Genomic and phenomic predictions help capture low-effect alleles promoting seed germination in oilseed rape in addition to QTL analyses.

KEY MESSAGE: Phenomic prediction implemented on a large diversity set can efficiently predict seed germination, capture low-effect favorable alleles that are not revealed by GWAS and identify promising genetic resources. Oilseed rape faces many challenges, especially at the beginning of its developmental cycle. Achieving rapid and uniform seed germination could help to ensure a successful establishment and therefore enabling the crop to compete with weeds and tolerate stresses during the earliest developmental stages. The polygenic nature of seed germination was highlighted in several studies, and more knowledge is needed about low- to moderate-effect underlying loci in order to enhance seed germination effectively by improving the genetic background and incorporating favorable alleles. A total of 17 QTL were detected for seed germination-related traits, for which the favorable alleles often corresponded to the most frequent alleles in the panel. Genomic and phenomic predictions methods provided moderate-to-high predictive abilities, demonstrating the ability to capture small additive and non-additive effects for seed germination. This study also showed that phenomic prediction estimated phenotypic values closer to phenotypic values than GEBV. Finally, as the predictive ability of phenomic prediction was less influenced by the genetic structure of the panel, it is worth using this prediction method to characterize genetic resources, particularly with a view to design prebreeding populations.

Thiourea improves yield and quality traits of Brassica napus L. by upregulating the antioxidant defense system under high temperature stress.

High temperature stress influences plant growth, seed yield, and fatty acid contents by causing oxidative damage. This study investigated the potential of thiourea (TU) to mitigate oxidative stress and restoring seed oil content and quality in canola. The study thoroughly examined three main factors: (i) growth conditions-control and high temperature stress (35 °C); (ii) TU supplementation (1000 mg/L)-including variations like having no TU, water application at the seedling stage, TU application at seedling stage (BBCH Scale-39), water spray at anthesis stage, and TU application at anthesis stage (BBCH Scale-60); (iii) and two canola genotypes, 45S42 and Hiola-401, were studied separately. High temperature stress reduced growth and tissue water content, as plant height and relative water contents were decreased by 26 and 36% in 45S42 and 27 and 42% Hiola-401, respectively, resulting in a substantial decrease in seed yield per plant by 36 and 38% in 45S42 and Hiola-401. Seed oil content and quality parameters were also negatively affected by high temperature stress as seed oil content was reduced by 32 and 35% in 45S42 and Hiola-401. High-temperature stress increased the plant stress indicators like malondialdehyde, H2O2 content, and electrolyte leakage; these indicators were increased in both canola genotypes as compared to control. Interestingly, TU supplementation restored plant performance, enhancing height, relative water content, foliar chlorophyll (SPAD value), and seed yield per plant by 21, 15, 30, and 28% in 45S42; 19, 13, 26, and 21% in Hiola-401, respectively, under high temperature stress as compared to control. In addition, seed quality, seed oil content, linoleic acid, and linolenic acid were improved by 16, 14, and 22% in 45S42, and 16, 11, and 23% in Hiola-401, as compared to control. The most significant improvements in canola seed yield per plant were observed when TU was applied at the anthesis stage. Additionally, the research highlighted that canola genotype 45S42 responded better to TU applications and exhibited greater resilience against high temperature stress compared to genotype Hiola-401. This interesting study revealed that TU supplementation, particularly at the anthesis stage, improved high temperature stress tolerance, seed oil content, and fatty acid profile in two canola genotypes.

Genetic control of root morphology in response to nitrogen across rapeseed diversity.

Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.

Effect of methyl jasmonate and GA3 on canola (Brassica napus L.) growth, antioxidants activity, and nutrient concentration cultivated in salt-affected soils.

Salinity stress is a significant challenge in agricultural production. When soil contains high salts, it can adversely affect plant growth and productivity due to the high concentration of soluble salts in the soil water. To overcome this issue, foliar applications of methyl jasmonate (MJ) and gibberellic acid (GA3) can be productive amendments. Both can potentially improve the plant's growth attributes and flowering, which are imperative in improving growth and yield. However, limited literature is available on their combined use in canola to mitigate salinity stress. That's why the current study investigates the impact of different levels of MJ (at concentrations of 0.8, 1.6, and 3.2 mM MJ) and GA3 (0GA3 and 5 mg/L GA3) on canola cultivated in salt-affected soils. Applying all the treatments in four replicates. Results indicate that the application of 0.8 mM MJ with 5 mg/L GA3 significantly enhances shoot length (23.29%), shoot dry weight (24.77%), number of leaves per plant (24.93%), number of flowering branches (26.11%), chlorophyll a (31.44%), chlorophyll b (20.28%) and total chlorophyll (27.66%) and shoot total soluble carbohydrates (22.53%) over control. Treatment with 0.8 mM MJ and 5 mg/L GA3 resulted in a decrease in shoot proline (48.17%), MDA (81.41%), SOD (50.59%), POD (14.81%) while increase in N (10.38%), P (15.22%), and K (8.05%) compared to control in canola under salinity stress. In conclusion, 0.8 mM MJ + 5 mg/L GA3 can improve canola growth under salinity stress. More investigations are recommended at the field level to declare 0.8 mM MJ + 5 mg/L GA3 as the best amendment for alleviating salinity stress in different crops.

Genetic dissection of Brassica napus seed vigor after aging.

KEY MESSAGE: Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3 years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78%-17.22% of the phenotypic variance for seed vigor-related traits after aging. We further demonstrated that seed vigor-related traits were positively correlated with oil content (OC) but negatively correlated with unsaturated fatty acids (FAs). Some pleiotropic QTLs that collectively regulate OC, FAs, and seed vigor, such as uq.A8, uq.A3-2, uq.A9-2, and uq.C3-1, were identified. The transcriptomic results from extreme pools of DH lines with distinct seed vigor phenotypes during accelerated aging revealed that various biological pathways and metabolic processes (such as glutathione metabolism and reactive oxygen species) were involved in seed vigor. Through integration of QTL analysis and RNA-Seq, a regulatory network for the control of seed vigor was constructed. Importantly, a candidate (BnaOLE4) from cqSW-C2-3 was selected for functional analysis, and transgenic lines overexpressing BnaOLE4 showed increased seed vigor after artificial aging. Collectively, these results provide novel information on QTL and potential candidate genes for molecular breeding for improved seed storability.

Veterinary antibiotics differ in phytotoxicity on oilseed rape grown over a wide range of concentrations.

Residues of veterinary antibiotics are a worldwide problem of increasing concern due to their persistence and diverse negative effects on organisms, including crops, and limited understanding of their phytotoxicity. Therefore, this study aimed to compare the phytotoxic effects of veterinary antibiotics tetracycline (TC) and ciprofloxacin (CIP) applied in a wide range of concentrations on model plant oilseed rape (Brassica napus). Overall phytotoxicity of 1-500 mg kg-1 of TC and CIP was investigated based on morphological, biochemical, and physiological plant response. Photosystem II (PSII) performance was suppressed by TC even under environmentally relevant concentration (1 mg kg-1), with an increasing effect proportionally to TC concentration in soil. In contrast, CIP was found to be more phytotoxic than TC when applied at high concentrations, inducing a powerful oxidative burst, impairment of photosynthetic performance, collapse of antioxidative protection and sugar metabolism, and in turn, complete growth retardation at 250 and 500 mg kg-1 CIP treatments. Results of our study suggest that TC and CIP pollution do not pose a significant risk to oilseed rapes in many little anthropogenically affected agro-environments where TC or CIP concentrations do not exceed 1 mg kg-1; however, intensive application of manure with high CIP concentrations (more than 50 mg kg-1) might be detrimental to plants and, in turn, lead to diminished agricultural production and a potential risk to human health.

Efficiency of nitrogen, gibberellic acid and potassium on canola production under sub-tropical regions of Pakistan.

The global demand for crop production is rapidly growing due to the continued rise in world population. Crop productivity varies generally with soil nutrient profile and climate. The optimal use of fertilizers might help to attain higher crop yield in canola. To circumvent nutrient imbalance issues in soil, two separate field trials were conducted to determine (a) the best source of nitrogen (N) between ammonium sulfate (NH4)2SO4) and ammonium nitrate (NH4NO3), (b) significance of gibberellic acid (GA3) and potassium (K), in an attempt to enhance canola yield and yield attributes. Both experiments were carried out in randomized complete block design (RCBD) with three replicates. The nitrogen source in the form of NH4)2SO4 (0, 10, 20 and 30 kg/ha) and NH4NO3 (0, 50, 75 and 100 kg/ha) was applied in the rhizosphere after 3 and 7 weeks of sowing, referred to as experiment 1 (E1). In another separate experiment (E2), the canola crop was sprayed with four level of GA3 (0, 10, 15, 30 g/ha) and K (0, 2.5, 3.5, 6 g/ha) individually or in combination by using hydraulic spryer, 30 days after sowing (DAS). The data was collected at different growth stages of canola and analyzed statistically. The E1 trail showed that N fortification in the form of NH4NO3 (100 kg/ha) and (NH4)2SO4 (30 kg/ha) had a positive effect on the plant height, number of branches, fruiting zone, seed yield per plant, seed yield per hectare of canola except oil percentage. Moreover, canola plants (E2) also displayed a significant improvement on all studied features with high doses of GA3 (30 g/ha) and K (6 g/ha) individualy and in combined form. The correlation coefficient analysis of (NH4)2SO4 and NH4NO3 was highly significant to plant height, number of branches, fruiting zone, seed yield per plant, seed yield per hectare of canola In a nutshell, compared to both source of N, NH4NO3 was more efficient and readily available source of N. GA3 being a growth elicitor and potassium as a micronutrient serve as potential source to improve yield and to manage nutrient profile of canola.

Non-specific phospholipase C4 hydrolyzes phosphosphingolipids and phosphoglycerolipids and promotes rapeseed growth and yield.

Phosphorus is a major nutrient vital for plant growth and development, with a substantial amount of cellular phosphorus being used for the biosynthesis of membrane phospholipids. Here, we report that NON-SPECIFIC PHOSPHOLIPASE C4 (NPC4) in rapeseed (Brassica napus) releases phosphate from phospholipids to promote growth and seed yield, as plants with altered NPC4 levels showed significant changes in seed production under different phosphate conditions. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated knockout of BnaNPC4 led to elevated accumulation of phospholipids and decreased growth, whereas overexpression (OE) of BnaNPC4 resulted in lower phospholipid contents and increased plant growth and seed production. We demonstrate that BnaNPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in vitro, and plants with altered BnaNPC4 function displayed changes in their sphingolipid and glycerolipid contents in roots, with a greater change in glycerolipids than sphingolipids in leaves, particularly under phosphate deficiency conditions. In addition, BnaNPC4-OE plants led to the upregulation of genes involved in lipid metabolism, phosphate release, and phosphate transport and an increase in free inorganic phosphate in leaves. These results indicate that BnaNPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in rapeseed to enhance phosphate release from membrane phospholipids and promote growth and seed production.

Winter warming post floral initiation delays flowering via bud dormancy activation and affects yield in a winter annual crop.

Winter annual life history is conferred by the requirement for vernalization to promote the floral transition and control the timing of flowering. Here we show using winter oilseed rape that flowering time is controlled by inflorescence bud dormancy in addition to vernalization. Winter warming treatments given to plants in the laboratory and field increase flower bud abscisic acid levels and delay flowering in spring. We show that the promotive effect of chilling reproductive tissues on flowering time is associated with the activity of two FLC genes specifically silenced in response to winter temperatures in developing inflorescences, coupled with activation of a BRANCHED1-dependent bud dormancy transcriptional module. We show that adequate winter chilling is required for normal inflorescence development and high yields in addition to the control of flowering time. Because warming during winter flower development is associated with yield losses at the landscape scale, our work suggests that bud dormancy activation may be important for effects of climate change on winter arable crop yields.

BABY BOOM regulates early embryo and endosperm development.

The BABY BOOM (BBM) AINTEGUMENTA-LIKE (AIL) AP2/ERF domain transcription factor is a major regulator of plant cell totipotency, as it induces asexual embryo formation when ectopically expressed. Surprisingly, only limited information is available on the role of BBM during zygotic embryogenesis. Here we reexamined BBM expression and function in the model plant Arabidopsis thaliana (Arabidopsis) using reporter analysis and newly developed CRISPR mutants. BBM was expressed in the embryo from the zygote stage and also in the maternal (nucellus) and filial (endosperm) seed tissues. Analysis of CRISPR mutant alleles for BBM (bbm-cr) and the redundantly acting AIL gene PLETHORA2 (PLT2) (plt2-cr) uncovered individual roles for these genes in the timing of embryo progression. We also identified redundant roles for BBM and PLT2 in endosperm proliferation and cellularization and the maintenance of zygotic embryo development. Finally, we show that ectopic BBM expression in the egg cell of Arabidopsis and the dicot crops Brassica napus and Solanum lycopersicon is sufficient to bypass the fertilization requirement for embryo development. Together these results highlight roles for BBM and PLT2 in seed development and demonstrate the utility of BBM genes for engineering asexual embryo development in dicot species.

Salt­responsive transcriptome analysis of canola roots reveals candidate genes involved in the key metabolic pathway in response to salt stress.

Salinity is a major constraint on crop growth and productivity, limiting sustainable agriculture in arid regions. Understanding the molecular mechanisms of salt-stress adaptation in canola is important to improve salt tolerance and promote its cultivation in saline lands. In this study, roots of control (no salt) and 200 mM NaCl-stressed canola seedlings were collected for RNA-Seq analysis and qRT-PCR validation. A total of 5385, 4268, and 7105 DEGs at the three time points of salt treatment compared to the control were identified, respectively. Several DEGs enriched in plant signal transduction pathways were highly expressed under salt stress, and these genes play an important role in signaling and scavenging of ROS in response to salt stress. Transcript expression in canola roots differed at different stages of salt stress, with the early-stages (2 h) of salt stress mainly related to oxidative stress response and sugar metabolism, while the late-stages (72 h) of salt stress mainly related to transmembrane movement, amino acid metabolism, glycerol metabolism and structural components of the cell wall. Several families of TFs that may be associated with salt tolerance were identified, including ERF, MYB, NAC, WRKY, and bHLH. These results provide a basis for further studies on the regulatory mechanisms of salt stress adaptation in canola.

Combined application of zinc and iron-lysine and its effects on morpho-physiological traits, antioxidant capacity and chromium uptake in rapeseed (Brassica napus L.).

Environmental contamination of chromium (Cr) has gained substantial consideration worldwide because of its high levels in the water and soil. A pot experiment using oil seed crop (rapeseed (Brassica napus L.)) grown under different levels of tannery wastewater (0, 33, 66 and 100%) in the soil using the foliar application of zinc (Zn) and iron (Fe)-lysine (lys) has been conducted. Results revealed that a considerable decline in the plant growth and biomass elevates with the addition of concentrations of tannery wastewater. Maximum decline in plant height, number of leaves, root length, fresh and dry biomass of root and leaves were recorded at the maximum level of tannery wastewater application (100%) compared to the plants grown without the addition of tannery wastewater (0%) in the soil. Similarly, contents of carotenoid and chlorophyll, gas exchange parameters and activities of various antioxidants (superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX)) were also reduced significantly (P < 0.05) with the increasing concentration of tannery wastewater (33, 66 and 100%) in the soil. In addition, a combined application of Zn and Fe-lys reduced the accumulation and uptake of toxic Cr, while boosting the uptake of essential micronutrients such as Zn and Fe in different tissues of the plants. Results concluded that exogenous application of micronutrients chelated with amino acid successfully mitigate Cr stress in B. napus. Under field conditions, supplementation with these micronutrient-chelated amino acids may be an effective method for alleviating metal stress in other essential seed crops.

Gene expression profiling reveals transcription factor networks and subgenome bias during Brassica napus seed development.

We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole-genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive-lethal phenotype. Global mRNA profiling revealed lower accumulation of Cn subgenome transcripts relative to the An subgenome. Subgenome-specific transcription factor networks identified distinct transcription factor families enriched in each of the An and Cn subgenomes early in seed development. Analysis of laser-microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the An subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cn subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the An and Cn genomes of the whole B. napus seed can identify valuable targets for seed development research and that -omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.

Role of beneficial microbes with nitrogen and phosphorous levels on canola productivity / Papel de microbes benéficos em associação com níveis de nitrogênio e fósforo na produtividade de canola

A research was conducted to evaluate the impact of various nitrogen and phosphorus levels along with beneficial microbes to enhance canola productivity. The research was carried out at Agronomy Research Farm, The University of Agriculture Peshawar in winter 2016-2017. The experiment was conducted in randomized complete block factorial design. The study was comprised of three factors including nitrogen (60, 120 and 180 kg ha-¹), phosphorous (70, 100 and 130 kg ha-¹) and beneficial microbes (with and without BM). A control treatment with no N, P and BM was also kept for comparison. Application of beneficial microbes significantly increased pods plant, seed pod, seed filling duration, 1000 seed weight, biological yield and seed yield as compared to control plots. Nitrogen applied at the rate of 180 kg ha-¹ increased pods plant-¹, seed pod, seed filling duration, seed weight, biological yield and seed yield. Maximum pods plant-¹, seed pod, early seed filling, heavier seed weight, biological yield, seed yield, and harvest index were observed in plots treated with 130 kg.ha-¹ phosphorous. As comparison, the combine treated plots have more pods plant-¹, seeds pod-¹, seed filling duration, heaviest seeds, biological yield, seed yield and harvest index as compared to control plots. It is concluded that application of beneficial microbes with N and P at the rate of 180 kg ha-¹ and 130 kg ha-¹, respectively, increased yield and its attributes for canola.

Uma pesquisa foi realizada para avaliar o impacto de vários níveis de nitrogênio e fósforo, juntamente com micróbios benéficos, para aumentar a produtividade da canola. A pesquisa foi realizada no inverno de 2016-17 no Agronomy Research Farm, Universidade de Agricultura do Peshawar. O experimento foi conduzido por planejamento fatorial aleatorizado em blocos. O estudo focou-se em três fatores, incluindo o teor de nitrogênio, N, (60, 120 e 180 kg.ha-¹), o teor de fósforo, P, (70, 100 e 130 kg ha-¹) e a presença de micróbios benéficos (com BM e sem BM). Para fins de comparação, um tratamento controle sem N, P e BM também foi incluído no estudo. A aplicação de micróbios benéficos aumentou significativamente as vagens das plantas e de sementes, a duração do enchimento das sementes, o peso de 1000 sementes, o rendimento biológico e o rendimento de sementes em comparação com os resultados do controle. O nitrogênio aplicado na taxa de 180 kg ha-¹ aumentou as vagens por planta, vagem, duração do enchimento, peso da semente, rendimento biológico e rendimento de sementes. Vagens máximas por planta, vagem, enchimento precoce de sementes, peso maior de semente, rendimento biológico, rendimento de sementes e índice de colheita foram observados em parcelas tratadas com 130 kg.ha-¹ de fósforo. Em comparação aos blocos cultivados de controle, os blocos cultivados tratados combinados têm mais vagens por planta e sementes por vagem, maior duração do enchimento das sementes, maior número de sementes mais pesadas e maior rendimento biológico, rendimento de sementes e índice de colheita. Conclui-se que a aplicação de micróbios benéficos junto com N e P nas doses de 180 kg ha-¹ e 130 kg ha-¹, respectivamente, aumentou a produtividade e atributos de produtividade para a canola.

A novel locus (Bnsdt2) in a TFL1 homologue sustaining determinate growth in Brassica napus.

BACKGROUND: The determinate growth habits is beneficial for plant architecture modification and the development of crops cultivars suited to mechanized production systems. Which play an important role in the genetic improvement of crops. In Brassica napus, a determinate inflorescence strain (4769) has been discovered among doubled haploid (DH) lines obtained from a spring B. napus × winter B. napus cross, but there are few reports on it. We fine mapped a determinate inflorescence locus, and evaluated the effect of the determinate growth habit on agronomic traits. RESULTS: In this study, we assessed the effect of the determinate growth habit on agronomic traits. The results showed that determinacy is beneficial for reducing plant height and flowering time, advancing maturity, enhancing lodging resistance, increasing plant branches and maintaining productivity. Genetic analysis in the determinate (4769) and indeterminate (2982) genotypes revealed that two independently inherited recessive genes (Bnsdt1, Bnsdt2) are responsible for this determinate growth trait. Bnsdt2 was subsequently mapped in BC2 and BC3 populations derived from the combination 2982 × 4769. Bnsdt2 could be delimited to an approximately 122.9 kb region between 68,586.2 kb and 68,709.1 kb on C09. BLAST analysis of these candidate intervals showed that chrC09g006434 (BnaC09.TFL1) is homologous to TFL1 of A. thaliana. Sequence analysis of two alleles identified two non-synonymous SNPs (T136C, G141C) in the first exon of BnaC09.TFL1, resulting in two amino acid substitutions (Phe46Leu, Leu47Phe). Subsequently, qRT-PCR revealed that BnaC09.TFL1 expression in shoot apexes was significantly higher in NIL-4769 than in 4769, suggesting its essential role in sustaining the indeterminate growth habit. CONCLUSIONS: In this study, the novel locus Bnsdt2, a recessive genes for determinate inflorescence in B. napus, was fine-mapped to a 68,586.2 kb - 68,709.1 kb interval on C09. The annotated genes chrC09g006434 (BnaC09.TFL1) that may be responsible for inflorescence traits were found.

Quantitative Trait Locus Mapping Combined with RNA Sequencing Reveals the Molecular Basis of Seed Germination in Oilseed Rape.

Rapid and uniform seed germination improves mechanized oilseed rape production in modern agricultural cultivation practices. However, the molecular basis of seed germination is still unclear in Brassica napus. A population of recombined inbred lines of B. napus from a cross between the lower germination rate variety 'APL01' and the higher germination rate variety 'Holly' was used to study the genetics of seed germination using quantitative trait locus (QTL) mapping. A total of five QTLs for germination energy (GE) and six QTLs for germination percentage (GP) were detected across three seed lots, respectively. In addition, six epistatic interactions between the QTLs for GE and nine epistatic interactions between the QTLs for GP were detected. qGE.C3 for GE and qGP.C3 for GP were co-mapped to the 28.5-30.5 cM interval on C3, which was considered to be a novel major QTL regulating seed germination. Transcriptome analysis revealed that the differences in sugar, protein, lipid, amino acid, and DNA metabolism and the TCA cycle, electron transfer, and signal transduction potentially determined the higher germination rate of 'Holly' seeds. These results contribute to our knowledge about the molecular basis of seed germination in rapeseed.

Transcriptome Analysis Reveals Roles of Anthocyanin- and Jasmonic Acid-Biosynthetic Pathways in Rapeseed in Response to High Light Stress.

Rapeseed (Brassica napus) is one of the major important oil crops worldwide and is largely cultivated in the Qinghai-Tibetan plateau (QTP), where long and strong solar-radiation is well-known. However, the molecular mechanisms underlying rapeseed's response to light stress are largely unknown. In the present study, the color of rapeseed seedlings changed from green to purple under high light (HL) stress conditions. Therefore, changes in anthocyanin metabolism and the transcriptome of rapeseed seedlings cultured under normal light (NL) and HL conditions were analyzed to dissect how rapeseed responds to HL at the molecular level. Results indicated that the contents of anthocyanins, especially glucosides of cyanidin, delphinidin, and petunidin, which were determined by liquid chromatography-mass spectrometry (LC-MS), increased by 9.6-, 4.2-, and 59.7-fold in rapeseed seedlings exposed to HL conditions, respectively. Next, RNA-sequencing analysis identified 7390 differentially expressed genes (DEGs), which included 4393 up-regulated and 2997 down-regulated genes. Among the up-regulated genes, many genes related to the anthocyanin-biosynthetic pathway were enriched. For example, genes encoding dihydroflavonol reductase (BnDFR) and anthocyanin synthase (BnANS) were especially induced by HL conditions, which was also confirmed by RT-qPCR analysis. In addition, two PRODUCTION OF ANTHOCYANIN PIGMENTATION 2 (BnPAP2) and GLABRA3 (BnGL3) genes encoding MYB-type and bHLH-type transcription factors, respectively, whose expression was also up-regulated by HL stress, were found to be associated with the changes in anthocyanin biosynthesis. Many genes involved in the jasmonic acid (JA)-biosynthetic pathway were also up-regulated under HL conditions. This finding, which is in agreement with the well-known positive regulatory role of JA in anthocyanin biosynthesis, suggests that the JA may also play a key role in the responses of rapeseed seedlings to HL. Collectively, these data indicate that anthocyanin biosynthesis-related and JA biosynthesis-related pathways mediate HL responses in rapeseed. These findings collectively provide mechanistic insights into the mechanisms involved in the response of rapeseed to HL stress, and the identified key genes may potentially be used to improve HL tolerance of rapeseed cultivars through genetic engineering or breeding strategies.

Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing.

BACKGROUND: Brassica napus is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been used successfully for rapeseed hybrid production in China. MicroRNAs (miRNAs) play crucial regulatory roles in various plant growth, development, and stress response processes. However, reports on miRNAs that regulate the pollen development of GMS lines in B. napus are few. RESULTS: In this study, 12 small RNA and transcriptome libraries were constructed and sequenced for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines, namely, "6251AB" and "6284AB". At the same time, 12 small RNA and transcriptome libraries were also constructed and sequenced for the flower buds from the fertile and sterile lines of two dominant GMS (DGMS) lines, namely, "4001AB" and "4006AB". Based on the results, 46 known miRNAs, 27 novel miRNAs on the other arm of known pre-miRNAs, and 44 new conserved miRNAs were identified. Thirty-five pairs of novel miRNA-3p/miRNA-5p were found. Among all the identified miRNAs, fifteen differentially expressed miRNAs with over 1.5-fold change between flower buds of sterile and fertile lines were identified, including six differentially expressed miRNAs between "4001A" and "4001B", two differentially expressed miRNAs between "4006A" and "4006B", four differentially expressed miRNAs between "6251A" and "6251B", and ten differentially expressed miRNAs between "6284A" and "6284B". The correlation analysis of small RNA and transcriptome sequencing was conducted. And 257 candidate target genes were predicted for the 15 differentially expressed miRNAs. The results of 5' modified RACE indicated that BnaA09g48720D, BnaA09g11120D, and BnaCnng51960D were cleaved by bna-miR398a-3p, bna-miR158-3p and bna-miR159a, respectively. Among the differentially expressed miRNAs, miR159 was chosen to analyze its function. Overexpression of bna-miR159 in Arabidopsis resulted in decreased seed setting rate, and shortened siliques, illustrating that miR159 may regulate the fertility and silique development in rapeseed. CONCLUSIONS: Our findings provide an overview of miRNAs that are potentially involved in GMS and pollen development. New information on miRNAs and their related target genes are provided to exploit the GMS mechanism and reveal the miRNA networks in B. napus.

Sensitivity analysis of the CROPGRO-Canola model in China: A case study for rapeseed.

Increasing domestic rapeseed production is an important national goal in China. Researchers often use tools such as crop models to determine optimum management practices for new varieties to increased production. The CROPGRO-Canola model has not been used to simulate rapeseed in China. The overall goal of this work was to identify key inputs to the CROPGRO-Canola model for calibration with limited datasets in the Yangtze River basin. First, we conducted a global sensitivity analysis to identify key genetic and soil inputs that have a large effect on simulated days to flowering, days to maturity, yield, above-ground biomass, and maximum leaf area index. The extended Fourier amplitude test method (EFAST) sensitivity analysis was performed for a single year at 8 locations in the Yangtze River basin (spatial analysis) and for seven years at a location in Wuhan, China (temporal analysis). The EFAST software was run for 4520 combinations of input parameters for each site and year, resulting in a sensitivity index for each input parameter. Parameters were ranked using the top-down concordance method to determine relative sensitivity. Results indicated that the model outputs of days to flowering, days to maturity, yield, above-ground biomass, and maximum leaf area index were most sensitive to parameters that affect the duration of critical growth periods, such as emergence to flowering, and temperature response to these stages, as well as parameters that affect total biomass at harvest. The five model outputs were also sensitive to several soil parameters, including drained upper and lower limit (SDUL and SLLL) and drainage rate (SLDR). The sensitivity of parameters was generally spatially and temporally stable. The results of the sensitivity analysis were used to calibrate and evaluate the model for a single rapeseed experiment in Wuhan, China. The model was calibrated using two seasons and evaluated using three seasons of data. Excellent nRMSE values were obtained for days to flowering (≤1.71%), days to maturity (≤ 1.48%), yield (≤ 9.96%), and above-ground biomass (≤ 9.63%). The results of this work can be used to guide researchers on model calibration and evaluation across the Yangtze River basin in China.