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

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.

MiRNA-mediated Changes in DNA Methylation Affect the Expression of Genes Involved in the Thickness of Pod Canopy Trait in Brassica Napus

“…Increased methylation in the promoter region of a gene inhibits gene expression, while demethylation in the promoter region of a gene promotes gene expression [39]. We combined the current results with our previously reported transcriptome data [1] and identi ed 26 genes in the high-TPC materials that were signi cantly hypermethylated in their promoter regions compared to the low-TPC materials in B. napus ower buds, resulting in signi cant decreases in their expression ( Fig. 11A and Supplementary Table 1).…”

“…GWAS identi ed four, ve, and seven SNPs for FEBH, FEBN, and PH, respectively, in B. napus and uncovered many genes associated with these traits [5]. We recently reported that TPC is regulated by miRNAs and identi ed many candidate genes for TPC based on RNA-Seq and miRNA pro ling analyses [1]. Many genes involved in nitrogen-related responses were dramatically differentially expressed in high-vs. low-TPC lines, such as ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15 [1], suggesting that nitrogen metabolism plays important roles in regulating TPC in B. napus.…”

“…Thickness of pod canopy (TPC), i.e., the thickness of the plant canopy from the bottom-most effective (seed-bearing) pod to the uppermost effective pod, is a key trait that determines the three-dimensional structure of plants. TPC is directly related to other important traits, such as economic yield (EY, grain weight per plant), plant height (PH), pod terminal height (PTH), stem height (SH), rst effective branch height (FEBH), height of the lowest pod (HLP), rst effective branch number (FEBN), main in orescence effective length (MIEL), and rst uneffective branch number (FUBN) [1]. Hence, understanding the molecular mechanism of TPC could shed light on the formation of plant architecture and help breeders further increase production in B. napus.…”

“…We recently reported that TPC is regulated by miRNAs and identi ed many candidate genes for TPC based on RNA-Seq and miRNA pro ling analyses [1]. Many genes involved in nitrogen-related responses were dramatically differentially expressed in high-vs. low-TPC lines, such as ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15 [1], suggesting that nitrogen metabolism plays important roles in regulating TPC in B. napus. DNA methylation is a critical epigenetic modi cation in many plants.…”

Phenotypic Differences Among and Within Extant Populations of Chrysanthemum Arcticum L. and C. a. Subsp. Arcticum

“…Plant height was measured using a standard ruler (30 cm) placed vertically from the tallest point of the canopy of an in orescence (if owering) or from the tallest leaf (if non owering) to the soil line (base of the plant). In orescence length was measured from the bracts to the top of the plant [51]. The color of each leaf, ower ray oret (petals) and disc oret were determined using the Royal Horticultural Society [24] chart with the visual appearance under natural sunlight in the greenhouse.…”