PXMP4 promotes gastric cancer cell epithelial-mesenchymal transition via the PI3K/AKT signaling pathway.

BACKGROUND: Peroxisomal membrane protein 4 (PXMP4), a member of the peroxisome membrane protein PXMP2/4 family, participates in the progression of several malignant cancers. Nevertheless, the effect of PXMP4 in the development of gastric cancer (GC) is still unknown. As a result, the focus of this investigation was to elucidate the potential mechanisms of PXMP4 in GC. METHODS AND RESULTS: Firstly, bioinformatics analysis results showed higher expression of PXMP4 in GC tissues. Secondly, clinical analysis of 57 patients with GC revealed correlations between PXMP4 expression and differentiation, depth of invasion, as well as TNM stage. Furthermore, individuals with elevated PXMP4 expression in GC exhibited an unfavorable prognosis. In vitro data showed the involvement of knockdown/overexpression of PXMP4 in the proliferation, invasion, and migration of GC cells, and triggering the epithelial-mesenchymal transition (EMT) of GC cells through the activation of the PI3K/AKT signaling pathway. LY294002, a PI3K/AKT inhibitor, inhibited the expression of PI3K/AKT-related proteins but did not affect the expression of PXMP4. CONCLUSIONS: These findings indicate that PXMP4 potentially functions as an upstream molecule in the PI3K/AKT pathway, governing the EMT process in GC.

QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat.

BACKGROUND: Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs. RESULTS: Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation. CONCLUSIONS: Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.

Mapping QTLs for 1000-grain weight and genes controlling hull type using SNP marker in Tartary buckwheat (Fagopyrum tataricum).

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its thick and tough hull, which has greatly limited the development of the Tartary buckwheat processing industry. The construction of high-resolution genetic maps serves as a basis for identifying quantitative trait loci (QTLs) and qualitative trait genes for agronomic traits. In this study, a recombinant inbred lines (XJ-RILs) population derived from a cross between the easily dehulled Rice-Tartary type and Tartary buckwheat type was genotyped using restriction site-associated DNA (RAD) sequencing to construct a high-density SNP genetic map. Furthermore, QTLs for 1000-grain weight (TGW) and genes controlling hull type were mapped in multiple environments. RESULTS: In total, 4151 bin markers comprising 122,185 SNPs were used to construct the genetic linkage map. The map consisted of 8 linkage groups and covered 1444.15 cM, with an average distance of 0.35 cM between adjacent bin markers. Nine QTLs for TGW were detected and distributed on four loci on chromosome 1 and 4. A major locus detected in all three trials was mapped in 38.2-39.8 cM region on chromosome 1, with an LOD score of 18.1-37.0, and explained for 23.6-47.5% of the phenotypic variation. The genes controlling hull type were mapped to chromosome 1 between marker Block330 and Block331, which was closely followed by the major locus for TGW. The expression levels of the seven candidate genes controlling hull type present in the region between Block330 and Block336 was low during grain development, and no significant difference was observed between the parental lines. Six non-synonymous coding SNPs were found between the two parents in the region. CONCLUSIONS: We constructed a high-density SNP genetic map for the first time in Tartary buckwheat. The mapped major loci controlling TGW and hull type will be valuable for gene cloning and revealing the mechanism underlying grain development and easy dehulling, and marker-assisted selection in Tartary buckwheat.

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed.

Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.

Assembly and comparison of two closely related Brassica napus genomes.

As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.

CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics.

The Central Carbon Metabolic Flux Database (CeCaFDB, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. It encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information gathered from hundreds of journal articles. In addition to its comprehensive literature-derived data, the CeCaFDB supports a common text search function among the data and interactive visualization of the curated flux distributions with compartmentation information based on the Cytoscape Web API, which facilitates data interpretation. The CeCaFDB offers four modules to calculate a similarity score or to perform an alignment between the flux distributions. One of the modules was built using an inter programming algorithm for flux distribution alignment that was specifically designed for this study. Based on these modules, the CeCaFDB also supports an extensive flux distribution comparison function among the curated data. The CeCaFDB is strenuously designed to address the broad demands of biochemists, metabolic engineers, systems biologists and members of the -omics community.

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.

KEY MESSAGE: The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.).

KEY MESSAGE: This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations. Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F2 population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.

[High performance liquid chromatography coupled with electrospray tandem mass spectrometry for the analysis of dicyandiamide and melamine residues in milk and milk products].

OBJECTIVE: To establish a sensitive method for the analysis of dicyanodiamide and melamine residue in milk and milk products by, hydrophilic interaction liquid chromatography coupled with electrospray tandem mass spectrometry. METHODS: Samples were extracted with 2.5% (V/V) formic acid solution. Acetonitrile was used to precipitate proteins. The separation was carried on Acquity UPLC BEH Amide column (100 mm x 2.1 mm x 1.7 mm) by gradient elution with acetonitrile - water as mobile phase. Identification was achieved by electrospray ionization (ESI) in positive mode using multiple reaction monitoring, and quantified with external standards. RESULTS: The dicyanodiamide and melamine were linear in the range of 5.0 - 1000.0 µg/L with correlation coefficient of 0.9995 for dicyanodiamide and 0.9997 for melamine. The detection limit of the method were 10.0 µg/kg for dicyanodiamide and melamine. The spiked at three levels ranged 86.0% - 100.0% (0.050 mg/kg), 90.0% - 104.0% (1.0 mg/kg) and 90.0% - 100.1% (10.0 mg/kg). And the relative standard derivations were lower than 1.06% -7.77%. The within-day precisions were 2.35% (dicyanodiamide) and 3.44% (melamine), and the inter-day precision 3.87% (dicyanodiamide) and 5.39% (melamine). CONCLUSION: The method was sensitive, accurate and precise. It can be used in monitoring quality of milk production and daily analysis of milk and milk products.

[Evaluation of nutrient level and its factors of breast milk in Shenzhen City].

OBJECTIVE: To investigate the nutrient level for Fat and Nutrient Elements (Ca, K, Na, Mg, Fe and Zn) in Breast Milk and its factors in Shenzhen, China. Eventually we can evaluate the nutrient study for local infants and provide a more reasonable basis for infants breast-feeding. METHODS: 235 breast milk (1 - 2 months postpartum) samples were collected in three districts of Shenzhen during the year of 2011 to 2013. Fat content was analyzed by Soxlet Extraction System, and elements contents were determined by ICP - OES. RESULTS: The average content of fat was 3.73 g/100 ml. The average concentrations of Ca, K, Na, Mg, Fe and Zn in breast milk from Shenzhen were 296.55, 531.45, 188.96, 28.22, 0.27 and 2.36 mg/L, respectively. CONCLUSION: The average contents of fat and elements of Ca, K in the breast milk from Shenzhen were within the reference ranges provided by the World Health Organization (WHO). However, the levels for element of Fe and Mg were much lower than the reference ranges, and the levels for Na and Zn were relative higher when compared with the standard. No significant difference in six nutrients among three districts in Shenzhen were found, however, the significant difference in each element was found compared with that from other cities or countries. Furthermore Zinc daily intake for local infant reached the level of recommended nutrient intake (RNI), however other nutrients were under the adequate intake level (AI) which was set by Chinese nutrition society (CNS).

Deep Learning Insights into the Dynamic Effects of Photodynamic Therapy on Cancer Cells.

Photodynamic therapy (PDT) shows promise in tumor treatment, particularly when combined with nanotechnology. This study examines the impact of deep learning, particularly the Cellpose algorithm, on the comprehension of cancer cell responses to PDT. The Cellpose algorithm enables robust morphological analysis of cancer cells, while logistic growth modelling predicts cellular behavior post-PDT. Rigorous model validation ensures the accuracy of the findings. Cellpose demonstrates significant morphological changes after PDT, affecting cellular proliferation and survival. The reliability of the findings is confirmed by model validation. This deep learning tool enhances our understanding of cancer cell dynamics after PDT. Advanced analytical techniques, such as morphological analysis and growth modeling, provide insights into the effects of PDT on hepatocellular carcinoma (HCC) cells, which could potentially improve cancer treatment efficacy. In summary, the research examines the role of deep learning in optimizing PDT parameters to personalize oncology treatment and improve efficacy.

A study of the role of multiple layer-by-layer assembled bionic extracellular matrix in promoting wound healing via activation of the Wnt signaling pathway.

Wound healing is a multicellular collaborative process in which the adhesion and proliferation of fibroblasts in the wound is the basis for ensuring rapid wound healing, and in this process, it can promote the regeneration and remodeling of tissue and extracellular matrix. Studies have shown that Arg-Gly-Asp adhesive peptide (RGD) and basic fibroblast growth factor (bFGF) can stimulate the adhesion and proliferation of fibroblasts by activating the Wnt/ß-catenin signaling pathway, respectively. This study adopts the principle of layer-by-layer self-assembly, and the binding force formed by electrostatic attraction and Schiff base was used to combine bFGF and RGD with collagen membrane to form a biomimetic membrane that is non-cytotoxic with strong biocompatibility that could promote soft tissue healing. The surface characteristics of MLCM and the sustained release concentration of bFGF in vitro were measured, and the effects of MLCM on cell viability, proliferation, migration, and wound healing by means of Wnt/catenin pathways were studied through cell experiments and animal experiments under the comparison of negative control groups and positive control groups. The results showed that MLCM could stimulate wound healing more actively and had a positive effect on cell activity, proliferation, and migration. During wound healing, MLCM activates the Wnt/ß-catenin signaling pathway and inhibition of Wnt/ß-catenin signaling pathway significantly reduces the positive effects of MLCM on wound healing.

De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa.

Interspecific hybridization is a significant evolutionary force as well as a powerful method for crop breeding. Partial substitution of the AA subgenome in Brassica napus (A(n) A(n) C(n) C(n) ) with the Brassica rapa (A(r) A(r) ) genome by two rounds of interspecific hybridization resulted in a new introgressed type of B. napus (A(r) A(r) C(n) C(n) ). In this study, we construct a population of recombinant inbred lines of the new introgressed type of B. napus. Microsatellite, intron-based and retrotransposon markers were used to characterize this experimental population with genetic mapping, genetic map comparison and specific marker cloning analysis. Yield-related traits were also recorded for identification of quantitative trait loci (QTLs). A remarkable range of novel genomic alterations was observed in the population, including simple sequence repeat (SSR) mutations, chromosomal rearrangements and retrotransposon activations. Most of these changes occurred immediately after interspecific hybridization, in the early stages of genome stabilization and derivation of experimental lines. These novel genomic alterations affected yield-related traits in the introgressed B. napus to an even greater extent than the alleles alone that were introgressed from the A(r) subgenome of B. rapa, suggesting that genomic changes induced by interspecific hybridization are highly significant in both genome evolution and crop improvement.

Age and gender differences in static and dynamic balance of Chinese preschool children.

Objectives: Balance is a crucial ability of early age, but there is conflicting evidence with regard to age and gender differences in preschool children's balance ability. Additionally, there are several tools available to measure balance, yet, wide variation in their use has restricted the capacity to synthesize the reference values. Therefore, the primary purpose of this study was to investigate the balance ability of preschool-aged children and determine how it is moderated by age and gender. The analysis pertained to determining whether different testing methods affect the results of static or dynamic balancing ability to provide a basis for normative balance ability data for healthy boys and girls between 3 and 6 years of age. Method: Six hundred and nineteen preschool children (296 boys and 323 girls) aged 3-6 years participated in the study. The static balance (SB) was assessed with children standing on one leg (OST) and in a tandem stance (TS) with respect to time. The balance beam test (BBT) and functional reach test (FRT) were used to evaluate dynamic balance (DB) by measuring the time spent and the distance reached, respectively. Result: The results revealed significant differences in OST with respect to gender (η2 = 0.037, p < 0.001), TS (η2 = 0.026, p < 0.001) and FRT (η2 = 0.016, p = 0.002); the girls performed better than boys on most balance tests except on BBT (η2 = 0.000, p = 0.596). Age had positive effects on the static and dynamic balance performance on the OST (η2 = 0.336, p < 0.001), TS (η2 = 0.205, p < 0.001), BBT (η2 = 0.367, p < 0.001) and FRT (η2 = 0.392, p < 0.001). Older children performed better than their younger counterparts. No significant interactions between age groups and sex were found. Conclusion: This study revealed that static and dynamic balance stability in preschool-aged children was affected by gender and age. Gender dimorphism is present in preschool children, older girls displayed better postural stability than boys, and balance performance improved with age. In addition, the study provides age- and gender-specific balance performance reference values for preschool children across multiple methods, which can be used to monitor static and dynamic balance development.

The compensation incentive effect of athletes: A structural equation model.

This study explores the compensation incentive effect of athletes. Based on the related literature, we proposed theoretical hypotheses on the compensation incentive effect and established an assessment index system of the compensation incentive effect for athletes. A structural equation model was used to test the survey data of 352 athletes in six provinces to discover the truth of the compensation incentive effect. The results suggested that direct economic compensation satisfaction, direct non-economic compensation satisfaction, and indirect non-economic compensation satisfaction had significant positive effects on the compensation incentive effect of athletes, while indirect economic compensation satisfaction showed no significant effect. Moreover, the evaluation results of athletes' compensation incentive effect showed that direct economic compensation satisfaction contributed the most to the influence factor of the compensation incentive effect. Therefore, the evaluation of athletes' compensation incentive effect should focus on variables of direct economic compensation satisfaction, i.e., basic compensation satisfaction, bonus income satisfaction, and subsidy satisfaction. Finally, some strategies and recommendations were suggested to improve the compensation design for athletes.

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq.

BACKGROUND: The complete and accurate human reference genome is important for functional genomics researches. Therefore, the incomplete reference genome and individual specific sequences have significant effects on various studies. RESULTS: we used two RNA-Seq datasets from human brain tissues and 10 mixed cell lines to investigate the completeness of human reference genome. First, we demonstrated that in previously identified ~5 Mb Asian and ~5 Mb African novel sequences that are absent from the human reference genome of NCBI build 36, ~211 kb and ~201 kb of them could be transcribed, respectively. Our results suggest that many of those transcribed regions are not specific to Asian and African, but also present in Caucasian. Then, we found that the expressions of 104 RefSeq genes that are unalignable to NCBI build 37 in brain and cell lines are higher than 0.1 RPKM. 55 of them are conserved across human, chimpanzee and macaque, suggesting that there are still a significant number of functional human genes absent from the human reference genome. Moreover, we identified hundreds of novel transcript contigs that cannot be aligned to NCBI build 37, RefSeq genes and EST sequences. Some of those novel transcript contigs are also conserved among human, chimpanzee and macaque. By positioning those contigs onto the human genome, we identified several large deletions in the reference genome. Several conserved novel transcript contigs were further validated by RT-PCR. CONCLUSION: Our findings demonstrate that a significant number of genes are still absent from the incomplete human reference genome, highlighting the importance of further refining the human reference genome and curating those missing genes. Our study also shows the importance of de novo transcriptome assembly. The comparative approach between reference genome and other related human genomes based on the transcriptome provides an alternative way to refine the human reference genome.

Structural and functional comparative mapping between the Brassica A genomes in allotetraploid Brassica napus and diploid Brassica rapa.

Brassica napus (AACC genome) is an important oilseed crop that was formed by the fusion of the diploids B. rapa (AA) and B. oleracea (CC). The complete genomic sequence of the Brassica A genome will be available soon from the B. rapa genome sequencing project, but it is not clear how informative the A genome sequence in B. rapa (A(r)) will be for predicting the structure and function of the A subgenome in the allotetraploid Brassica species B. napus (A(n)). In this paper, we report the results of structural and functional comparative mapping between the A subgenomes of B. napus and B. rapa based on genetic maps that were anchored with bacterial artificial chromosomes (BACs)-sequence of B. rapa. We identified segmental conservation that represented by syntenic blocks in over one third of the A genome; meanwhile, comparative mapping of quantitative trait loci for seed quality traits identified a dozen homologous regions with conserved function in the A genome of the two species. However, several genomic rearrangement events, such as inversions, intra- and inter-chromosomal translocations, were also observed, covering totally at least 5% of the A genome, between allotetraploid B. napus and diploid B. rapa. Based on these results, the A genomes of B. rapa and B. napus are mostly functionally conserved, but caution will be necessary in applying the full sequence data from B. rapa to the B. napus as a result of genomic rearrangements in the A genome between the two species.

Estimating the impact of ground ozone concentrations on crop yields across China from 2014 to 2018: A multi-model comparison.

Ground level ozone exerts a strong impact on crop yields, yet how to properly quantify ozone induced yield losses in China remains challenging. To this end, we employed a series of O3-crop models to estimate ozone induced yield losses in China from 2014 to 2018. The outputs from all models suggested that the total Relative Yield Losses (RYL) of wheat in China from 2014 to 2018 was 18.4%-49.3% and the total RYL of rice was 6.2%-52.9%. Consequently, the total Crop Production Losses (CPL) of wheat and rice could reach 63.9-130.4 and 28.3-35.4 million tons, and the corresponding Total Economic Losses (TEL) could reach 20.5-44.7 and 11.0-15.3 billion dollars, stressing the great importance and urgency of national ozone management. Meanwhile, the estimation outputs highlighted the large variations between different regional O3-crop models when applying to large scales. Instead of applying one unified O3-crop models to all regions across China, we also explored the strategy of employing specific O3-crop models in corresponding (and neighboring) regions to estimate ozone induced yield loss in China. The comparison of two strategies suggested that the mean value from multiple models may still present an inconsistent over/underestimation trend for different crops. Therefore, it is a preferable strategy to employ corresponding O3-crop models in different regions for estimating the national crop losses caused by ozone pollution. However, the severe lack of regional O3-crop models in most regions across China makes a robust estimation of national yield losses highly challenging. Given the large variations between O3-crop interactions across regions, a systematic framework with massive regional O3-crop models should be properly designed and implemented.

Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa.

BACKGROUND: The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). RESULTS: In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. CONCLUSION: The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napus.

Yield is the most important and complex trait for the genetic improvement of crops. Although much research into the genetic basis of yield and yield-associated traits has been reported, in each such experiment the genetic architecture and determinants of yield have remained ambiguous. One of the most intractable problems is the interaction between genes and the environment. We identified 85 quantitative trait loci (QTL) for seed yield along with 785 QTL for eight yield-associated traits, from 10 natural environments and two related populations of rapeseed. A trait-by-trait meta-analysis revealed 401 consensus QTL, of which 82.5% were clustered and integrated into 111 pleiotropic unique QTL by meta-analysis, 47 of which were relevant for seed yield. The complexity of the genetic architecture of yield was demonstrated, illustrating the pleiotropy, synthesis, variability, and plasticity of yield QTL. The idea of estimating indicator QTL for yield QTL and identifying potential candidate genes for yield provides an advance in methodology for complex traits.