Transcriptome and Small RNA Sequencing Reveal the Mechanisms Regulating Harvest Index in Brassica napus

Abstract

Harvest index (HI), the ratio of harvested seed weight to total aboveground biomass weight, is an economically critical value reflecting the convergence of complex agronomic traits. HI values in rapeseed (Brassica napus) remain much lower than in other major crops, and the underlying regulatory network is largely unknown. In this study, we performed mRNA and small RNA sequencing to reveal the mechanisms shaping HI in B. napus during the seed-filling stage. A total of 8,410 differentially expressed genes (DEGs) between high-HI and low-HI accessions in four tissues (silique pericarp, seed, leaves, and stem) were identified. Combining with co-expression network, 72 gene modules were identified, and a key gene BnaSTY46 was found to participate in retarded establishment of photosynthetic capacity to influence HI. Further research found that the genes involved in circadian rhythms and response to stimulus may play important roles in HI and that their transcript levels were modulated by differentially expressed microRNAs (DEMs), and we identified 903 microRNAs (miRNAs), including 46 known miRNAs and 857 novel miRNAs. Furthermore, transporter activity-related genes were critical to enhancing HI in good cultivation environments. Of 903 miRNAs, we found that the bna-miR396–Bna.A06SRp34a/Bna.A01EMB3119 pair may control the seed development and the accumulation of storage compounds, thus contributing to higher HI. Our findings uncovered the underlying complex regulatory network behind HI and offer potential approaches to rapeseed improvement.

Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield

“…Therefore, while improving the photosynthetic efficiency, it is also important to improve the transport and distribution capacity of photoassimilates. Collaboration of “source-flow-sink” as the main factor affecting photosynthate allocation, sufficient source, smooth flow, and large storage capacity is the ideal breeding target and helps to maximize the transport and distribution capacity of photosynthates to balance source–sink dynamics [ 46 ]. Numerous studies on source and sink systems have been conducted that can be seen when we search for critical information, but less progress has been made in crops’ understanding of flow and the vascular bundles (mostly the phloem) systems.…”

Identification of miRNAs Interacting with Abscisic Acid to Regulate Fatty Acid Metabolism

“…By sequencing high-and low-oil-content rapeseed seeds, 302 differentially expressed miRNAs were identified, and further analysis through degradation sequencing and bioinformatics revealed that nine target genes may be involved in seed oil synthesis [19]. Analysis of the transcriptomes of different rapeseed varieties with varying harvest indices revealed that miRNAs are associated with the rapeseed harvest index, with bna-miR396 potentially controlling seed development and enhancing the harvest index [20]. In addition to rapeseed, miRNAs involved in oil and lipid biosynthesis have been identified in other oil crops as well.…”