. Combined with analysis of physiological data, we suggest that ABA positively regulates tuberization in D. opposita. This study will serve as an empirical foundation for future molecular studies and for the propagation of D. opposita germplasm in field crops.
Highlights
Yams (Dioscorea spp.) are a tuberous crop in many tropical and subtropical regions, such as West Africa, East and South Asia, and the Caribbean
In order to perform an expression profiling study, here we divided the process of microtuber formation into the following three stages based on appearance changes of the leaf-axil region and the microtuber emergence (Figure 1): initial explant (EXP), axillary bud proliferation after three weeks (BUD), and microtuber visible after four weeks (MTV)
Through analyzing the Kyoto Encyclopedia of Genes and Genomes MTV (KEGG) enrichment data on the differentially expressed genes (DEGs) of BUD vs. EXP and MTV vs. EXP comparisons, we found that the biosynthesis of amino acids, carbon metabolism, and phenylpropanoid biosynthesis is significantly differently expressed in the BUD vs. EXP and speculated that the biosynthesis of amino acids, followed by carbon metabolism and phenylpropanoid biosynthesis, may play key regulatory roles during microtuber induction of D. opposita
Summary
Yams (Dioscorea spp.) are a tuberous crop in many tropical and subtropical regions, such as West Africa, East and South Asia, and the Caribbean. Dioscorea opposita (Chinese yam) is one of the four famous Chinese herbs produced in Huaiqing area, it is a very popular edible plant and has long been cultivated to promote human health and longevity through diet, and it is the 2nd most commonly grown tuberous crop in China after potato. D. opposita has drawn more and more research attentions on its biology, pathology, and cultivation [1, 2]. Especially virus infections that resulted from vegetative propagation, are a serious issue for field production of D. opposita. The production of virus-free plants through plant tissue culture is widely used in the Dioscorea genus to avoid virus infections of plant materials [3,4,5]. Microtubers are small tubers originated from plant tissues in vitro. The study of microtuber induction and formation has attracted more and more attention [8, 9]
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