基于全基因组 sRNA 和 mRNA 转录组学分析的萝卜（Raphanus sativus L.）主根增粗的动态调控机制研究。

Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.).

机构信息

National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.

College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China.

出版信息

BMC Plant Biol. 2020 Aug 8;20(1):373. doi: 10.1186/s12870-020-02585-z.

DOI:10.1186/s12870-020-02585-z

PMID:32770962

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7414755/

Abstract

BACKGROUND

Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size.

RESULTS

A total of 2606 differentially expressed genes (DEGs) were shared between 'NAU-DY' (large acicular) and 'NAU-YB' (medium obovate), which were significantly enriched in 'phenylpropanoid biosynthesis', 'glucosinolate biosynthesis', and 'starch and sucrose metabolism' pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between 'NAU-DY' and 'NAU-YH' (small circular), whereas 12 miRNAs exhibited specific differential expression in 'NAU-DY'. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis.

CONCLUSION

This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.

摘要

背景

直根是主要的可食用器官，最终决定萝卜的产量和品质。然而，萝卜直根加粗的精确分子机制仍有待进一步研究。本研究通过 RNA-seq 从三个不同根大小的近交系中鉴定了参与萝卜直根加粗的关键基因。

结果

'NAU-DY'（长针形）和'NAU-YB'（中卵形）之间共鉴定到 2606 个差异表达基因（DEGs），这些基因显著富集在苯丙烷生物合成、硫苷生物合成和淀粉和蔗糖代谢途径中。同时，'NAU-DY'和'NAU-YH'（圆形）之间共鉴定到 16 个差异表达 miRNA（DEM），而'NAU-DY'中 12 个 miRNA 表现出特异性差异表达。关联分析表明，miR393a-bHLH77、miR167c-ARF8 和 miR5658-APL 可能是直根类型变异的生物学现象的关键因素，并提出了直根加粗和发育的假设调控模型。此外，通过 RT-qPCR 分析对几个关键基因，包括 SUS1、EXPB3 和 CDC5 进行了特征和分析。