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Plant height, a key agronomic trait, affects crop structure, photosynthesis, and thus the final yield and seed quality. The combination of digital cameras on unmanned aerial vehicles (UAVs) and use of structure from motion have enabled high-throughput crop canopy height estimation. However, the focus of prior research has mainly been on plot-level height prediction, neglecting precise estimations for individual plants. This study aims to explore the potential of UAV RGB images with mask region-based convolutional neural network (Mask-RCNN) for high-throughput phenotyping of individual-level height (IH) in oilseed rape at different growth stages. Field-measured height (FH) of nine sampling plants in each subplot of the 150 subplots was obtained by manual measurement after the UAV flight. An instance segmentation model for oilseed rape with data augmentation based on the Mask-RCNN model was developed. The IHs were then used to obtain plot-level height based on individual-level height (PHIH). The results show that Mask-RCNN performed better than the conventional Otsu method with the F1 score increased by 60.8% and 26.6% under high and low weed pressure, respectively. The trained model with data augmentation achieved accurate crop height estimation based on overexposed and underexposed UAV images, indicating the model's applicability in practical scenarios. The PHIH can be predicted with the determination coefficient (r2) of 0.992, root mean square error (RMSE) of 4.03 cm, relative root mean square error (rRMSE) of 7.68%, which outperformed the results in the reported studies, especially in the late bolting stage. The IHs of the whole growth stages of oilseed can be predicted by this method with an r2 of 0.983, RMSE of 2.60 cm, and rRMSE of 7.14%. Furthermore, this method enabled a comprehensive Genome-wide association study (GWAS) in a 293-accession genetic population. The GWAS identified 200 and 65 statistically significant single nucleotide polymorphisms (SNPs), which were tightly associated with 28 and 11 candidate genes, at the late bolting and flowering stages, respectively. These findings demonstrated that the proposed method is promising for accurate estimations of IHs in oilseed rape as well as exploring the variations within the subplot, thus providing great potential for high-throughput plant phenotyping in crop breeding. [ABSTRACT FROM AUTHOR]

Nitrogen is essential for improving the seed oil yield of rapeseed (Brassica napus L.). However, the molecular mechanism by which increased nitrogen rates impact seed oil content is largely unknown. Therefore, a field experiment was conducted to determine how three nitrogen application rates (120, 240, and 360 kg ha−1) regulated seed oil content via transcriptomic analysis. The results showed that the seed yield and the protein and total N contents increased from N1 to N3, with average increases of 57.2%, 16.9%, and 79.5%, respectively. However, the seed oil content significantly decreased from N1 to N3, with an average decrease of 8.6%. These results were repeated over a number of years. The quantity of oil protein bodies observed under a transmission electron microscope was in accordance with the ultimate seed oil and protein contents. As the nitrogen application rate increased, a substantial number of genes involved in the photosynthesis, glycolysis, and phenylpropanoid biosynthesis pathways were up-regulated, as were TF families, such as AP2/ERF, MYB, and NAC. The newly identified genes were mainly involved in carbohydrate, lipid, and amino acid metabolism. Metabolic flux analysis showed that most of the genes involved in glycolysis and fatty acid biosynthesis had higher transcript levels in the early development stages. Our results provide new insights into the molecular regulation of rapeseed seed oil content through increased nitrogen application rates. [ABSTRACT FROM AUTHOR]

Rapeseed (Brassica napus L.) is a typical polyploid crop and one of the most important oilseed crops worldwide. With the rapid progress on high-throughput sequencing technologies and the reduction in sequencing cost, large-scale genomic data of a specific crop have become available. However, raw sequence data are mostly deposited in the sequence read archive of the National Center of Biotechnology Information and the European Nucleotide Archive, which is freely accessible to all researchers. Extensive tools for practical purposes should be developed to efficiently utilize these large raw data. Here, we report a web-based rapeseed genomic variation database (BnaGVD, http://rapeseed.biocloud.net/home) from which genomic variations, such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) across a worldwide collection of rapeseed accessions, can be referred. The current release of the BnaGVD contains 34,591,899 high-quality SNPs and 12,281,923 high-quality InDels and provides search tools to retrieve genomic variations and gene annotations across 1,007 accessions of worldwide rapeseed germplasm. We implement a variety of built-in tools (e.g. BnaGWAS, BnaPCA and BnaStructure) to help users perform in-depth analyses. We recommend this web resource for accelerating studies on the functional genomics and the screening of molecular markers for rapeseed breeding. [ABSTRACT FROM AUTHOR]

Background: Rapeseed (Brassica napus L.) is an important oil crop world-widely cultivated, and seed oil content (SOC) is one of the most important traits for rapeseed. To increase SOC, many efforts for promoting the function of genes on lipid biosynthesis pathway have been previously made. However, seed oil formation is a dynamic balance between lipid synthesis and breakdown. It is, therefore, also reasonable to weaken or eliminate the function of genes involved in lipid degradation for a higher final SOC. Results: We applied a genome-wide association study (GWAS) on SOC in a collection of 290 core germplasm accessions. A total of 2,705,480 high-quality SNPs were used in the GWAS, and we identified BnaC07g30920D, a patatin-like lipase (PTL) gene, that was associated with SOC. In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region of BnaC07g30920D were associated with the significant reduction of SOC, leading to a 4.7–6.2% reduction of SOCs. We performed in silico analysis to show a total of 40 PTLs, which were divided into four clades, evenly distributed on the A and C subgenomes of Brassica napus. RNA-seq analysis unveiled that BnPTLs were preferentially expressed in reproductive tissues especially maturing seeds. Conclusions: We identified BnaC07g30920D, a BnPTL gene, that was associated with SOC using GWAS and performed in silico analysis of 40 PTLs in Brassica napus. The results enrich our knowledge about the SOC formation in rapeseed and facilitate the future study in functional characterization of BnPTL genes. [ABSTRACT FROM AUTHOR]

Summary: Plant‐based oils are valuable agricultural products, and seed oil content (SOC) is the major yield component in oil crops. Increasing SOC has been successfully targeted through the selection and genetic modification of oil biosynthesis. The SOC in rapeseed declined during the seed maturation and eventually caused the final accumulated seed oil quantity. However, genes involved in oil degradation during seed maturity are not deeply studied so far. We performed a candidate gene association study using a worldwide collection of rapeseed germplasm. We identified SEED FATTY ACID REDUCER (SFAR) genes, which had a significant effect on SOC and fatty acid (FA) composition. SFAR genes belong to the GDSL lipases, and GDSL lipases have a broad range of functions in plants. After quantification of gene expression using RNA‐seq and quantitative PCR, we used targeted (CRISPR‐Cas mediated) and random (chemical) mutagenesis to modify turnover rates of seed oil in winter rapeseed. For the first time, we demonstrate significant increase of SOC in a crop after knocking out members of the BnSFAR4 and BnSFAR5 gene families without pleiotropic effects on seed germination, vigour and oil mobilization. Our results offer new perspectives for improving oil yield by targeted mutagenesis. [ABSTRACT FROM AUTHOR]

Key message: We provided a gene pool of moderate size for selecting or manipulating the candidate genes that favour the acquisition of seed dormancy, shedding light on the elevation of seed oil content in oilseed rape by blocking lipid degradation in developing seeds. In oilseed rape, the association between the germination potential of premature seeds and the final level of seed lipids, and the underlying mechanism, is elusive. Here, we investigated phenotypic differences in the germination percentage of premature seeds in a collection of oilseed rape cultivars. We compared the dynamic lipid accumulation between the deep-, moderate- and non-dormant genotypes and compared the transcriptomes of the seeds at 40 days after pollination between multiple pairs of deep- and non-dormant genotypes. We identified a wide range of differences in germination percentage of premature seeds and the association between the germination potential and the change of fatty acid content at late stage of seed maturation. The comparisons of transcriptomes between deep- and non-dormant seeds revealed the genetic basis for the dormant difference, e.g. the different expression levels of the genes involved in gibberellic and abscisic acid biosynthesis and/or signalling, fatty acid metabolic pathways, and the structure of seed cell wall. We provided a gene pool of moderate size for selecting or manipulating the candidate genes that favour the acquisition of seed dormancy, shedding light on the elevation of seed oil content in oilseed rape by blocking lipid degradation in developing seeds. [ABSTRACT FROM AUTHOR]

Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome‐wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy‐ and glabrous‐leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy‐ and glabrous‐leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy‐leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous‐leaf SAMs. Spraying of exogenous auxin (8 μm) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape. Our genome‐wide association study in oilseed rape identified new genes, such as BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b, that associate with leaf trichome formation, indicating the role of sugar and auxin signalling in leaf trichome initiation of oilseed rape. [ABSTRACT FROM AUTHOR]

Flavonoids are involved in many physiological processes in plants. TRANSPARENT TESTA 4 (TT4) acts at the first step of flavonoid biosynthesis, and the loss of TT4 function causes a lack of flavonoid. Flavonoid deficiency is reportedly the main cause of increased fatty acid content in pale‐coloured oilseeds, but details regarding the relationship between seed flavonoids and fatty acid biosynthesis are elusive. In this work, we applied a genetic strategy combined with biochemical and cytological assays to determine the effect of seed flavonoids on the biosynthesis of fatty acids in Arabidopsis thaliana. We showed that TT4‐mediated flavonoids negatively affect embryonic fatty acid biosynthesis. A crossing experiment indicated that seed flavonoid biosynthesis and the impact of this process on fatty acid biosynthesis were controlled in a maternal line‐dependent manner. Loss of TT4 function activated glycolysis in seed embryos, thereby enhancing fatty acid biosynthesis, but did not improve seed mucilage production. Moreover, loss of TT4 function reduced PIN‐FORMED 4 expression and subsequently increased auxin accumulation in embryos. Pharmacologically and genetically elevated auxin levels enhanced seed fatty acid biosynthesis. These results indicated that flavonoids affect fatty acid biosynthesis by carbon source reallocation via regulation of WRINKLE1 and auxin transport. In this work, we showed that TT4‐mediated flavonoids negatively affect embryonic fatty acid biosynthesis. Flavonoid biosynthesis and its impact on fatty acid biosynthesis were maternally controlled. Flavonoids affect fatty acid biosynthesis by carbon source reallocation with the regulation of WRINKLE1 and auxin transport. [ABSTRACT FROM AUTHOR]