Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato.

The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants.

Interactions between plants and bacterial communities for phytoremediation of petroleum-contaminated soil.

Plants can stimulate the microbes to degrade ubiquitous petroleum hydrocarbons (PHCs), which has prompted a novel view on rhizoremediation. In the present study, the degradation rate of PHCs was investigated and 16S rRNA gene analysis was performed to investigate the PHC-degrading bacteria in petroleum-contaminated soil with different plants. Mirabilis jalapa (M. jalapa) has a higher PHC degradation rate than Lolium perenne (L. perenne) under petroleum contamination. The bacterial diversity in rhizospheric soil was decreased but the relative abundance of Actinobacteriota, Proteobacteria, and Candidatus Saccharibacteria were significant increased on 45 days petroleum-contaminated rhizospheric soil. In addition, the relative expression of PHC degradation-related genes, the content of malic acid and citric acid of the root exudates in the two plants was significantly increased in response to petroleum stress. The content of citric acid increased 11.9 times in M. jalapa and 3.4 times in L. perenne, respectively, in response to petroleum stress. These results indicate that M. jalapa changes the hydrocarbon-degrading microbial community to enhance the degradation of PHCs by root exudates and phytostimulation.

Towards interpretable machine learning for observational quantification of soil heavy metal concentrations under environmental constraints.

Monitoring heavy metal concentrations in soils is central to assessing agricultural production safety. Satellite observations permit inferring concentrations from spectrum, thereby contributing to the prevention and control of soil heavy metal pollution. However, heavy metals exhibit weak spectral responses, particularly at low and medium concentrations, and are predominantly influenced by other soil components. Machine learning (ML)-driven modelling can produce predictions but lacks interpretability. Here, we present an interpretable ML framework for concentration quantification modelling and investigated the contributions of spectral and environmental factors-pH and organic carbon-to the estimation of metals with multiple concentration gradients, as analysed through SHAP (SHapley Additive exPlanations) data derived from four learning-based scenarios. The results indicated that scenarios SHC (spectral, pH, and organic carbon) and SH (spectral and pH) were the most optimal for chromium (Cr) [RPD = 1.42, Adj R2 = 0.62], and cadmium (Cd) [RPD = 1.80, Adj R2 = 0.80]. Under environmental constraints, the spectral predictability for Cr and Cd was improved by 67 % and 87 %, respectively. We concluded that interpretable modelling, utilising both spectral and soil environmental factors, holds significant potential for estimating heavy metals across concentration gradients. It is recommended that samples with higher organic carbon content and lower pH be selected to enhance Cr and Cd predictions. An advanced grasp of interpretable predictions facilitates earlier warning of heavy metal contamination and guides the formulation of robust sampling strategies.

Water optical properties over or around coral reefs in the coastal region: implications for coral reef remote sensing.

Coral reefs inhabit clear oceanic-type waters to turbid coastal regimes. For shallow coastal water environments, the coral reefs from remote sensing will be substantially influenced by the complexity and heterogeneity of the optical properties of water. Through a set of bio-optical and chemical measurements in July 2019 around Xidao Island, Sanya, China, we explored spatial variations of water components' concentrations (including suspended solids, phytoplankton, and dissolved organic carbon) and the optical absorptions (i.e., particulate pigments, detritus, and colored dissolved organic matter) in waters over or around coral reefs; further analysis of their influences upon the remote sensing reflectance (Rrs(λ)) of water was performed. It was observed that the bio-optical and chemical properties of the waters over or around coral reefs were spatially and vertically heterogeneous for different sampling sites. As expected, the suspended solids dominated the optical properties of coral reefs waters in areas of Xidao Island, which evidently influenced the Rrs(λ), especially for the surface waters (Pearson r > 0.60, p < 0.01). In addition, the dissolved organic carbon concentrations exhibited significant relations to the Rrs(λ) both in surface and bottom water layers, whereas the colored dissolved organic matter showed a weak negative correlation with the Rrs(λ). These findings will support the mapping and monitoring benthic habitats with remote sensing imagery in coastal regions, especially when a removal of the influence by particulate sediments was available.

Heterologous expression of MirMAN enhances root development and salt tolerance in Arabidopsis.

Introduction: ß-Mannanase is a plant cell wall remodeling enzyme involved in the breakdown of hemicellulose and plays an important role in growth by hydrolyzing the mannan-like polysaccharide, but its function in adaptation to salt stress has been less studied. Methods: Based on cloned the mannanase (MAN) gene from Mirabilis jalapa L., the study was carried out by heterologously expressing the gene in Arabidopsis thaliana, and then observing the plant phenotypes and measuring relevant physiological and biochemical indicators under 150 mM salt treatment. Results and discussion: The results indicate that MirMAN is a protein with a glycohydrolase-specific structural domain located in the cell wall. We first found that MirMAN reduced the susceptibility of transgenic Arabidopsis thaliana to high salt stress and increased the survival rate of plants by 38%. This was corroborated by the following significant changes, including the reduction in reactive oxygen species (ROS) levels, increase in antioxidant enzyme activity, accumulation of soluble sugars and increase of the expression level of RD29 in transgenic plants. We also found thatthe heterologous expression of MirMAN promoted root growth mainly by elongating the primary roots and increasing the density of lateral roots. Meanwhile, the expression of ARF7, ARF19, LBD16 and LBD29 was up-regulated in the transgenic plants, and the concentration of IAA in the roots was increased. Those results indicate that MirMAN is involved in the initiation of lateral root primordia in transgenic plants through the IAA-ARF signalling pathway. In conclusion, MirMAN improves plant salt tolerance not only by regulating ROS homeostasis, but also by promoting the development of lateral roots. Reflecting the potential of the MirMAN to promote root plastic development in adaptation to salt stress adversity.

Molecular characterization and expression analysis of the remorin genes in tomato (Solanum lycopersicum L.).

Remorin (REMs) are plant-specific and plasma membrane-associated proteins that play an essential role in the growth and development of plants and adaptations to adverse environments. To our knowledge, a genome-scale investigation of the REM genes in tomato has never been systematically studied. In this study, a total of 17 SlREM genes were identified in the tomato genome using bioinformatics methods. Our results demonstrated that the 17 members of SlREM were classified into 6 groups based on phylogenetic analysis and unevenly distributed on the eight chromosomes of tomato. There were 15 REM homologous gene pairs between tomato and Arabidopsis. The SlREM gene structures and motif compositions were similar. Promoter sequence analysis showed that the SlREM gene promoters contained some tissue-specific, hormones and stress-related cis-regulatory elements. Expression analysis based on qRT-PCR (Real-time quantitative PCR) analysis showed that SlREM family genes were were differentially expressed in different tissues, and they responded to ABA, MeJA, SA, low-temperature, drought and NaCl treatments. These results potentially provide relevant information for further research on the biological functions of SlREM family genes.

Coupled retrieval of heavy metal nickel concentration in agricultural soil from spaceborne hyperspectral imagery.

Widespread soil contamination endangers public health and undermines global attempts to achieve the United Nations Sustainable Development Goals. Due to the lack of relevant studies and low precision of spaceborne spectroscopy, estimating soil heavy metal concentrations is challenging. In this study, we developed a coupled retrieval to qualify the heavy metal nickel (Ni) concentration in agricultural soil from spaceborne hyperspectral imagery. The retrieval couples spectral feature extraction from multi-scale discrete wavelet transform (DWT) and dimension reduction (DR), optimal band combination algorithm to five machine learning retrieval models using tree-based ensemble learning, neural network-based, and kernel-based. The comparison between the retrievals and Ni measurements shows that the DWT combined with t-distributed stochastic neighbor embedding (tSNE) coupled extreme gradient boosting (XGboost) retrieval model exhibited the best prediction for the validation dataset. Moreover, due to the integration of six statistical indicators of model performance and the fitted slope of the regression line, the retrieval framework can produce more robust and accurate predictions than those that rely on correlation coefficients. The demonstrated potential of spaceborne hyperspectral remote sensing to provide accurate quantitative measurements of soil heavy metal concentrations will serve as a reference for agricultural plot applications worldwide.

Quantitative proteomics analysis of tomato root cell wall proteins in response to salt stress.

Cell wall proteins perform diverse cellular functions in response to abiotic and biotic stresses. To elucidate the possible mechanisms of salt-stress tolerance in tomato. The 30 d seedlings of two tomato genotypes with contrasting salt tolerances were transplanted to salt stress (200 mM NaCl) for three days, and then, the cell wall proteins of seedling roots were analyzed by isobaric tags for relative and absolute quantification (iTRAQ). There were 82 and 81 cell wall proteins that changed significantly in the salt-tolerant tomato IL8-3 and the salt-sensitive tomato M82, respectively. The proteins associated with signal transduction and alterations to cell wall polysaccharides were increased in both IL8-3 and M82 cells wall in response to salt stress. In addition, many different or even opposite metabolic changes occurred between IL8-3 and M82 in response to salt stress. The salt-tolerant tomato IL8-3 experienced not only significantly decreased in Na+ accumulation but also an obviously enhanced in regulating redox balance and cell wall lignification in response to salt stress. Taken together, these results provide novel insight for further understanding the molecular mechanism of salt tolerance in tomato.

Comprehensive screening of low nitrogen tolerant maize based on multiple traits at the seedling stage.

Background: Plants tolerant to low nitrogen are a quantitative trait affected by many factors, and the different parameters were used for stress-tolerant plant screening in different investigations. But there is no agreement on the use of these indicators. Therefore, a method that can integrate different parameters to evaluate stress tolerance is urgently needed. Methods: Six maize genotypes were subject to low nitrogen stress for twenty days. Then seventeen traits of the six maize genotypes related to nitrogen were investigated. Nitrogen tolerance coefficient (NTC) was calculated as low nitrogen traits to high nitrogen traits. Then principal component analysis was conducted based on the NTC. Based on fuzzy mathematics theory, a D value (decimal comprehensive evaluation value) was introduced to evaluate maize tolerant to low nitrogen. Results: Three maize (SY998, GEMS42-I and GEMS42-II) with the higher D value have better growth and higher nitrogen accumulation under low nitrogen conditions. In contrast, Ji846 with the lowest D value has the lowest nitrogen accumulation and biomass in response to nitrogen limitation. These results indicated that the D value could help to screen low nitrogen tolerant maize, given that the D value was positively correlated with low nitrogen tolerance in maize seedlings. Conclusions: The present study introduced the D value to evaluate stress tolerance. The higher the D value, the greater tolerance of maize to low nitrogen stress. This method may reduce the complexity of the investigated traits and enhance the accuracy of stress-tolerant evaluation. In addition, this method not only can screen potentially tolerant germplasm for low-nitrogen tolerance quickly, but also can comprise the correlated traits as many as possible to avoid the one-sidedness of a single parameter.

Alternative splicing and duplication of PI-like genes in maize.

Alternative splicing and duplication provide the possibility of functional divergence of MADS-box genes. Compared with its Arabidopsis counterpart PI gene, Zmm16 in maize recruits a new role in carpel abortion and floral asymmetry, whereas the other two duplicated genes, Zmm18/29, have not yet been attributed to any function in flower development as a typical B class gene does. Here, alternatively spliced transcripts of three PIL genes were analyzed, among which we described the candidate functional isoforms and analyzed the potential effects of alternative splicing (AS) on protein-protein interactions as well, then their phylogenetic relationships with orthologs in typical grasses were further analyzed. Furthermore, we compared the cis-acting elements specific for three maize PIL genes, especially the elements related to methyl jasmonate (MeJA) and gibberellic acid (GA), both hormones involved in the sex-determination process in maize. Together with the results from the co-expression networks during reproductive organ development, we speculated that, due to duplication and alternative splicing, Zmm18/29 may play a role in GA- and MeJA-related developmental process. These results provide novel clues for experimental validation of the evolutional meaning of maize PIL genes.

Remote Sensing Evaluation of Total Suspended Solids Dynamic with Markov Model: A Case Study of Inland Reservoir across Administrative Boundary in South China.

Accurate and quantitative assessment of the impact of natural environmental changes and human activities on total suspended solids (TSS) concentration is one of the important components of water environment protection. Due to the limits of traditional cross-sectional point monitoring, a novel water quality evaluation method based on the Markov model and remote sensing retrieval is proposed to realize the innovation of large-scale spatial monitoring across administrative boundaries. Additionally, to explore the spatiotemporal characteristics and driving factors of TSS, a new three-band remote sensing model of TSS was built by regression analysis for the inland reservoir using the synchronous field spectral data, water quality samples and remote sensing data in the trans-provincial Hedi Reservoir in the Guangdong and Guangxi Provinces of South China. The results show that: (1) The three-band model based on the OLI sensor explained about 82% of the TSS concentration variation (R2=0.81, N=34,  p value<0.01) with an acceptable validation accuracy (RMSE=6.24 mg/L,MRE=18.02%, N=15), which is basically the first model of its kind available in South China. (2) The TSS concentration has spatial distribution characteristics of high upstream and low downstream, where the average TSS at 31.54 mg/L in the upstream are 2.5 times those of the downstream (12.55 mg/L). (3) Different seasons and rainfall are important factors affecting the TSS in the upstream cross-border area, the TSS in the dry season are higher with average TSS of 33.66 mg/L and TSS are negatively correlated with rainfall from upstream mankind activity. Generally, TSS are higher in rainy seasons than those in dry seasons. However, the result shows that TSS are negatively correlated with rainfall, which means human activities have higher impacts on water quality than climate change. (4) The Markov dynamic evaluation results show that the water quality improvement in the upstream Shijiao Town is the most obvious, especially in 2018, the improvement in the water quality level crossed three levels and the TSS were the lowest. This study provided a technical method for remote sensing dynamic monitoring of water quality in a large reservoir, which is of great significance for remediation of the water environment and the effective evaluation of the river and lake chief system in China.

Using continous wavelet analysis for monitoring wheat yellow rust in different infestation stages based on unmanned aerial vehicle hyperspectral images.

Yellow rust is the most extensive disease in wheat cultivation, seriously affecting crop quality and yield. This study proposes sensitive wavelet features (WFs) for wheat yellow rust monitoring based on unmanned aerial vehicle hyperspectral imagery of different infestation stages [26 days after inoculation (26 DAI) and 42 DAI]. Furthermore, we evaluated the monitoring ability of WFs and vegetation indices on wheat yellow rust through linear discriminant analysis and support vector machine (SVM) classification frameworks in different infestation stages, respectively. The results show that WFs-SVM have promising potential for wheat yellow rust monitoring in both the 26 DAI and 42 DAI stages.

Normalized Method for Land Surface Temperature Monitoring on Coastal Reclaimed Areas.

The temporal analysis of land surface temperature (LST) has generally been studied using data from the same season, as temperature varies greatly over time. However, the cloud cover in thermal remotely sensed images and the coarse resolution of passive sensor system significantly limits data availability of same season for comparative temporal analysis in many parts of the world. To address this problem, we propose a new method for temporal monitoring of surface temperature based on LST normalization (LSTn); deploying the average open water temperature to normalize LST when monitoring temporal change in the surface temperature of newly coastal reclaimed areas. This method was applied in the Lingding Bay area, Guangdong Province, Southern China. Original LST and LSTn values were calculated for years 1987, 1997, 2007, and 2017. In contrast to the original LST, results show that LSTn can reduce seasonal variability when monitoring temporal change in surface temperatures. Additionally, LSTn revealed pronounced differences between the temperature of impervious surfaces and other land cover types. This method offers more robust detection of surface urban heat islands than original LST in newly developed coastal areas.

Recombinant Expression and Bioactivity Comparison of Four Typical Fungal Immunomodulatory Proteins from Three Main Ganoderma Species.

BACKGROUND: More than a dozen of fungal immunomodulatory proteins (FIPs) have been identified to date, most of which are from Ganoderma species. However, little is known about the similarities and differences between different Ganoderma FIPs' bioactivities. In the current study, two FIP genes termed FIP-gap1 and FIP-gap2 from G. applanatum, along with LZ-8 and FIP-gsi, another two representative Ganoderma FIP genes from G. lucidum and G. sinense were functionally expressed in Pichia. Subsequently, bioactivities of four recombinant Ganoderma FIPs were demonstrated and compared. RESULTS: All the four Ganoderma FIP genes could be effectively expressed in P. pastoris GS115 at expression levels ranging from 197.5 to 264.3 mg L- 1 and simply purified by one step chromatography using HisTrap™ FF prepack columns. Amino acid sequence analysis showed that they all possessed the FIP conserved fragments. The homologies of different Ganoderma FIPs were from 72.6 to 86.4%. In vitro haemagglutination exhibited that FIP-gap1, FIP-gsi and LZ-8 could agglutinate human, sheep and mouse red blood cells but FIP-gap2 agglutinated none. Besides, the immunomodulation activities of these Ganoderma FIPs were as: rFIP-gap2 > rFIP-gap1 > rLZ-8 and rFIP-gsi in terms of proliferation stimulation and cytokine induction on murine splenocytes. Additionally, the cytotoxic activity of different FIPs was: rFIP-gap1 > rLZ-8 > rFIP-gsi > rFIP-gap2, examined by their inhibition of three human carcinomas A549, Hela and MCF-7. CONCLUSIONS: Taken together, four typical Ganoderma FIP genes could be functionally expressed in P. pastoris, which might supply as feasible efficient resources for further study and application. Both similarities and differences were indeed observed between Ganoderma FIPs in their amino acid sequences and bioactivities. Comprehensively, rFIP-gaps from G. applanatum proved to be more effective in immunomodulation and cytotoxic assays in vitro than rLZ-8 (G. lucidum) and rFIP-gsi (G. sinense).

Compared the physiological response of two petroleum tolerant-contrasting plants to petroleum stress.

Petroleum not only benefits the world economy but also contaminates the soil. In order to select the plants tolerant to petroleum, the physiological response of two petroleum tolerant-contrasting plants, Mirabilis jalapa and Orychophragmus violace, were investigated in variation of petroleum-contaminated soils (0, 5, 10, 20, and 40 g petroleum per kg soil) for 120 d. Petroleum degradation rate, seeds germination rate, free proline, and superoxide dismutase and peroxidase activities of M. jalapa were higher than that of O. violace under petroleum stress. However, the decrease rate of soluble protein, plant height, chlorophyll, and root fresh weight was greater in O. violace as compared to M. jalapa. Pearson correlation coefficient analysis was conducted, which indicated that the higher tolerance of M. jalapa was correlated with the higher level of free proline and antioxidative enzyme activities. Besides, the 10 g petroleum per kg soil may be appropriate for petroleum-tolerant plants selection, in which petroleum significantly restrain growth in O. violace but not in M. jalapa.

The spatial and temporal variation of total suspended solid concentration in Pearl River Estuary during 1987-2015 based on remote sensing.

The movement and migration of total suspended solid (TSS) are the essential component of global material cycling and change. Based on the TSS concentrations retrieved from 112 scenes of Landsat remote sensing imageries during 1987-2015, the spatial and temporal variations of TSS concentration in high flow season and low flow seasons of six sub-regions (west shoal, west channel, middle shoal, east channel, east shoal and Pearl River Estuary Chinese White Dolphin National Nature Reserve and its adjacent waters (NNR)) of Pearl River Estuary (PRE) were analyzed and compared by statistical simulation. It was found that TSS concentrations in east and west shoals were about 23mg/L and 64mg/L higher than that of the middle shoal, respectively. There was a significant decreasing trend of TSS concentration from the northwest (223.7mg/L) to southeast (51.4mg/L) of study area, with an average reduction of 5.86mg/Lperkm, which mainly attributes to unique interaction of runoff and tide in PRE. In high flow season, there existed a significant and definite annual cycle period (5-8years) of TSS concentration change primarily responding to the periodic variation of precipitation. There were five full-fledged period changes of TSS detected in west shoal and west channel (the years of changes in 1988, 1994, 1998, 2003, 2010, 2015), while there were the last four cycle periods found in middle shoal, east channel, east shoal and NNR only. TSS concentrations in shoals and channels of PRE showed a significant decreased trend mainly due to the dam construction at the same time, with an average annual TSS concentration decrease of 5.7-10.1mg/L in high flow season from 1988 to 2015. There was no significant change trend of TSS concentration in NNR before 2003, but the TSS concentration decreased significantly after the establishment of the NNR since June 2003, with an average annual decrease of 9.7mg/L from 2004 to 2015. It was deduced that man-made protection measures had a great influence on the variation trend and intensity of TSS concentration in PRE, but had little effect on the cycle of TSS changes, indicating that the cyclical change is a very strong natural law. In low flow season, there was no significant change trend of TSS concentrations in PRE except that TSS concentrations in west channel and middle shoal showed a weak increasing trend (2.1mg/L and 2.9mg/L, respectively), which is probably because of controlled discharge for avoiding the intrusion of saltwater in PRE. Evidently, the change trend and cycle periods of TSS concentration in high- and low-flow seasons in six sub-regions of PRE had significant difference. The decreasing trend and cycle periods of TSS concentration mainly occurred in high flow season. The change trend and cycle periods of TSS concentration in low flow season was relatively small in PRE. The study shows that long series mapping of Landsat remote sensing images is an effective way to help understanding the spatial and temporal variation of TSS concentrations of estuaries and coasts, and to increase awareness of environmental change and human activity effects.

Quantitative proteomics analysis reveals the tolerance of Mirabilis jalapa L. to petroleum contamination.

Petroleum is not only an important energy resource but is also a major soil pollutant. To gain better insight into the adaptability mechanism of Mirabilis jalapa to petroleum-contaminated soil, the protein profiles of M. jalapa root were investigated using label-free quantitative proteomics technique. After exposing to petroleum-contaminated soil for 24 h, 34 proteins significantly changed their protein abundance and most of the proteins increased in protein abundance (91.18%). Combined with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as data from previous studies, our results revealed that M. jalapa enhanced tolerance to petroleum by changing antioxidation and detoxification, cell wall organization, amino acid and carbohydrate metabolism, transportation and protein process, and so on. These metabolism alterations could result in the production and secretion of low molecular carbohydrate, amino acid, and functional protein, which enhanced the bioavailability of petroleum and reducing the toxicity of the petroleum. Taken together, these results provided novel information for better understanding of the tolerance of M. jalapa to petroleum stress.

Comparative analysis of Brassica napus plasma membrane proteins under phosphorus deficiency using label-free and MaxQuant-based proteomics approaches.

Phosphorus (P) deficiency is a primary constraint for plant growth in terrestrial ecosystems. To better understand the genotypic differences in the adaptation mechanism of Brassica napus to P deficiency, we purified the plasma membrane (PM) from the roots of two genotypes: P-efficient "Eyou Changjia" and P-inefficient "B104-2". Combining label-free quantitative proteomics with the MaxQuant approach, a total of 71 proteins that significantly changed in abundances were identified in the two genotypes in response to P-free starvation, including 31 in "Eyou Changjia" and 40 in "B104-2". Based on comparative genomics study, 28 proteins were mapped to the confidence intervals of quantitative trait loci (QTLs) for P efficiency related traits. Seven decreased proteins with transporter activity were found to be located in the PM by subcellular localization analyses. These proteins involved in intracellular protein transport and ATP hydrolysis coupled proton transport were mapped to the QTL for P content and dry weight. Compared with "B104-2", more decreased proteins referring to transporter activity were found in "Eyou Changjia", showing that substance exchange was decreased in response to short-term P-free starvation. Together with the finding, more decreased proteins functioning in signal transduction and protein synthesis/degradation suggested that "Eyou Changjia" could slow the progression of growth and save more P in response to short-term P-free starvation. BIOLOGICAL SIGNIFICANCE: P deficiency seriously limits the production and quality of B. napus. Roots absorb water and nutrients and anchor the plant in the soil. Therefore, to study root PM proteome under P stress would be helpful to understand the adaptation mechanism for P deficiency. However, PM proteome analysis in B. napus has been seldom reported due to the high hydrophobicity and low abundance of PM. Thus, we herein investigated the PM proteome alteration of roots in two B. napus genotypes, with different P deficient tolerances, in response to P-free starvation. The present study offers new insights and novel information for better understanding the adaptative response to P deficiency in B. napus.

Data in support of proteomic and comparative genomic analysis reveal adaptability of Brassica napus to phosphorus-deficient stress.

This data article contains data related to the research article titled proteomic and comparative genomic analysis reveal adaptability of Brassica napus to phosphorus-deficient stress [1]. Proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient 'Eyou Changjia' and P-inefficient 'B104-2', under long-term low phosphorus (P) and short-term P-free starvation was investigated, and then comparative gnomic analysis was conducted to interpret the interrelation of the differential abundance protein species responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. The report concluded with the results that nearly 50% of the identified protein species was mapped in the confidence intervals of QTLs for P efficiency related traits. The tables presented here represented the detail information of protein spots detected, as well as protein species identified.

Proteomic and comparative genomic analysis reveals adaptability of Brassica napus to phosphorus-deficient stress.

Given low solubility and immobility in many soils of the world, phosphorus (P) may be the most widely studied macronutrient for plants. In an attempt to gain an insight into the adaptability of Brassica napus to P deficiency, proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient 'Eyou Changjia' and P-inefficient 'B104-2', under long-term low P stress and short-term P-free starvation conditions were investigated, and proteomic combined with comparative genomic analyses were conducted to interpret the interrelation of differential abundance protein species (DAPs) responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. P-efficient 'Eyou Changjia' had higher dry weight and P content, and showed high tolerance to low P stress compared with P-inefficient 'B104-2'. A total of 146 DAPs were successfully identified by MALDI TOF/TOF MS, which were categorized into several groups including defense and stress response, carbohydrate and energy metabolism, signaling and regulation, amino acid and fatty acid metabolism, protein process, biogenesis and cellular component, and function unknown. 94 of 146 DAPs were mapped to a linkage map constructed by a B. napus population derived from a cross between the two genotypes, and 72 DAPs were located in the confidence intervals of QTLs for P efficiency related traits. We conclude that the identification of these DAPs and the co-location of DAPs with QTLs in the B. napus linkage genetic map provide us novel information in understanding the adaptability of B. napus to P deficiency, and helpful to isolate P-efficient genes in B. napus. BIOLOGICAL SIGNIFICANCE: Low P seriously limits the production and quality of B. napus. Proteomics and genetic linkage map were widely used to study the adaptive strategies of B. napus response to P deficiency, proteomic combined with comparative genetic analysis to investigate the correlations between DAPs and QTLs are scarce. Thus, we herein investigated proteome alteration of the roots and leaves in two B. napus genotypes, with different P-deficient tolerances, in response to long-term low P stress and short-term P-free starvation by 2-DE. And comparative genomic was conducted to map the DAPs to the linkage map of B. napus by sequence alignment. The present study offers new insights into adaptability mechanism of B. napus to P deficiency and provides novel information in map-based cloning to isolate the genes in B. napus and scientific improvement of P-efficient in practice.