A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is ...critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.
Summary
Hitherto, most quantitative trait loci of maize growth and biomass yield have been identified for a single time point, usually the final harvest stage. Through this approach cumulative ...effects are detected, without considering genetic factors causing phase‐specific differences in growth rates. To assess the genetics of growth dynamics, we employed automated non‐invasive phenotyping to monitor the plant sizes of 252 diverse maize inbred lines at 11 different developmental time points; 50 k SNP array genotype data were used for genome‐wide association mapping and genomic selection. The heritability of biomass was estimated to be over 71%, and the average prediction accuracy amounted to 0.39. Using the individual time point data, 12 main effect marker‐trait associations (MTAs) and six pairs of epistatic interactions were detected that displayed different patterns of expression at various developmental time points. A subset of them also showed significant effects on relative growth rates in different intervals. The detected MTAs jointly explained up to 12% of the total phenotypic variation, decreasing with developmental progression. Using non‐parametric functional mapping and multivariate mapping approaches, four additional marker loci affecting growth dynamics were detected. Our results demonstrate that plant biomass accumulation is a complex trait governed by many small effect loci, most of which act at certain restricted developmental phases. This highlights the need for investigation of stage‐specific growth affecting genes to elucidate important processes operating at different developmental phases.
Significance Statement
Most genetic studies of biomass accumulation or yield in crops have focused on a single growth stage, but agronomic traits are complex and controlled by many genes, each with small effect. Here we use high‐throughput non‐invasive phenotyping to show that genetic effects on maize biomass accumulation differ across developmental phases, that there are complex interactions of loci with developmental progression, that allele effects and epistatic interaction patterns change over time, and that functional mapping can uncover additional genetic factors. Our results indicate that continuous assessment of growth dynamics coupled with transcript profiling will aid in detecting superior stage‐specific genes/alleles and thus provide a powerful tool for crop improvement.
Detailed and standardized protocols for plant cultivation in environmentally controlled conditions are an essential prerequisite to conduct reproducible experiments with precisely defined treatments. ...Setting up appropriate and well defined experimental procedures is thus crucial for the generation of solid evidence and indispensable for successful plant research. Non-invasive and high throughput (HT) phenotyping technologies offer the opportunity to monitor and quantify performance dynamics of several hundreds of plants at a time. Compared to small scale plant cultivations, HT systems have much higher demands, from a conceptual and a logistic point of view, on experimental design, as well as the actual plant cultivation conditions, and the image analysis and statistical methods for data evaluation. Furthermore, cultivation conditions need to be designed that elicit plant performance characteristics corresponding to those under natural conditions. This manuscript describes critical steps in the optimization of procedures for HT plant phenotyping systems. Starting with the model plant Arabidopsis, HT-compatible methods were tested, and optimized with regard to growth substrate, soil coverage, watering regime, experimental design (considering environmental inhomogeneities) in automated plant cultivation and imaging systems. As revealed by metabolite profiling, plant movement did not affect the plants' physiological status. Based on these results, procedures for maize HT cultivation and monitoring were established. Variation of maize vegetative growth in the HT phenotyping system did match well with that observed in the field. The presented results outline important issues to be considered in the design of HT phenotyping experiments for model and crop plants. It thereby provides guidelines for the setup of HT experimental procedures, which are required for the generation of reliable and reproducible data of phenotypic variation for a broad range of applications.
Post-hospital discharge mortality is high among undernourished children in many low and middle-income countries. Although a number of quantitative studies have highlighted a range of potential ...socio-cultural, economic and health system factors influencing paediatric post-discharge treatment-seeking and recovery, few studies have explored family and provider perspectives of the post-discharge period in-depth.
This work was part of a large, multi-country prospective cohort study, the Childhood Acute Illness and Nutrition (CHAIN) Network. We conducted a qualitative sub-study to understand the post-discharge treatment-seeking and recovery experiences of families of undernourished children aged 2-23 months admitted in a rural and urban icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh) hospital. Methods included repeat in-depth interviews (73 interviews in total) with 29 family members of 17 purposively selected children. These data were supplemented by interviews with 33 health workers, and by observations in hospitals and homes.
Important drivers of treatment-seeking perceived to support recovery included advice provided to family members while in hospital, media campaigns on hygiene practice, availability of free treatment, and social and financial support from family members, relatives and neighbours. Key perceived challenges included low household incomes, mothers having to juggle multiple responsibilities in addition to caring for the sick child, lack of support (sometimes violence) from the child's father, and family members' preference for relatively accessible drug shops, physicians or healers over hospital admission.
Development of interventions that address the challenges that families face is essential to support post-discharge adherence to medical advice and recovery. Potential interventions include strengthening information giving during hospitalization on what post-discharge care is needed and why, reducing direct and indirect costs associated with hospital visits, engaging fathers and other 'significant others' in post-discharge advice, and building mobile phone-based support for follow-up care.
Tomato (Solanum lycopersicon) is among the most consumed vegetables across the globe. In most parts of Kenya, tomato production is characterized by low quality and huge losses due to pests and ...diseases. The most prevelance tomato diseases are caused by bacteria and fungi, most common being bacterial wilt. This study determined the prevalence of Ralstonia solanacearum in tomato farms in Meru South sub-county. The Prevalence of bacterial wilt was carried out by conducting a survey across agroecological zones in Meru South. Study farms were randomly selected. Data on the frequency of occurrence, severity, and impacts of the disease were collected by observation and administration of questionnaires to the farmers. The study broadens the understanding of R. solancaerum prevalence in Meru South sub-county.
Infant feeding in the context of human immunodeficiency virus (HIV) poses unique challenges to mothers and healthcare workers in balancing the perceived risks of HIV transmission and nutritional ...requirements. We aimed to describe the decision-making processes around infant feeding at a rural HIV clinic in Kenya.
We used a qualitative study design. Between March and August 2011, we conducted in-depth interviews (
= 9) and focus group discussions (
= 10) with purposively selected hospital and community respondents at Kilifi County Hospital, Kenya. These respondents had all experienced of infant feeding in the context of HIV. These interviews were informed by prior structured observations of health care worker interactions with carers during infant feeding counselling sessions.
Overall, women living with HIV found it difficult to adhere to the HIV infant feeding guidance. There were three dominant factors that influenced decision making processes: 1) Exclusive breastfeeding was not the cultural norm, therefore practising it raised questions within the family and community about a mother's parenting capabilities and HIV status. 2) Women living with HIV lacked autonomy in decision-making on infant feeding due to socio-cultural factors. 3) Non-disclosure of HIV status to close members due to the stigma.
Infant feeding decision-making by women living with HIV in rural Kenya is constrained by a lack of autonomy, stigma and poverty. There is an urgent need to address these challenges through scaling up psycho-social and gender empowerment strategies for women, and introducing initiatives that promote the integration of HIV infant feeding strategies into other child health services.
Phenomic prediction of maize hybrids Edlich-Muth, Christian; Muraya, Moses M.; Altmann, Thomas ...
BioSystems,
August 2016, 2016-Aug, 2016-08-00, 20160801, Letnik:
146
Journal Article
Recenzirano
Phenomic experiments are carried out in large-scale plant phenotyping facilities that acquire a large number of pictures of hundreds of plants simultaneously. With the aid of automated image ...processing, the data are converted into genotype-feature matrices that cover many consecutive days of development. Here, we explore the possibility of predicting the biomass of the fully grown plant from early developmental stage image-derived features. We performed phenomic experiments on 195 inbred and 382 hybrid maizes varieties and followed their progress from 16 days after sowing (DAS) to 48 DAS with 129 image-derived features. By applying sparse regression methods, we show that 73% of the variance in hybrid fresh weight of fully-grown plants is explained by about 20 features at the three-leaf-stage or earlier. Dry weight prediction explained over 90% of the variance. When phenomic features of parental inbred lines were used as predictors of hybrid biomass, the proportion of variance explained was 42 and 45%, for fresh weight and dry weight models consisting of 35 and 36 features, respectively. These models were very robust, showing only a small amount of variation in performance over the time scale of the experiment. We also examined mid-parent heterosis in phenomic features. Feature heterosis displayed a large degree of variance which resulted in prediction performance that was less robust than models of either parental or hybrid predictors. Our results show that phenomic prediction is a viable alternative to genomic and metabolic prediction of hybrid performance. In particular, the utility of early-stage parental lines is very encouraging.
Tomato production is characterized by inconsistent quality and yields due to biotic constraints such as fungal foliar diseases. Information on the occurrence of the diseases in different ...agro-ecological zones of Kenya is scanty. This study assessed the occurrence of early blight, late blight and Septoria spot diseases in tomato farms in five agro-ecological zones (AEZ) of Kirinyaga County in Kenya (UM2, UM3, UM4, LM3 and LM4) using cross sectional survey method. Macro plots were systematically established diagonally in tomato farms and were used to assess disease incidence and severity. Incidences and severity data were subjected to analysis of variance (ANOVA) using Krukal wallis H test at α = 0.05. Median comparison was performed using Steel Dwass Critchlow Fligner with bonferroni adjustment in Statistical Analysis System (SAS) version 9.4. Incidences and severity of early blight, late blight and Septoria spot in tomato farms were significantly different (p< 0.05) among the villages and agro-ecological zones. Incidence of early blight ranged from 35.7% to 76.65% with severity ranging from 17.15% to 50.87%. The incidence of Septoria spot ranged from 23.56% to 93.42% with severity ranging from 16.67% to 44.44%. The incidence of late blight ranged from 33.33% to 86.63% with severity ranging from 16.67% to 33.33%. The incidence of early blight was significantly higher in AEZ UM3 (Median= 75%), the incidence of Septoria spot was significantly higher in AEZ LM4 (Median = 83.33%) while the incidence of late blight was significantly higher in AEZ UM3 (Median= 50%). The severity of early blight was significantly higher in AEZ UM3 (Median = 38.89%), Septoria spot was significantly severe in AEZ LM4 (Median = 40.28%) while severity of late blight was significantly higher in AEZ UM4 (Median= 32.72%). It can be concluded that the incidences and severity of the three foliar fungal diseases of tomato differed in different AEZ of Kirinyaga County. These findings serve as a baseline study and can be used to enlighten farmers on tomato fungal diseases in the area. However, there is a need for studies to evaluate predisposing factors and to determine the economic impact of foliar fungal diseases of tomatoes in Kirinyaga County. Fundam Appl Agric 2022; 7(1.000): 31-46
Objective: Even though dynamic multidisciplinary team discussions are crucial for end-of-life care management and decisions concerning chronic obstructive pulmonary disease (COPD), the details of the ...discussion contents remain poorly understood. This study aimed to identify essential considerations in decision-making for patients with chronic respiratory diseases to enhance a consensus-based approach. Materials and Methods: A qualitative content analysis of focus group conversations on published clinical case reports in the Japanese community about end-of-life care for patients with chronic respiratory disorders was conducted. The cases were searched through Igaku Chuo Zasshi (ICHUSHI) and Google in February 2021, using the keywords: "COPD", "chronic respiratory diseases", and "end-of-life care". A total of 41 healthcare professionals participated in the focus group discussions. Results: Four major themes evolved from the qualitative content analysis: unpredictable disease prognosis and stages, low awareness of patients on disease severity, acute exacerbations, and home oxygen therapy (HOT). The participants perceived that assessment of severity and prognosis in chronic respiratory diseases such as COPD was a core discussion point to enhance patients' decision-making. The study's findings also indicated that healthcare providers evaluate the influence of acute aggravation of the condition on patients' perceived health status and decision-making. Conclusion: The study reaffirms the significance of informed consent in patients with chronic respiratory disease. It details how, after a thorough assessment of disease severity, patients are given personalized explanations of standardized HOT. This approach ensures they fully understand the unpredictable nature and various stages of their condition resulting from acute exacerbations.Objective: Even though dynamic multidisciplinary team discussions are crucial for end-of-life care management and decisions concerning chronic obstructive pulmonary disease (COPD), the details of the discussion contents remain poorly understood. This study aimed to identify essential considerations in decision-making for patients with chronic respiratory diseases to enhance a consensus-based approach. Materials and Methods: A qualitative content analysis of focus group conversations on published clinical case reports in the Japanese community about end-of-life care for patients with chronic respiratory disorders was conducted. The cases were searched through Igaku Chuo Zasshi (ICHUSHI) and Google in February 2021, using the keywords: "COPD", "chronic respiratory diseases", and "end-of-life care". A total of 41 healthcare professionals participated in the focus group discussions. Results: Four major themes evolved from the qualitative content analysis: unpredictable disease prognosis and stages, low awareness of patients on disease severity, acute exacerbations, and home oxygen therapy (HOT). The participants perceived that assessment of severity and prognosis in chronic respiratory diseases such as COPD was a core discussion point to enhance patients' decision-making. The study's findings also indicated that healthcare providers evaluate the influence of acute aggravation of the condition on patients' perceived health status and decision-making. Conclusion: The study reaffirms the significance of informed consent in patients with chronic respiratory disease. It details how, after a thorough assessment of disease severity, patients are given personalized explanations of standardized HOT. This approach ensures they fully understand the unpredictable nature and various stages of their condition resulting from acute exacerbations.
Breast cancer remains the most commonly diagnosed cancer among women, affecting 34 women per every 100,000. This has led to high number of fatalities annually, which need to be mitigated. ...Establishing alternative conventional therapies such as working on mindfulness-based stress (MBS) may be a good alternative to improve prognosis and survival rate of breast cancer patients. However, there is little information on the effects of MBS factors on breast cancer survival. The objective of this study is to predict the effect of MBS factors on breast cancer survival rate among women in Meru and Nyeri Counties using Cox Proportional Hazard Model. Both primary data and secondary data were used. Primary data was obtained using a structured questionnaire from the breast cancer survivors and the medical practioners, while secondary data was obtained from records at Meru teaching and referral hospital and Nyeri level five hospital for the period 2012 to 2017. The MBS variables included cost burden of treatment, stress on diagnosis, prolonged time taken to access treatment, poor diet, alcohol use, physical activity and lack of awareness. . This study used mixed method research design. Data obtained were analysed using R software. Kaplain-Meier estimators were used to estimate the varying effects of MBS factors on survival rate. Log-rank test was used to perform comparisons of survival curves on the patients’ survival rate considering age. The likelihood ratio test showed that MBS factors are significant in predicting hazard rates ( X2= 66.7, p = 0.0000119). Treatment period, lack of awareness, ease of coping with stress and observing the right diet were also found to significantly (p < 0.05) affect breast cancer survival rate. Access of treatment immediately after diagnosis, availing the right information to the patients, helping patients to cope easily with stress and observing the right diet were found to be the best estimators in increasing breast cancer survival rate. The study showed the importance of using model in predicting breast cancer survival rates, which can greatly improve breast cancer prognosis.
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