Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus.

Qing Chen,Yaodong Hu,Xiaorong Wang,Yan Wang,Yueyang Hu,Haoru Tang,Bo Sun,Xunju Liu

doi:10.1155/2018/8084032

Abstract

The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.

Highlights

The genus Rubus L. comprises 900–1000 species and has a worldwide distribution with various climatic adaptations [1]
In Hyun et al.’s study of R. occidentalis from the perspective of fruit morphology and phenological traits [7], transcriptome analysis involved mRNA isolated only from fruits sampled 20 days after anthesis at an intermediate stage of ripening [6]
Sixteen pathways were enriched across the whole fruit developmental process, including those of genes involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis, among others (Figures 2–4)

Summary

Introduction

The genus Rubus L. comprises 900–1000 species and has a worldwide distribution (excluding Antarctica) with various climatic adaptations [1]. Blackberries and raspberries are the most commonly cultivated fruits in these two subgenera They are deemed functional fruits, mainly due to being rich sources of healthpromoting antioxidant or “nutraceutical” compounds (i.e., anthocyanins, phenolics, and ellagic acid) in fresh fruits [2] and anticancer properties in fruit extracts [3]. As a first step towards understanding gene expression during fruit ripening in R. coreanus, this study presents results of a comprehensive analysis of transcriptome data from fruits at three representative developmental stages. Both de novo and reference-guided assembly were carried out to maximize the possibility of finding potential transcripts. It is hoped that exploration of the genetics of R. coreanus may prove to be a profitable endeavor by providing valuable information for Rubus breeding

Results and Discussion

Conclusions

Materials and Methods

Conflicts of Interest