Editorial: Regulation and manipulation of nutrient-controlling genes in crops

Agriculture, food, and health sectors are largely disconnected because little has been done to consider the complex relationship between agricultural production, food consumption, human nutrition, health, and the food supply chain. As society develops, a healthy diet has becoming increasingly important for humans. Unhealthy diets and nutritional imbalance are highly correlated with several common chronic diseases, such as obesity, cardiovascular disease, and some cancers (Lee et al., 2011). The staples of a healthy diet usually come from crops, and the nutritional qualities of these crops, including the chemical composition of food crops, are essential considerations for a healthy diet. For example, the ratio between amylose and amylopectin in rice and the ratio between saturated and unsaturated fatty acids—particularly the percentage of oleic acid—are both related to human health (Goddard et al., 1984; Mozaffarian et al., 2006). Another major issue is the presence, or absence, of some nutritional components that are essential for human health, such as lysine in rice and tocopherol in the oils (Wang and Galili, 2016; Martin and Li, 2017). All of these require a better understanding of genetic regulation and the interaction between those genes encoding these traits (Martin and Li, 2017). This Research Topic focuses on the genetic control of important nutrients in crops, the identification of important QTLs combining large effective modern genetic tools such as GWAS analysis, multiple omics analysis on nutrients, gene-controlling nutrients function assays, and the manipulation of genes, such as gene transferring and genome editing. The aim of this Research Topic is to identify key genes and understand the genetic control of nutrients in order to provide healthy foods for humans. The Research Topic includes three original research articles, one systematic review, and one mini review on the subject of carbohydrate-containing and oil-bearing crops

Dynamic genome evolution in a model fern

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

Floral initiation in response to planting date reveals the key role of floral meristem differentiation prior to budding in canola (Brassica napus L.)

In Brassica napus, floral development is a decisive factor in silique formation, and it is influenced by many cultivation practices including planting date. However, the effect of planting date on floral initiation in canola is poorly understood at present. A field experiment was conducted using a split plot design, in which three planting dates (early, 15 Sep, middle, 1 Oct, and late, 15 Oct) served as main plot and five varieties differing in maturity (1358, J22, Zhongshuang 11, Zheshuang 8, and Zheyou 50) employed as subplot. The purpose of this study was to shed light on the process of floral meristem (FM) differentiation, the influence of planting date on growth period (GP) and floral initiation, and silique formation. The main stages of FM developments can be divided into four stages: first, the transition from shoot apical meristem to FM; second, flower initiation; third, gynoecium and androecium differentiation; and fourth, bud formation. Our results showed that all genotypes had increased GPs from sowing to FM differentiation as planting date was delayed while the GPs from FM differentiation to budding varied year by year except the very early variety, 1358. Based on the number of flowers present at the different reproductive stages, the flowers produced from FM differentiation to budding closely approximated the final silique even though the FM differentiated continuously after budding and peaked generally at the middle flowering stage. The ratio of siliques to maximum flower number ranged from 48% to 80%. These results suggest that (1) the period from FM differentiation to budding is vital for effective flower and silique formation although there was no significant correlation between the length of the period and effective flowers and siliques, and (2) the increased number of flowers from budding were generally ineffective. Therefore, maximizing flower numbers prior to budding will improve silique numbers, and reducing FM degeneration should also increase final silique formation. From the results of our study, we offer guidelines for planting canola varieties that differ in maturity in order to maximize effective flower numbers

Effect of branch position on seed weight and oil content in canola (<i>Brassica napus</i> L.)

Increasing seed weight and oil content are the main pathways to increase canola seed oil yield. The effect of branch position on seed weight and oil content has not been previously reported in canola. Field experiments were conducted to explore the impact of branch position on seed weight and oil content. Four canola genotypes, Zheyou 50, Zhongshuang 11, Zheyou 18, and Zheshuang 8, were used to evaluate seed weight, oil content, carbohydrate profile, and nitrogen content in the main inflorescence and branches from the top to the bottom of the main stem. Seed weight and oil content decreased from the main inflorescence to the lower branches in the four genotypes. Lower carbohydrate and nitrogen content in the seed and low transport efficiency of the two chemical compounds in the silique and branches were responsible for the lower seed weight and oil content in Zheshuang 8 and Zheyou 18, respectively. However, the decreasing seed weight and oil content in the branches did not correspond with decreasing carbohydrate and nitrogen content in the branches from the top to the bottom. The result suggested complex carbohydrate and nitrogen metabolism in the canola seed in the different branches

Multi-Omics Analysis Reveals That Anthocyanin Degradation and Phytohormone Changes Regulate Red Color Fading in Rapeseed (<i>Brassica napus</i> L.) Petals

Flower color is an important trait for the ornamental value of colored rapeseed (Brassica napus L.), as the plant is becoming more popular. However, the color fading of red petals of rapeseed is a problem for its utilization. Unfortunately, the mechanism for the process of color fading in rapeseed is unknown. In the current study, a red flower line, Zhehuhong, was used as plant material to analyze the alterations in its morphological and physiological characteristics, including pigment and phytohormone content, 2 d before flowering (T1), at flowering (T2), and 2 d after flowering (T3). Further, metabolomics and transcriptomics analyses were also performed to reveal the molecular regulation of petal fading. The results show that epidermal cells changed from spherical and tightly arranged to totally collapsed from T1 to T3, according to both paraffin section and scanning electron microscope observation. The pH value and all pigment content except flavonoids decreased significantly during petal fading. The anthocyanin content was reduced by 60.3% at T3 compared to T1. The content of three phytohormones, 1-aminocyclopropanecarboxylic acid, melatonin, and salicylic acid, increased significantly by 2.2, 1.1, and 30.3 times, respectively, from T1 to T3. However, auxin, abscisic acid, and jasmonic acid content decreased from T1 to T3. The result of metabolomics analysis shows that the content of six detected anthocyanin components (cyanidin, peonidin, pelargonidin, delphinidin, petunidin, and malvidin) and their derivatives mainly exhibited a decreasing trend, which was in accordance with the trend of decreasing anthocyanin. Transcriptomics analysis showed downregulation of genes involved in flavonol, flavonoid, and anthocyanin biosynthesis. Furthermore, genes regulating anthocyanin biosynthesis were preferentially expressed at early stages, indicating that the degradation of anthocyanin is the main issue during color fading. The corresponding gene-encoding phytohormone biosynthesis and signaling, JASMONATE-ZIM-DOMAIN PROTEIN, was deactivated to repress anthocyanin biosynthesis, resulting in fading petal color. The results clearly suggest that anthocyanin degradation and phytohormone regulation play essential roles in petal color fading in rapeseed, which is a useful insight for the breeding of colored rapeseed

Chlorophyll and carbohydrate metabolism in developing silique and seed are prerequisite to seed oil content of Brassica napus L.

Background: Although the seed oil content in canola is a crucial quality determining trait, the regulatory mechanisms of its formation are not fully discovered. This study compared the silique and seed physiological characteristics including fresh and dry weight, seed oil content, chlorophyll content, and carbohydrate content in a high oil content line (HOCL) and a low oil content line (LOCL) of canola derived from a recombinant inbred line in 2010, 2011, and 2012. The aim of the investigation is to uncover the physiological regulation of silique and seed developmental events on seed oil content in canola. Results: On average, 83% and 86% of silique matter while 69% and 63% of seed matter was produced before 30 days after anthesis (DAA) in HOCL and LOCL, respectively, over three years. Furthermore, HOCL exhibited significantly higher fresh and dry matter at most developmental stages of siliques and seeds. From 20 DAA, lipids were deposited in the seed of HOCL significantly faster than that of LOCL, which was validated by transmission electron microscopy, showing that HOCL accumulates considerable more oil bodies in the seed cells. Markedly higher silique chlorophyll content was observed in HOCL consistently over the three consecutive years, implying a higher potential of photosynthetic capacity in siliques of HOCL. As a consequence, HOCL exhibited significantly higher content of fructose, glucose, sucrose, and starch mainly at 20 to 45 DAA, a key stage of seed lipid deposition. Moreover, seed sugar content was usually higher than silique indicating the importance of sugar transportation from siliques to seeds as substrate for lipid biosynthesis. The much lower silique cellulose content in HOCL was beneficial for lipid synthesis rather than consuming excessive carbohydrate for cell wall. Conclusions: Superior physiological characteristics of siliques in HOCL showed advantage to produce more photosynthetic assimilates, which were highly correlated to seed oil contents

Effects of Low Nighttime Temperature on Fatty Acid Content in Developing Seeds from <i>Brassica napus</i> L. Based on RNA-Seq and Metabolome

Brassica napus L. is a vital plant oil resource worldwide. The fatty acid biosynthesis and oil accumulation in its seeds are controlled by several genetic and environmental factors, including daytime and nighttime temperatures. We analyzed changes in oleic and erucic acid content in two double haploid (DH) lines, DH0729, a weakly temperature-sensitive line, and DH0815, a strongly temperature-sensitive line, derived from B. napus plants grown at different altitudes (1600, 1800, 2000, 2200, and 2400 m a.s.l., 28.85° N, 112.35° E) and nighttime temperatures (20/18, 20/16, 20/13 and 20/10 °C, daytime/nighttime temperature). Based on medium- and long-chain fatty acid metabolites, the total oleic acid content 35 and 43 days after flowering was significantly lower in low nighttime temperature (LNT, 20/13 °C) plants than in high nighttime temperature (HNT, 20/18 °C) plants (HNT: 58–62%; LNT: 49–54%; an average decrease of 9%), and the total erucic acid content was significantly lower in HNT than in LNT plants (HNT: 1–2%; LNT: 8–13%; an average increase of 10%). An RNA-seq analysis showed that the expression levels of SAD (LOC106366808), ECR (LOC106396280), KCS (LOC106419344), KAR (LOC106367337), HB1(LOC106430193), and DOF5 (LOC111211868) in STSL seeds increased under LNT conditions. In STSL seeds, a base mutation in the cis-acting element involved in low-temperature responsiveness (LTR), the HB1 and KCS promoter caused loss of sensitivity to low temperatures, whereas that of the KCS promoter caused increased sensitivity to low temperatures

Genetic characterization of a new radish introgression line carrying the restorer gene for Ogura CMS in Brassica napus.

Creating a homologous restorer line for Ogura cytoplasmic male sterility (Ogu-CMS) in Brassica napus is meaningful for the wider application of Ogu-CMS system in rapeseed production. Previously, an independent development of a new Ogu-CMS restorer line (CLR650) was reported locally from crossing between Raphanobrassica (AACCRR, 2n = 56) and B. napus and a new version of Ogu CMS lines CLR6430 derived from CLR650 was characterized in this study. The results showed that the fertility restoration gene in CLR6430 presented a distorted segregation in different segregating populations. However, the majority of somatic cells from roots had a regular chromosome number (2n = 38) and no radish signal covered a whole chromosome was detected using GISH. Thirty-two specific markers derived from the introgressed radish fragments were developed based on the re-sequencing results. Unique radish insertions and differences between CLR6430 and R2000 were also identified through both radish-derived markers and PCR product sequences. Further investigations on the genetic behaviors, interactions between the fertility restoration and other traits and specific molecular markers to the introgression in CLR6430 were also conducted in this study. These results should provide the evidence of nucleotide differences between CLR6430 and R2000, and the specific markers will be helpful for breeding new Ogura restore lines in future

Variation of carbohydrates and macronutrients during the flowering stage in canola (Brasscia napus L.) plants with contrasting seed oil content

Determination of dynamics of the physiological traits that affect the seed oil content in canola (Brassica napus L.) is essential for high seed oil content breeding programs. The main purpose of the present experiments was to explore the relationship between seed oil content and carbohydrates, N and P content of various canola aboveground tissues during flowering stage using two recombinant inbred lines RILS. Two field experiments were performed simultaneously in both 2010 and 2011. In experiment 1, seed yield and quality were compared between two RILs with contrasting seed oil content, that is, high oil content line (HOCL) and low oil content line (LOCL) at 50.4% and 41.4%, respectively. In experiment 2, our results showed the HOCL produced markedly more biomass in the reproductive organs by 9.9% and 30% at 35 days after anthesis (DAA) in 2010 and 2011, respectively. Furthermore, compared with LOCL, HOCL accumulated higher fructose, sucrose, and P content in the reproductive organs at the late flowering stage, with an average increment of 85.0%, 31.1%, and 12.4% at 35 DAA, respectively. However, the mean N content in the reproductive organs of HOCL was 17.27% lower than that in LOCL at 35DAA. These results reveal the importance of the higher reproductive organ C/N ratio in the regulation of the higher seed oil content of HOCL. Therefore, the C/N ratio of the reproductive organ may be a useful physiological indicator to screen canola lines for high seed oil content in future breeding program

How Antioxidants, Osmoregulation, Genes and Metabolites Regulate the Late Seeding Tolerance of Rapeseeds (<i>Brassica napus</i> L.) during Wintering

Rapeseed seeding dates are largely delayed under the rice–rape rotation system, but how rapeseeds adapt to the delayed environment remains unclear. Here, five seeding dates (20 October, 30 October, 10 November, 20 November and 30 November, T1 to T5) were set and the dynamic differences between two late-seeding-tolerant (LST) and two late-seeding-sensitive (LSS) rapeseed cultivars were investigated in a field experiment. The growth was significantly repressed and the foldchange (LST/LSS) of yield increased from 1.50-T1 to 2.64-T5 with the delay in seeding. Both LST cultivars showed higher plant coverage than the LSS cultivars according to visible/hyperspectral imaging and the vegetation index acquired from an unmanned aerial vehicle. Fluorescence imaging, DAB and NBT staining showed that the LSS cultivars suffered more stress damage than the LST cultivars. Antioxidant enzymes (SOD, POD, CAT, APX) and osmoregulation substances (proline, soluble sugar, soluble protein) were decreased with the delay in seeding, while the LST cultivar levels were higher than those of the LSS cultivars. A comparative analysis of transcriptomes and metabolomes showed that 55 pathways involving 123 differentially expressed genes (DEGs) and 107 differentially accumulated metabolites (DAMs) participated in late seeding tolerance regulation, while 39 pathways involving 60 DEGs and 68 DAMs were related to sensitivity. Levanbiose, α-isopropylmalate, s-ribosyl-L-homocysteine, lauroyl-CoA and argino-succinate were differentially accumulated in both cultivars, while genes including isocitrate dehydrogenase, pyruvate kinase, phosphoenolpyruvate carboxykinase and newgene_7532 were also largely regulated. This study revealed the dynamic regulation mechanisms of rapeseeds on late seeding conditions, which showed considerable potential for the genetic improvement of rapeseed