The complete mitochondrial genome sequences of Brassica napus varieties NY18 and 088018

Brassica napus variety NY18 and 088018 are female and male parents of the national registered variety Ningza 1818, respectively. Here, we determined the complete mitochondrial genomes of these two varieties. The genome sizes of NY18 and 088018 were 221,864 bp and 222,015 bp, respectively. Both genomes contained 40 protein-coding genes, 21 tRNA genes, and three rRNA genes. Considerable structural variations existed between the two mitochondrial genomes, which were separated into five syntenic regions. Phylogenetic analysis using the maximum-likelihood method showed that the mitochondrial sequences of B. napus were closely clustered, forming a single clade which had a relatively close relationship with the clade formed by B. rapa, B. juncea, and B. oleracea

Ethylene response factor BnERF2-like (ERF2.4) from Brassica napus L. enhances submergence tolerance and alleviates oxidative damage caused by submergence in Arabidopsis thaliana

Ethylene response factor proteins play an important role in regulating a variety of stress responses in plants, but their exact functions in submergence stress are not well understood. In this study, we isolated BnERF2.4 from Brassica napus L. to study its function in submergence tolerance. The expression of the BnERF2.4 gene in B. napus and the expression of antioxidant enzyme genes in transgenic Arabidopsis were analyzed by quantitative RT-PCR. The expression of BnERF2.4 was induced by submergence in B. napus and the overexpression of BnERF2.4 in Arabidopsis increased the level of tolerance to submergence and oxidative stress. A histochemical method detected lower levels of H2O2, O2•− and malondialdehyde (MDA) in transgenic Arabidopsis. Compared to the wild type, transgenic lines also had higher soluble sugar content and higher activity of antioxidant enzymes, which helped to protect plants against the oxidative damage caused by submergence. It was concluded that BnERF2.4 increased the tolerance of plants to submergence stress and may be involved in regulating soluble sugar content and the antioxidant system in defense against submergence stress

A Novel Method for Long Time Series Passive Microwave Soil Moisture Downscaling over Central Tibet Plateau

The coarse scale of passive microwave surface soil moisture (SSM) is not suitable for regional agricultural and hydrological applications such as drought monitoring and irrigation management. The optical/thermal infrared (OTI) data-based passive microwave SSM downscaling method can effectively improve its spatial resolution to fine scale for regional applications. However, the estimation capability of SSM with long time series is limited by OTI data, which are heavily polluted by clouds. To reduce the dependence of the method on OTI data, an SSM retrieval and spatio-temporal fusion model (SMRFM) is proposed in the study. Specifically, a model coupling in situ data, MODerate-resolution Imaging Spectro-radiometer (MODIS) OTI data, and topographic information is developed to retrieve MODIS SSM (1 km) using the least squares method. Then the retrieved MODIS SSM and the spatio-temporal fusion model are employed to downscale the passive microwave SSM from coarse scale to 1 km. The proposed SMRFM is implemented in a grassland dominated area over Naqu, central Tibet Plateau, for Advanced Microwave Scanning Radiometer—Earth Observing System sensor (AMSR-E) SSM downscaling in unfrozen period. The in situ SSM and Noah land surface model 0.01° SSM are used to validate the estimated MODIS SSM with long time series. The evaluations show that the estimated MODIS SSM has the same temporal resolution with AMSR-E and obtains significantly improved detailed spatial information. Moreover, the temporal accuracy of estimated MODIS SSM against in situ data (r = 0.673, μbRMSE = 0.070 m3/m3) is better than the AMSR-E (r = 0.661, μbRMSE = 0.111 m3/m3). In addition, the temporal r of estimated MODIS SSM is obviously higher than that of Noah data. Therefore, this suggests that the SMRFM can be used to estimate MODIS SSM with long time series by AMSR-E SSM downscaling in the study. Overall, the study can provide help for the development and application of microwave SSM-related scientific research at the regional scale

A Novel Method for Long Time Series Passive Microwave Soil Moisture Downscaling over Central Tibet Plateau

The coarse scale of passive microwave surface soil moisture (SSM) is not suitable for regional agricultural and hydrological applications such as drought monitoring and irrigation management. The optical/thermal infrared (OTI) data-based passive microwave SSM downscaling method can effectively improve its spatial resolution to fine scale for regional applications. However, the estimation capability of SSM with long time series is limited by OTI data, which are heavily polluted by clouds. To reduce the dependence of the method on OTI data, an SSM retrieval and spatio-temporal fusion model (SMRFM) is proposed in the study. Specifically, a model coupling in situ data, MODerate-resolution Imaging Spectro-radiometer (MODIS) OTI data, and topographic information is developed to retrieve MODIS SSM (1 km) using the least squares method. Then the retrieved MODIS SSM and the spatio-temporal fusion model are employed to downscale the passive microwave SSM from coarse scale to 1 km. The proposed SMRFM is implemented in a grassland dominated area over Naqu, central Tibet Plateau, for Advanced Microwave Scanning Radiometer—Earth Observing System sensor (AMSR-E) SSM downscaling in unfrozen period. The in situ SSM and Noah land surface model 0.01° SSM are used to validate the estimated MODIS SSM with long time series. The evaluations show that the estimated MODIS SSM has the same temporal resolution with AMSR-E and obtains significantly improved detailed spatial information. Moreover, the temporal accuracy of estimated MODIS SSM against in situ data (r = 0.673, μbRMSE = 0.070 m3/m3) is better than the AMSR-E (r = 0.661, μbRMSE = 0.111 m3/m3). In addition, the temporal r of estimated MODIS SSM is obviously higher than that of Noah data. Therefore, this suggests that the SMRFM can be used to estimate MODIS SSM with long time series by AMSR-E SSM downscaling in the study. Overall, the study can provide help for the development and application of microwave SSM-related scientific research at the regional scale

Genetic Dissection and Germplasm Selection of the Low Crude Fiber Component in <i>Brassica napus</i> L. Shoots

Background: Brassica napus is one of the most important oil crops in the world, and B. napus shoots are nutrient-rich fresh vegetables. The crude fiber (CF) component is one of the most important factors affecting the taste quality of B. napus shoots, but the factors underlying the desirable low-CF trait remain poorly understood. Methods: In this study, a high-density single-nucleotide polymorphism (SNP) map was used to map quantitative trait loci (QTLs) for five CF-related traits in a recombinant inbred population. Results: A total of 49 QTLs were obtained in four environments, including eleven, twelve, eight, twelve and six QTLs for content of neutral detergent fiber, acid detergent fiber, acid detergent lignin, hemicellulose and cellulose, respectively. The phenotypic variation explained by single QTL ranged from 4.62% to 14.76%. Eight of these QTLs were further integrated into four unique QTLs, which controlled two different traits simultaneously. Five CF-component-related candidate genes were identified, among which BnaC03g07110D and BnaC07g21271D were considered to be the most likely candidate genes. In addition, five lines with low CF content were selected, which can be used as excellent germplasm resources in breeding. Conclusions: The QTLs identified in this study will contribute to our understanding of the genetic mechanism of CF and can be used as targets for reducing CF content in B. napus shoots. In addition, this study also provided excellent germplasm resources for low CF content breeding

Unconditional and conditional QTL analyses of seed fatty acid composition in Brassica napus L.

Abstract Background The fatty acid composition of B. napus’ seeds determines the oil’s nutritional and industrial values, and affects seed germination. Many studies have reported correlations among C16:0, C18:0, C18:1, C18:2 and C18:3 based on phenotypic data; however, the genetic basis of the fatty acid composition in B. napus is still not well understood. Results In this study, unconditional and conditional quantitative trail locus (QTL) mapping analyses were conducted using a recombinant inbred line in six environments. In total, 21 consensus QTLs each for C16:0, C18:0 and C18:2, 16 for C18:1 and 22 for C18:3 were detected by unconditional mapping. The QTLs with overlapping confidence intervals were integrated into 71 pleiotropically unique QTLs by meta-analysis. Two major QTLs, uuqA5–6 and uuqA5–7, simultaneously affected the fatty acids, except C18:0, in most of environments, with the homologous genes fatty acid desaturase 2 (FAD2) and glycerol-3-phosphate sn-2-acyltransferase 5 (GPAT5) occurring in the confidence interval of uuqA5–6, while phosphatidic acid phosphohydrolase 1 (PAH1) was assigned to uuqA5–7. Moreover, 49, 30, 48, 60 and 45 consensus QTLs were detected for C16:0, C18:0, C18:1, C18:2 and C18:3, respectively, by the conditional mapping analysis. In total, 128 unique QTLs were subsequently integrated from the 232 conditional consensus QTLs. A comparative analysis revealed that 63 unique QTLs could be identified by both mapping methodologies, and 65 additional unique QTLs were only identified in conditional mapping. Conclusions Thus, conditional QTL mapping for fatty acids may uncover numerous additional QTLs that were inhibited by the effects of other traits. These findings provide useful information for better understanding the genetic relationships among fatty acids at the QTL level

Quantitative Trait Transcripts Mapping Coupled with Expression Quantitative Trait Loci Mapping Reveal the Molecular Network Regulating the Apetalous Characteristic in Brassica napus L.

The apetalous trait of rapeseed (Brassica napus, AACC, 2n = 38) is important for breeding an ideal high-yield rapeseed with superior klendusity to Sclerotinia sclerotiorum. Currently, the molecular mechanism underlying the apetalous trait of rapeseed is unclear. In this study, 14 petal regulators genes were chosen as target genes (TGs), and the expression patterns of the 14 TGs in the AH population, containing 189 recombinant inbred lines derived from a cross between apetalous “APL01” and normal “Holly,” were analyzed in two environments using qRT-PCR. Phenotypic data of petalous degree (PDgr) in the AH population were obtained from the two environments. Both quantitative trait transcript (QTT)-association mapping and expression QTL (eQTL) analyses of TGs expression levels were performed to reveal regulatory relationships among TGs and PDgr. QTT mapping for PDgr determined that PLURIPETALA (PLP) was the major negative QTT associated with PDgr in both environments, suggesting that PLP negatively regulates the petal development of line “APL01.” The QTT mapping of PLP expression levels showed that CHROMATIN-REMODELING PROTEIN 11 (CHR11) was positively associated with PLP expression, indicating that CHR11 acts as a positive regulator of PLP expression. Similarly, QTT mapping for the remaining TGs identified 38 QTTs, associated with 13 TGs, and 31 QTTs, associated with 10 TGs, respectively, in the first and second environments. Additionally, eQTL analyses of TG expression levels showed that 12 and 11 unconditional eQTLs were detected in the first and second environment, respectively. Based on the QTTs and unconditional eQTLs detected, we presented a hypothetical molecular regulatory network in which 14 petal regulators potentially regulated the apetalous trait in “APL01” through the CHR11-PLP pathway. PLP acts directly as the terminal signal integrator negatively regulating petal development in the CHR11-PLP pathway. These findings will aid in the understanding the molecular mechanism underlying the apetalous trait of rapeseed

DataSheet1_Both organic fertilizer and biochar applications enhanced soil nutrition but inhibited cyanobacterial community in paddy soils.docx

Cyanobacteria plays an important role in other ecological processes in paddy soils, particularly in terms of nitrogen input to the ecosystem. Organic fertilizer and biochar are common soil amendment materials used to preserve soil health in agricultural intensification background. However, the consequent increase in soil nutrition may inhibit soil cyanobacteria, therefore decreasing nitrogen fixation and changes other soil processes. To test this hypothesis, we established a 2 × 2 full factorial experiment in a paddy field in South China, which included four treatments: Ctr (control, receiving no organic fertilization or biochar addition), +OF (organic fertilizer application only), +BC (biochar application only), and +Mix (organic fertilizer and biochar applications). The soil cyanobacterial community was analyzed using metagenomics technology, and 14 soil property variables were measured. The results suggested that organic fertilizer was effective in enhancing nutrient levels, leading to a significant increase in extractable and soluble nitrogen, phosphorus, and potassium. In contrast, biochar application had a stronger effect on total soil carbon, potassium, and soil pH. However, both organic fertilizer and biochar applications induced significant decreases in overall cyanobacterial abundance and species number. Dominant cyanobacterial organisms, particularly the two most abundant genera, Leptolyngbya and Phormidium, experienced a greater decrease compared to others. Canonical correlation analyses and structural equation models indicated that organic fertilizer and biochar applications affected soil cyanobacterial community mainly through soil available nitrogen and pH. In total, the present study highlighted that both organic fertilizer and biochar applications in paddy soils notably change soil physicochemical traits, inhibiting rather than benefiting cyanobacterial microorganisms, especially the dominant ones, and potentially reducing nitrogen input. Our study reveals the impacts of oragnic fertilizer and biochar applications in paddies on soil cyanobacteria and how the consequent changes in soil properties mediate this impact, thereby enhancing our understanding of the responses of different soil microbial groups to soil improvement measures.</p

Additional file 12: of Unconditional and conditional QTL analyses of seed fatty acid composition in Brassica napus L.

Conditional identified QTLs and consensus QTLs obtained for C18:1 in six environments. (XLS 47 kb

Additional file 7: of Unconditional and conditional QTL analyses of seed fatty acid composition in Brassica napus L.

The locations of conditional consensus QTLs associated with fatty acids in the AH map. Conditional consensus QTLs distributed across the C subgenome are shown in this figure, and QTLs on the A subgenome are supplied in Fig. 3. The linkage groups are represented by vertical bars. The locus name and genetic distance are listed on the right and left of the corresponding chromosomes, respectively. The red regions on the linkage groups indicate that these regions harbor QTLs identified by the conditional QTL mapping analysis. Different colors denote different traits as indicated in the bar shown at the lower right corner of the picture. (TIFF 6380 kb