Joint RNA-Seq and miRNA Profiling Analyses to Reveal Molecular Mechanisms in Regulating Thickness of Pod Canopy in Brassica napus.

Chen Chen,Qu Qu,Jian Jian,Lu Lu,Huo Huo,Li Li,Yang Yang

doi:10.3390/genes10080591

Abstract

Oilseed rape (Brassica napus) is the second largest oilseed crop worldwide. As an architecture component of B. napus, thickness of pod canopy (TPC) plays an important role in yield formation, especially under high-density cultivation conditions. However, the mechanisms underlying the regulation of TPC remain unclear. RNA and microRNA (miRNA) profiling of two groups of B. napus lines with significantly different TPC at the bolting with a tiny bud stage revealed differential expressions of numerous genes involved in nitrogen-related pathways. Expression of several nitrogen-related response genes, including ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15, was dramatically changed in the thick TPC lines compared to those in the thin TPC lines. Differentially expressed miRNAs also included many involved in nitrogen-related pathways. Expression of most target genes was negatively associated with corresponding miRNAs, such as miR159, miR6029, and miR827. In addition, 12 (including miR319, miR845, and miR158) differentially expressed miRNAs between two plant tissues sampled (stem apex and flower bud) were identified, implying that they might have roles in determining overall plant architecture. These results suggest that nitrogen signaling may play a pivotal role in regulating TPC in B. napus.

Highlights

Oilseed rape (Brassica napus, 2n = 38, AACC) is one of the most important oil crops in the world.With the ongoing decreases in arable land and increases in human population, crop yield improvement is a highly important goal
Thickness of pod canopy (TPC) is a key trait of B. napus, which can influence other important abundant phenotypes, according to our investigation, such as economic yield (EY, grain weight per plant), plant height (PH), pod terminal height (PTH), stem height (SH), first effective branch height (FVBH), height of the lowest pod (POH), first effective branch number (FVBN), main inflorescence effective length (MIVL), and first effective branch number (FIBN) (Figure 1 and Table S2)
The subjected plants used were taken from two sites on each plant, the stem apex, and a nearby tiny flower bud for transcriptome sequencing (Illumina HiSeq 2000, Illumina, San Diego, CA, USA), generating an average of ~43.47 million clean reads (39.96~50.53 million clean reads) from eight samples, with two biological repeats

Summary

Introduction

One strategy to increase yield is to focus on ideal-type breeding, i.e., plant architecture optimization, which has proved to be useful for improving crop adaptability to different environments and increasing seed and fruit yield [1,2,3,4,5,6]. B. napus plants, with direct relationships with other important traits (Figure 1). Plant architecture (PA) optimization is fundamental for crop yield improvement, but the genetic basis of many architectural traits in B. napus remains unknown. Plant architecture (PA) optimization is fundamental for cropPA yield improvement, the genetic in crop adaptation and yield potential [7,8]. Over the past two decades, numerous genes involved basis of many architectural traits in B. napus remains unknown. PA modifications play significant in plant phenotypic characteristics have been investigated unravel their molecular regulatory roles in crop adaptation and yield potential

Methods

Results

Conclusion