Genomic analysis of a major seed protein/oil QTL region on soybean linkage group I

The economic and nutritional value of soybeans is determined by its seed protein and oil contents. The genetic control of seed protein/oil is quantitative and many genomic regions associated with the regulation of these traits have been identified in soybean. The protein/oil quantitative trait locus (QTL) mapped to LG I (chromosome 20) is ubiquitous among high protein soybean lines. Identification of the candidate gene(s) underlying this major QTL would help us understand the genetic and molecular mechanisms regulating seed protein/oil accumulation in soybean. Map based cloning to identify the candidate genes for the LG I QTL was undertaken. A BAC based physical map of the region was developed by chromosome walking. Utilizing the genome sequence of soybean and the fine genetic mapping, the QTL region was delineated to an approximately 8.4 Mbp pericentromeric region on chromosome 20. Thirteen genes exhibiting differential expression in developing seeds of near isogenic-lines (NILs) contrasting in protein/oil contents, were identified as potential candidates for the QTL. The homoeologous region corresponding to the QTL region was identified on chromosome 10, spanning a 7.3 Mbp pericentromeric region. Evidence suggests these regions were products of the recent soybean genome duplication 10-14 million years ago (MYA). Comparative analysis of the two regions indicated that both regions are hot spots for retrotransposon accumulation. However, the chromosome 20 region showed preferential accumulation of retrotransposons. The extent of synteny was poor in the retrotransposon rich (gene poor) regions while the adjacent retrotransposon poor (gene rich) regions showed high levels of synteny and colinearity. The genes conserved across the regions showed evidence of sub-funtionalization. The conserved genes were evolving under purifying selection and were enriched for genes involved in stress responses and transcription regulation. The abundance of retrotransposons in these regions points to the likely role of retrotransposons in the evolution of these regions. A detailed study of the retrotransposon insertions in BAC-sized regions around the QTL indicated intergenic and intragenic insertions. The majority of retrotransposon accumulations in the regions studied, happened in the past two million years. Retrotransposon insertions and selection against the insertions could be the predominant forces driving the evolution of this major protein/oil QTL region in soybean

Impact of the upper tropospheric cooling trend over Central Asia on the Indian summer monsoon rainfall and the Bay of Bengal cyclone tracks

The Indian summer monsoon rainfall had three decade long alternate dry and wet epochs during the 150 years from 1840 to 1989. The dry epochs had frequent drought monsoons affecting agriculture, power generation and the overall economy of the country. A high percentage of severe cyclones in the Bay of Bengal moved northwards during the dry epochs causing disasters in Bangladesh, Myanmar and the Indian states of Odisha and West Bengal. These dry epochs have been shown to be associated with the cold phase of the Atlantic multi decadal oscillation in sea-surface temperature. Using the available tropospheric temperature (re-analysis) data since 1948, the recent dry epoch during 1960-89 which had 10 monsoon drought years was found to have cold upper tropospheric temperature anomaly over Central Asia. This cold anomaly region has also experienced a long-term cooling trend. Extrapolating the naturally occurring epochal nature of the ocean-atmosphere system into the future, we fear that the epoch 2020-49 is likely to be another dry one, and the cooling trend over the Asian continent is likely to make it even more severe in its impact than 1960-89. This article presents details of an ocean-atmosphere instability that generates frequent drought monsoons during dry epochs which needs urgent research

Quantitative variation in responses to root spatial constraint within <i>Arabidopsis thaliana</i>

Among the myriad of environmental stimuli that plants utilize to regulate growth and development to optimize fitness are signals obtained from various sources in the rhizosphere that give an indication of the nutrient status and volume of media available. These signals include chemical signals from other plants, nutrient signals, and thigmotropic interactions that reveal the presence of obstacles to growth. Little is known about the genetics underlying the response of plants to physical constraints present within the rhizosphere. In this study, we show that there is natural variation among Arabidopsis thaliana accessions in their growth response to physical rhizosphere constraints and competition. We mapped growth quantitative trait loci that regulate a positive response of foliar growth to short physical constraints surrounding the root. This is a highly polygenic trait and, using quantitative validation studies, we showed that natural variation in EARLY FLOWERING3 (ELF3) controls the link between root constraint and altered shoot growth. This provides an entry point to study how root and shoot growth are integrated to respond to environmental stimuli

Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana.

BackgroundGenome-wide association (GWA) is gaining popularity as a means to study the architecture of complex quantitative traits, partially due to the improvement of high-throughput low-cost genotyping and phenotyping technologies. Glucosinolate (GSL) secondary metabolites within Arabidopsis spp. can serve as a model system to understand the genomic architecture of adaptive quantitative traits. GSL are key anti-herbivory defenses that impart adaptive advantages within field trials. While little is known about how variation in the external or internal environment of an organism may influence the efficiency of GWA, GSL variation is known to be highly dependent upon the external stresses and developmental processes of the plant lending it to be an excellent model for studying conditional GWA.Methodology/principal findingsTo understand how development and environment can influence GWA, we conducted a study using 96 Arabidopsis thaliana accessions, &gt;40 GSL phenotypes across three conditions (one developmental comparison and one environmental comparison) and ∼230,000 SNPs. Developmental stage had dramatic effects on the outcome of GWA, with each stage identifying different loci associated with GSL traits. Further, while the molecular bases of numerous quantitative trait loci (QTL) controlling GSL traits have been identified, there is currently no estimate of how many additional genes may control natural variation in these traits. We developed a novel co-expression network approach to prioritize the thousands of GWA candidates and successfully validated a large number of these genes as influencing GSL accumulation within A. thaliana using single gene isogenic lines.Conclusions/significanceTogether, these results suggest that complex traits imparting environmentally contingent adaptive advantages are likely influenced by up to thousands of loci that are sensitive to fluctuations in the environment or developmental state of the organism. Additionally, while GWA is highly conditional upon genetics, the use of additional genomic information can rapidly identify causal loci en masse

Electronic cigarettes or vaping : are there any differences in the profiles, use and perceptions between a developed and a developing country?

The use of electronic cigarettes or vaping is currently increasing in popularity globally. Debate continues regarding their potential role for smoking cessation. We aimed to compare the profiles, use and perceptions of using e-cigarettes amongst online forum users in a developed and a developing country. A cross-sectional survey was conducted among members of different popular online forums in Australia and Bangladesh who were current or ex-users of e-cigarettes. There were 422 study participants, 261 (62%) from Australia and 161 (38%) from Bangladesh. The mean age was 36.3 (±12) years and 83% were men. Australians were more likely to be exclusive users of e-cigarettes (70% vs. 30%, AOR 3.05 [95% CI 1.63–5.71]), but less likely to be dual users of smoking and e-cigarettes (43% vs. 57%, 0.36 [0.19–0.69]); they were also more likely to mention that the perceived reasons for using were their low cost, good taste/flavour, safety and assistance in reducing or quitting smoking (66% vs. 34%, 5.10 [2.04–12.8]), but less likely to mention a social/cool image as a reason for use (23% vs. 77%, 0.11 [0.01–0.87]) compared with Bangladeshi participants. About two-thirds of the participants in both countries perceived the use of e-cigarettes as less addictive than cigarettes and more than three-quarters perceived them as less harmful. E-cigarette users in Australia were more likely to use them to reduce or quit cigarettes compared with those in Bangladesh, and dual use was common in Bangladesh. These findings warrant the consideration of precautions for promoting e-cigarettes as a harm reduction strategy for smoking cessation in developing countries, such as Bangladesh. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

Genetic variation in the nuclear and organellar genomes modulates stochastic variation in the metabolome, growth, and defense

Recent studies are starting to show that genetic control over stochastic variation is a key evolutionary solution of single celled organisms in the face of unpredictable environments. This has been expanded to show that genetic variation can alter stochastic variation in transcriptional processes within multi-cellular eukaryotes. However, little is known about how genetic diversity can control stochastic variation within more non-cell autonomous phenotypes. Using an Arabidopsis reciprocal RIL population, we showed that there is significant genetic diversity influencing stochastic variation in the plant metabolome, defense chemistry, and growth. This genetic diversity included loci specific for the stochastic variation of each phenotypic class that did not affect the other phenotypic classes or the average phenotype. This suggests that the organism's networks are established so that noise can exist in one phenotypic level like metabolism and not permeate up or down to different phenotypic levels. Further, the genomic variation within the plastid and mitochondria also had significant effects on the stochastic variation of all phenotypic classes. The genetic influence over stochastic variation within the metabolome was highly metabolite specific, with neighboring metabolites in the same metabolic pathway frequently showing different levels of noise. As expected from bet-hedging theory, there was more genetic diversity and a wider range of stochastic variation for defense chemistry than found for primary metabolism. Thus, it is possible to begin dissecting the stochastic variation of whole organismal phenotypes in multi-cellular organisms. Further, there are loci that modulate stochastic variation at different phenotypic levels. Finding the identity of these genes will be key to developing complete models linking genotype to phenotype

A study on association between intraocular pressure and myopia

Background: Myopia is one of the commonest ocular disorders and has been recognized as a risk factor for glaucoma. Aim of this study is to find the association between intraocular pressure (IOP) and different grades of myopia from low to high and compare it with emmetropia.Methods: Observational study done from January to May 2014. 178 eyes of 100 patients were divided into four groups according to their refractive status. Group 0 – Emmetropia (+0.5 to -0.5D), Group1- low myopia (-0.75 to -3.00D), Group 2 -moderate myopia (-3.00 to -5.00D) and Group 3 - high Myopia (>-5.00D).A complete ocular examination was done. Intraocular pressure was measured by standard Goldmann applanation tonometer.Results: Mean age of patients was 30.09 (range 11-47 years). The refraction ranged from +0.50D to -9.00D. Group 0 (emmetropia) included 84 eyes and mean IOP was 12.75 (SD: 2.18).Group 1 included 74 eyes with a mean IOP of 12.32 (SD: 2.44),Group 2 had 14 eyes with a mean IOP of 15.00 (SD:2.25)and Group 3 had 6 eyes with a mean I0P 18.5 (SD:0.7).There was no statistically significant difference in IOP between low myopic and emmetropic patients but the IOP in moderate and severe myopia was higher compared to emmetropic patients.                                                                                  Conclusions: There is statistically significant correlation (p<0.05) between IOP and myopia, in moderate and high myopia groups. The IOP was higher in those groups than in emmetropia and low myopia thereby increasing the risk of glaucoma in these patients.

Factors influencing the transition and retention of mental health nurses during the initial years of practice : scoping review

Aim: This review aims to identify the factors influencing the transition and retention of mental health nurses during the initial years of practice, recognize gaps in the literature and propose evidence-based strategies. Background: Mental health is a challenging specialty; recruitment, transition and retention of mental health nurses are known issues of concern. Evaluation: The present study undertakes a scoping review to identify factors influencing the transition and retention of mental health nurses during the initial years of practice and the gaps in that research domain. A literature search was conducted using electronic databases. To gain an understanding of the topic of interest, the review of the literature extended from 2000 to 2022. Key issues: Existing evidence focuses on specific perspectives of transition. There is limited literature on factors influencing transition and retention among mental health nurses. Findings suggested that personal and professional factors could influence the transition and retention of mental health nurses during the initial years of practice. The main themes identified were personal attributes and professional factors with a number of subthemes. Conclusion: The scoping review identified only a few studies, which showed personal and professional factors related to the transition and retention of mental health nurses at the early stages of their career. Implications for nursing management: Potential benefits of effective transition and support with the understanding of factors influencing transition and retention of early career mental health nurses will enhance staff morale, sustainability of the workforce and better patient outcomes. Additionally, a few recommendations for nurse managers and leaders to improve transitional experiences and retention of early career nurses are highlighted. © 2022 The Authors. Journal of Nursing Management published by John Wiley & Sons Ltd