Differentially expressed genes in Populus simonii×Populus nigra in response to NaCl stress using cDNA-AFLP

Salinity is an important environmental factor limiting growth and productivity of plants, and affects almost every aspect of the plant physiology and biochemistry. The objective of this study was to apply cDNA-AFLP and to identify differentially expressed genes in response to NaCl stress vs. no-stress in Populus simonii × Populus nigra in order to develop genetic resources for genetic improvement. Selective amplification with 64 primer combinations allowed the visualization of 4407 transcript-derived fragments (TDFs), and 2027 were differentially expressed. Overall, 107 TDFs were re-sequenced successfully, and 86 unique sequences were identified in 10 functional categories based on their putative functions. A subset of these genes was selected for real-time PCR validation, which confirmed the differential expression patterns in the leaf tissues under NaCl stress vs. no stress. Differential expressed genes will be studied further for association with salt or drought-tolerance in P. simonii×P. nigra. This study suggests that cDNA-AFLP is a useful tool to serve as an initial step for characterizing transcriptional changes induced by NaCl salinity stress in P. simonii×P. nigra and provides resources for further study and application in genetic improvement and breeding. All unique sequences have been deposited in the Genbank as accession numbers GW672587–GW672672 for public use

Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

<p>Abstract</p> <p>Background</p> <p>Lack of sufficient molecular markers hinders current genetic research in peanuts (<it>Arachis hypogaea </it>L.). It is necessary to develop more molecular markers for potential use in peanut genetic research. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining.</p> <p>Results</p> <p>In this study, we investigated 24,238 ESTs for the identification and development of SSR markers. In total, 881 SSRs were identified from 780 SSR-containing unique ESTs. On an average, one SSR was found per 7.3 kb of EST sequence with tri-nucleotide motifs (63.9%) being the most abundant followed by di- (32.7%), tetra- (1.7%), hexa- (1.0%) and penta-nucleotide (0.7%) repeat types. The top six motifs included AG/TC (27.7%), AAG/TTC (17.4%), AAT/TTA (11.9%), ACC/TGG (7.72%), ACT/TGA (7.26%) and AT/TA (6.3%). Based on the 780 SSR-containing ESTs, a total of 290 primer pairs were successfully designed and used for validation of the amplification and assessment of the polymorphism among 22 genotypes of cultivated peanuts and 16 accessions of wild species. The results showed that 251 primer pairs yielded amplification products, of which 26 and 221 primer pairs exhibited polymorphism among the cultivated and wild species examined, respectively. Two to four alleles were found in cultivated peanuts, while 3–8 alleles presented in wild species. The apparent broad polymorphism was further confirmed by cloning and sequencing of amplified alleles. Sequence analysis of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the microsatellite regions. In addition, a few single base mutations were observed in the microsatellite flanking regions.</p> <p>Conclusion</p> <p>This study gives an insight into the frequency, type and distribution of peanut EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated peanut. These EST-SSR markers could enrich the current resource of molecular markers for the peanut community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, and genetic diversity studies in cultivated peanut as well as related <it>Arachis </it>species. All of the 251 working primer pairs with names, motifs, repeat types, primer sequences, and alleles tested in cultivated and wild species are listed in Additional File <supplr sid="S1">1</supplr>.</p> <suppl id="S1"> <title> <p>Additional File 1</p> </title> <text> <p><b>List of EST-SSR primers developed from cultivated peanut ESTs</b>. The file contains a table that lists primer names, repeat motifs, primer sequences, allele number and product length for the newly developed EST-SSR markers.</p> </text> <file name="1471-2229-9-35-S1.xls"> <p>Click here for file</p> </file> </suppl

Impact of sudden stratospheric warmings on the neutral density, temperature and wind in the MLT region

In this study, the neutral density and horizontal wind observed by the four meteor radars, as well as the temperature measured by the Microwave Limb Sounder (MLS) onboard the Aura satellite are used to examine the response of neutral density, wind, and temperature in the MLT region to the stratospheric sudden warmings (SSWs) during 2005 to 2021 in the Northern Hemisphere. The four meteor radars include the Svalbard (78.3°N, 16°E) and Tromsø (69.6°N, 19.2°E) meteor radars at high latitudes and the Mohe (53.5°N, 122.3°E) and Beijing (40.3°N, 116.2°E) meteor radars at middle latitudes. The superposed epoch analysis results indicate that: 1) the neutral density over Svalbard and Tromsø at high latitude increased at the beginning of SSWs and decreased after the zonal mean stratospheric temperature reached the maximum. However, the neutral density over Mohe at midlatitudes decreased in neutral density at the beginning of SSW and increase after the zonal mean stratospheric temperature reached the maximum. 2) The zonal wind at high latitudes show a westward enhancement at the beginning of SSWs and then shows an eastward enhancement after the stratospheric temperature reaches maximum. However, the zonal wind at midlatitudes shows an opposite variation to at high latitudes, with an eastward enhancement at the onset and changing to westward enhancements after the stratospheric temperature maximum. The meridional winds at high and midlatitudes show a southward enhancement after the onset of SSW and then show a northward enhancement after the stratospheric temperature maximum. 3) In general, the temperature in the MLT region decreased throughout SSWs. However, as the latitudes decrease, the temperature cooling appears to lag a few days to the higher latitudes, and the degree of cooling will decrease relatively

Impact of sudden stratospheric warmings on the neutral density, temperature and wind in the MLT region

In this study, the neutral density and horizontal wind observed by the four meteor radars, as well as the temperature measured by the Microwave Limb Sounder (MLS) onboard the Aura satellite are used to examine the response of neutral density, wind, and temperature in the MLT region to the stratospheric sudden warmings (SSWs) during 2005 to 2021 in the Northern Hemisphere. The four meteor radars include the Svalbard (78.3°N, 16°E) and Tromsø (69.6°N, 19.2°E) meteor radars at high latitudes and the Mohe (53.5°N, 122.3°E) and Beijing (40.3°N, 116.2°E) meteor radars at middle latitudes. The superposed epoch analysis results indicate that: 1) the neutral density over Svalbard and Tromsø at high latitude increased at the beginning of SSWs and decreased after the zonal mean stratospheric temperature reached the maximum. However, the neutral density over Mohe at midlatitudes decreased in neutral density at the beginning of SSW and increase after the zonal mean stratospheric temperature reached the maximum. 2) The zonal wind at high latitudes show a westward enhancement at the beginning of SSWs and then shows an eastward enhancement after the stratospheric temperature reaches maximum. However, the zonal wind at midlatitudes shows an opposite variation to at high latitudes, with an eastward enhancement at the onset and changing to westward enhancements after the stratospheric temperature maximum. The meridional winds at high and midlatitudes show a southward enhancement after the onset of SSW and then show a northward enhancement after the stratospheric temperature maximum. 3) In general, the temperature in the MLT region decreased throughout SSWs. However, as the latitudes decrease, the temperature cooling appears to lag a few days to the higher latitudes, and the degree of cooling will decrease relatively

Expression Analysis of Stress-Related Genes in Kernels of Different Maize (Zea mays L.) Inbred Lines with Different Resistance to Aflatoxin Contamination

This research examined the expression patterns of 94 stress-related genes in seven maize inbred lines with differential expressions of resistance to aflatoxin contamination. The objective was to develop a set of genes/probes associated with resistance to A. flavus and/or aflatoxin contamination. Ninety four genes were selected from previous gene expression studies with abiotic stress to test the differential expression in maize lines, A638, B73, Lo964, Lo1016, Mo17, Mp313E, and Tex6, using real-time RT-PCR. Based on the relative-expression levels, the seven maize inbred lines clustered into two different groups. One group included B73, Lo1016 and Mo17, which had higher levels of aflatoxin contamination and lower levels of overall gene expression. The second group which included Tex6, Mp313E, Lo964 and A638 had lower levels of aflatoxin contamination and higher overall levels of gene expressions. A total of six “cross-talking” genes were identified between the two groups, which are highly expressed in the resistant Group 2 but down-regulated in susceptible Group 1. When further subjected to drought stress, Tex6 expressed more genes up-regulated and B73 has fewer genes up-regulated. The transcript patterns and interactions measured in these experiments indicate that the resistant mechanism is an interconnected process involving many gene products and transcriptional regulators, as well as various host interactions with environmental factors, particularly, drought and high temperature

Quaternary vegetation history in Hungary

Detailed information of SSR markers used for genotyping the RIL population. (XLSX 49 kb

Genetic linkage maps of white birches (\u3ci\u3eBetula platyphylla\u3c/i\u3e Suk. and \u3ci\u3eB. pendula\u3c/i\u3e Roth) based on RAPD and AFLP markers

A pseudo-testcross mapping strategy was used in combination with the random amplified polymorphism DNA (RAPD) and amplified fragment length polymorphism (AFLP) genotyping methods to develop two moderately dense genetic linkage maps for Betula platyphylla Suk. (Asian white birch) and B. pendula Roth (European white birch). Eighty F1 progenies were screened with 291 RAPD markers and 451 AFLP markers. We selected 230 RAPD and 362 AFLP markers with 1:1 segregation and used them for constructing the parent-specific linkage maps. The resultant map for B. platyphylla was composed of 226 markers in 24 linkage groups (LGs), and spanned 2864.5 cM with an average of 14.3 cM between adjacent markers. The linkage map for B. pendula was composed of 226 markers in 23 LGs, covering 2489.7 cM. The average map distance between adjacent markers was 13.1 cM. Clustering of AFLP markers was observed on several LGs. The availability of these white birch linkage maps will contribute to the molecular genetics and the implementation of marker-assisted selection in these important forest species

Association of serum selenium with anemia‐related indicators and risk of anemia

Abstract Few studies have examined the association of serum selenium with anemia‐related indicators and risk of anemia. We conducted a cross‐sectional analysis of 2,902 adults in 2003–2004 National Health and Nutrition Examination Survey database. Multivariable linear and logistic regression models were used to examine the association of serum selenium with anemia‐related indicators and risk of anemia. The nonlinear relationship was analyzed using a generalized additive model with the smoothing plot. A total of 1,472 males and 1,430 females with a mean age of 61.94 ± 13.73 years were included. Compared with the lowest quintile, the highest quintile of serum selenium was associated with increased level of serum iron (β = 12.44, 95% confidence interval [CI]: 7.14, 17.75, p < .001), mean corpuscular hemoglobin concentration (MCHC) (β = 0.14, 95%CI: 0.02, 0.26, p = .020), and hemoglobin (β = 0.40, 95%CI: 0.19, 0.61, p < .001), and decreased risk of anemia (odds ratio [OR] = 0.47, 95%CI: 0.28, 0.77, p = .002). Furthermore, smoothed plots suggested the nonlinear relationships between serum selenium and MCHC, hemoglobin level, and risk of anemia. Interestingly, on the left of inflection point, serum selenium was associated with decreased risk of anemia (OR = 0.972, 95%CI: 0.960, 0.985, p < .001), and then, the risk of anemia increased with increasing serum selenium concentration (OR = 1.011, 95%CI: 1.002, 1.021, p = .023). Future large‐scale, polycentric prospective studies should be conducted to verify our results

Potential Candidate Molecule of Photosystem II Inhibitor Herbicide—Brassicanate A Sulfoxide

Brassicanate A sulfoxide, a secondary metabolite of broccoli, exhibited the inhibition of weed growth, but its mechanism of action on weeds remains unclear. To elucidate the mechanism by which brassicanate A sulfoxide suppresses weeds, this study explores the interaction between brassicanate A sulfoxide and the photosystem II D1 protein through molecular docking and molecular dynamics simulations. This research demonstrates that brassicanate A sulfoxide interacts with the photosystem II D1 protein by forming hydrogen bonds with Phe-261 and His-214. The successful expression of the photosystem II D1 protein in an insect cell/baculovirus system validated the molecular docking and dynamics simulations. Biolayer interferometry experiments elucidated that the affinity constant of brassicanate A sulfoxide with photosystem II was 2.69 × 10−3 M, suggesting that brassicanate A sulfoxide can stably bind to the photosystem II D1 protein. The findings of this study contribute to the understanding of the mode of action of brassicanate A sulfoxide and also aid in the development of natural-product-based photosynthesis-inhibiting herbicides

Predicting potential distribution of the Rhinoncus sibiricus under climatic in China using MaxEnt.

In recent years, buckwheat (Fagopyrum spp.) is being increasingly damaged by the Siberian tortoise beetle (Rhinoncus sibiricus Faust). Adults and nymphs feed on leaf tissues and caulicles, thus damaging its stems and leaves. In this study, we investigated the habits, distribution, and environmental impact of R. sibiricus using MaxEnt, an ecological niche model. Geographic information about the infestation site from previous field surveys and climatic data from 2013 to 2018 were organized and optimized using R. The impact factors were calculated using MaxEnt software. The results indicate that population fluctuations in R. sibiricus are related to changes in temperature, humidity, and their spatial distribution. Under current climatic conditions, R. sibiricus is mainly distributed in northern China, with sporadic distribution in south-western China. The values for a survival probability threshold > 0.3 were: precipitation during the wettest month (bio13), 70.31-137.56 mm; mean temperature of the coldest quarter (bio11), -15.00-0.85°C; mean temperature of the warmest quarter (bio10), 11.88-23.16°C; precipitation during the coldest quarter (biol9), 0-24.39 mm. The main factors contributing > 70% to the models were precipitation during the wettest month and coldest quarter, and mean temperature during the warmest and coldest quarters. Under both future climate models, the center of the fitness zone moves northward. Our results will be useful in guiding administrative decisions and support farmers interested in establishing control and management strategies for R. sibiricus. This study could also serve as a reference for future research on other invasive pests