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The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

Rapeseed (Brassica napus L.) seedlings suffering from inappropriate growth substrate stress will present poor seedling quality. However, the regulatory mechanism for the production and scavenging of reactive oxygen species (ROS) caused by this type of stress remains unclear. In the current study, a split plot experiment design was implemented with two crop growth substrates—a rice growth substrate (RIS) and rapeseed growth substrate (RAS)—as the main plot and two genotypes—a hybrid and an open-pollinated variety (Zheyouza 1510 and Zheyou 51, respectively)—as the sub-plot. The seedling quality was assessed, and the ROS production/scavenging capacity was evaluated. Enzymatic and non-enzymatic systems, including ascorbic acid and glutathione metabolism, and RNA-seq data were analyzed under the two growth substrate treatments. The results revealed that rapeseed seedling quality decreased under RIS, with the plant height, maximum leaf length and width, and aboveground dry matter being reduced by 187.7%, 64.6%, 73.2%, and 63.8% on average, respectively, as compared to RAS. The main type of ROS accumulated in rapeseed plants was hydrogen peroxide, which was 47.8% and 14.1% higher under RIS than under RAS in the two genotypes, respectively. The scavenging of hydrogen peroxide in Zheyouza 1510 was the result of a combination of enzymatic systems, with significantly higher peroxidase (POD) and catalase (CAT) activity as well as glutathione metabolism, with significantly higher reduced glutathione (GSH) content, under RAS, while higher oxidized glutathione (GSSH) was observed under RIS. However, the scavenging of hydrogen peroxide in Zheyou 51 was the result of a combination of elevated oxidized ascorbic acid (DHA) under RIS and higher GSH content under RAS. The identified gene expression levels were in accordance with the observed enzyme expression levels. The results suggest that the cost of substituting RAS with RIS is a reduction in rapeseed seedling quality contributing to excessive ROS production and a reduction in ROS scavenging capacity. [ABSTRACT FROM AUTHOR]

Yield prediction is an important agriculture management for crop policy making. In recent years, unmanned aerial vehicles (UAVs) and spectral sensor technology have been widely used in crop production. This study aims to evaluate the ability of UAVs equipped with spectral sensors to predict oilseed rape yield. In an experiment, RGB and hyperspectral images were captured using a UAV at the seedling (S1), budding (S2), flowering (S3), and pod (S4) stages in oilseed rape plants. Canopy reflectance and spectral indices of oilseed rape were extracted and calculated from the hyperspectral images. After correlation analysis and principal component analysis (PCA), input spectral indices were screened to build yield prediction models using random forest regression (RF), multiple linear regression (MLR), and support vector machine regression (SVM). The results showed that UAVs equipped with spectral sensors have great potential in predicting crop yield at a large scale. Machine learning approaches such as RF can improve the accuracy of yield models in comparison with traditional methods (e.g., MLR). The RF-based training model had the highest determination coefficient (R2) (0.925) and lowest relative root mean square error (RRMSE) (5.91%). In testing, the MLR-based model had the highest R2 (0.732) and lowest RRMSE (11.26%). Moreover, we found that S2 was the best stage for predicting oilseed rape yield compared with the other growth stages. This study demonstrates a relatively accurate prediction for crop yield and provides valuable insight for field crop management. [ABSTRACT FROM AUTHOR]

Ogura cytoplasmic male sterility (CMS) is considered the rapeseed (Brassica napus L.) with the most potential to be utilized as a heterosis system worldwide, but it lacks sufficient restorers. In this study, root tip cell (RTC) mitotic and pollen mother cell (PMC) meiosis observations were compared to ensure the number of chromosomes and the formation of a chromosomal bridge using restorer lines R2000, CLR650, and Zhehuhong (a new restorer) as the experimental material. Further, molecular markers of exogenous chromosomal fragments were detected and the sequence and expression differences of restorer genes in the three lines were determined to identify the distinctive characteristics of Zhehuhong. The results showed that the number of chromosomes in Zhehuhong was stable (2n = 38), indicating that the exogenous radish chromosome segment had been integrated into the chromosome of Zhehuhong. Molecular marker detection revealed that Zhehuhong was detected at most loci, with only the RMA05 locus being missed. The exogenous radish chromosome segment of Zhehuhong differed from R2000 and CLR650. The pollen mother cells of Zhehuhong showed chromosome lagging in the meiotic metaphase I, meiotic anaphase I, and meiotic anaphase II, which was consistent with R2000 and CLR650. The restorer gene PPRB in Zhehuhong had 85 SNPs compared with R2000 and 119 SNPs compared with CLR650, indicating the distinctive characteristic of PPRB in Zhehuhong. In terms of the spatial expression of PPRB, the highest level was detected in the anthers in the three restorer lines. In addition, in terms of temporal expression, the PPRB gene expression of Zhehuhong was highest at a bud length of 4 mm. Our results clearly indicated that Zhehuhong is a new restorer line for the Ogura CMS system, which can be used further in rapeseed heterosis utilization. [ABSTRACT FROM AUTHOR]

The molecular mechanisms underlying anthocyanin-based flower coloration remain unknown in Brassica napus. To identify the key genes and metabolites associated with apricot and pink flower colors, metabolome, BSA-seq, and RNA-seq analyses were conducted on apricot-, pink-, yellow-, and white-flowered F2 B. napus. Yellow carotenoids and red anthocyanins were abundant in apricot petals, while colorless carotenoids and red anthocyanins accumulated in pink petals. Most carotenoid genes were not differentially regulated between apricot and yellow or between pink and white petals. Three regulator genes, BnaMYBL2 , BnaA07.PAP2 , and BnaTT8 , and structural genes in anthocyanin biosynthesis were dramatically enhanced in apricot and pink petals in comparison with yellow and white petals. Map-based cloning revealed that BnaA07.PAP2 is responsible for anthocyanin-based flower color and encodes a nucleus-localized protein predominantly expressed in apricot and pink flowers. Two insertions in the promoter region are responsible for the transcriptional activation of BnaA07.PAP2 in flowers. Introducing the BnaA07.PAP2 In-184-317 allele broadly activated the expression of anthocyanin-related genes and promoted anthocyanin accumulation in flowers, yielding color change from yellow to apricot. These findings illustrate the genetic basis of anthocyanin-based flower coloration and provide a valuable genetic resource for breeding varieties with novel flower colors in B. napus. [ABSTRACT FROM AUTHOR]

Naturally colored cotton (Gossypium hirsutum L.) fibers (CCFs) are eco-friendly for the textile industry because they omit the dyeing process and reduce harmful effluent liquor. However, the low yield and quality of CCFs have greatly affected their development. Limited information is available on the reasons for the low yield and quality of CCFs. The aim of this 2-yr investigation was to compare variations in chlorophyll concentration, net photosynthesis rate, monosaccharide concentration, and fiber yield and quality among white-fiber cotton (WFC), brown-fiber cotton (BFC), and green-fiber cotton (GFC). White-fiber cotton had the highest lint yield, which was on average 33.6 and 41.9% higher than that of BFC and GFC, respectively. Other yield components such as boll number and boll weight had similar trends in both years. The fiber length of GFC and BFC was reduced by 17.4 and 11.1%, respectively, compared with that of WFC. These results indicated that GFC had the lowest fiber yield and quality. Leaf chlorophyll concentration, net photosynthesis rate, and fructose and glucose concentrations of GFC were slightly higher than those of WFC, indicating its active photosynthesis. However, its vigorous vegetative growth had reduced its reproductive growth, partly resulting in low yield and quality. Brown-fiber cotton had the lowest leaf chlorophyll concentration and other photosynthetic indexes, leading to a lower amount of photosynthetic product and, hence, yield and quality.

Naturally colored cotton (Gossypium hirsutum L.) fibers (CCFs) are of interest in the textile industry because they require little dyeing and result in less environmental pollution. Pigmentation is one of the most important factors that differentiate CCFs from white cotton fiber (WCF) during fiber maturation. Many factors are involved in pigmentation, some of which we compared between CCFs and WCF with isogenetic backgrounds. These included the type of pigment, the activity of phenylalanine ammonia lyase (PAL), the concentration of total carbohydrates, and the type of soluble saccharide. We aimed to determine the causes of different fiber colors and found that flavonoids were the dominant type of pigment in the CCFs. At maturity (50 d post anthesis [DPA]), the WCF had only about 1/3 the amount of flavonoids as the brown cotton fiber (BCF) and 1/10 that of the green cotton fiber (GCF). During the course of fiber maturation (in particular, the stage before 8 DPA), CCFs had much higher PAL activity than the WCF. Of the fibers, the GCF had the highest concentration of carbohydrates over the course of maturation. However, higher concentrations of total carbohydrates did not always lead to higher concentrations of cellulose. This was very likely due to the synthesis of flavonoids and their derivatives consuming a large amount of carbohydrates that otherwise might be used for the synthesis of cellulose.

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]