Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice.

BACKGROUND: Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS: In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION: This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.

A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice.

Improving grain yield potential in rice is an important step toward addressing global food security challenges. The meta-QTL analysis offers stable and robust QTLs irrespective of the genetic background of mapping populations and phenotype environment and effectively narrows confidence intervals (CI) for candidate gene (CG) mining and marker-assisted selection improvement. To achieve these aims, a comprehensive bibliographic search for grain yield traits (spikelet fertility, number of grains per panicle, panicles number per plant, and 1000-grain weight) QTLs was conducted, and 462 QTLs were retrieved from 47 independent QTL research published between 2002 and 2022. QTL projection was performed using a reference map with a cumulative length of 2,945.67 cM, and MQTL analysis was conducted on 313 QTLs. Consequently, a total of 62 MQTLs were identified with reduced mean CI (up to 3.40 fold) compared to the mean CI of original QTLs. However, 10 of these MQTLs harbored at least six of the initial QTLs from diverse genetic backgrounds and environments and were considered the most stable and robust MQTLs. Also, MQTLs were compared with GWAS studies and resulted in the identification of 16 common significant loci modulating the evaluated traits. Gene annotation, gene ontology (GO) enrichment, and RNA-seq analyses of chromosome regions of the stable MQTLs detected 52 potential CGs including those that have been cloned in previous studies. These genes encode proteins known to be involved in regulating grain yield including cytochrome P450, zinc fingers, MADs-box, AP2/ERF domain, F-box, ubiquitin ligase domain protein, homeobox domain, DEAD-box ATP domain, and U-box domain. This study provides the framework for molecular dissection of grain yield in rice. Moreover, the MQTLs and CGs identified could be useful for fine mapping, gene cloning, and marker-assisted selection to improve rice productivity.

Participatory approach of preferred traits, production constraints and mitigation strategies: implications for soybean breeding in Guinea Savannah zone of Ghana.

Soybean production is concentrated in the Guinea Savannah agro-ecological zone of Ghana. However, its cultivation is plagued with a number of constraints leading to low yields. A participatory approach was, therefore, used to identify farmers' and processors' preferred soybean traits and production constraints, climate change effects and strategies employed for mitigating these effects in three districts within the soybean growing areas in Northern Ghana. The study revealed that 72.0 % and 68.8 % of farmers in the Tolon and Savelugu districts, respectively, used improved soybean seeds for planting their fields. Over 13.0 % of farmers indicated late maturity as the most important constraint, followed by manual threshing difficulty and terminal drought which results in low grain yield and poor quality. About 70.0 % of farmers opined that climate change effects are causing obvious shifts in the rainfall pattern. Majority of the farmers (94.6 %) indicated that the onset of peak rainfall has changed in the past decade. Almost 44.0% of farmers also indicated that severe drought has affected pods filling in the past. A third (33.3%) of farmers indicated that drought usually sets in at pod initiation. The farmers enumerated some of the effects of early cessation of the rainfall in soybean production as drying up of immature and green seed (28.3%), low grain yield (27.1%) and poor seed quality (22.1%). Some of the mitigation strategies employed by the farmers include early planting (40.0%) and mulching (25.0%) to retain soil moisture for enhanced growth of crops. The order of farmers' preferences new soybean varieties were shattering resistance (16.0%), high grain yield (14.0%), large seeds size (13.1%), and early maturity (11.8%), whereas processors preferred varieties with large seed size (30.6%), high protein content (28.7%), pest resistance (15.9%) and short cooking duration (12.7%). Both the farmers and processors indicated their willingness to pay more for seeds with the desired traits. These findings will aid soybean breeders in developing new varieties that possess desired traits preferred by both farmers and processors for increased soybean cultivation and utilization.

Women diagnosed with HIV and unknown HIV status perceived susceptibility to cervical cancer and perceived benefits of cervical cancer screening in Ghana: a cross-sectional study.

BACKGROUND: Cervical cancer is an issue of global health concern, and it seems to be the next epidemic in Sub-Saharan Africa after Human Immunodeficiency Virus (HIV). This study compared the perceptions of susceptibility to cervical cancer and benefits of cervical cancer screening among women diagnosed and those with unknown HIV status and determined the association between socio-demographic factors and HIV status. METHODS: A cross-sectional study was conducted with 600 women diagnosed with HIV and 600 women with unknown HIV status in the Central Region of Ghana. Convenience sampling was used and a structured interview schedule was the main data collection instrument. Data were analysed using frequencies, percentages, chi-square test and independent samples t-test. RESULTS: A high proportion of women diagnosed with HIV 94.8% (n = 569) and those with unknown HIV status 93.5% (n = 561) agreed that "screening can find cervical changes". Also, 58.0% (n = 348) of women diagnosed with HIV agreed that they have been in polygamous relationships so they may get cervical cancer. There was a statistically significant association between marital status (X2 = 167.071, p = 0.001), religion (X2 = 57.720, p = 0.001), level of education (X2 = 118.997, p = 0.001), employment status (X2 = 782.646, p = 0.001) and HIV status. A comparison of the mean difference for women diagnosed and those with unknown HIV status in relation to perceived benefits of cervical cancer screening showed a statistically significant difference (t = 7.418, df = 1198, p = 0.001). Nonetheless, there was no statistically significant difference in the means for women diagnosed and those with unknown HIV status regarding perceived susceptibility to cervical cancer (t = 0.935, df = 1198, p = 0.351). CONCLUSIONS: Women with HIV perceived higher benefits of cervical cancer screening. Perception of susceptibility to cervical cancer by women with and those without HIV need to be addressed in efforts to improve their health. Furthermore, interventions for women with HIV should consider some important sociodemographic factors.

Food Fingerprinting: Using a Two-Tiered approach to Monitor and Mitigate Food Fraud in Rice.

BACKGROUND: Rice is an important staple food that is consumed around the world. Like many foods, the price of rice varies considerably, from very inexpensive for a low-quality product to premium pricing for highly prized varieties from specific locations. Therefore, like other foods it is vulnerable to economically motivated adulteration through substitution or misrepresentation of inferior-quality rice for more expensive varieties. OBJECTIVE: In this article we describe results of a research project focused on addressing potential food fraud issues related to rice supplies in China, India, Vietnam, and Ghana. Rice fraud manifests differently in each country; therefore, tailored solutions were required. METHOD: Here we describe a two-tiered testing regime of rapid screening using portable Near Infrared technology supported by second tier testing using mass spectrometry-based analysis of suspicious samples. RESULTS: Portable Near Infrared spectroscopy models and laboratory-based Gas Chromatography-Mass Spectrometry methods were developed to differentiate between: high-value Basmati rice varieties and their potential adulterants; six Geographic Indicated protected rice varieties from specific regions within China; various qualities of rice in Ghana and Vietnam; and locally produced and imported rice in Ghana. Furthermore, an Inductively Coupled Plasma-Mass Spectrometry method was developed to support the Chinese rice varieties methods as well as a Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry method for quality differentiation in Vietnam. CONCLUSIONS/HIGHLIGHTS: This two-tier approach can provide a substantially increased level of testing through rapid screening outside of the laboratory with the reassurance of corroborating mass spectrometry-based laboratory analysis to support decision making.

Sonication, osmosonication and vacuum-assisted osmosonication pretreatment of Ghanaian garlic slices: Effect on physicochemical properties and quality characteristics.

This work aimed to assess the impact of sonication (US), osmosonication (US + OD) and vacuum-assisted osmosonication (V + US + OD) pretreatments on the quality of Ghanaian garlic prior to relative humidity convective drying. Hence, slices of fresh garlic subjected to US, US + OD and V + US + OD pretreatments were dried and the following assessed: antioxidant activities, total phenolic content (TPC), total flavonoid content (TFC), polyphenol oxidase (PPO) enzyme inactivation, rehydration ratio (RR), drying kinetics, energy consumption, chromatographic fingerprinting, allicin content and Fourier-transform infrared (FT-IR) spectroscopy. V + US + OD pretreatment gave the best results for antioxidant activities, TPC, TFC, RR and PPO enzyme inactivation. It also recorded the shortest drying time and was more energy efficient. Finally V + US + OD pretreatment maintained the chemical integrity of the finished product and recorded the highest content of allicin. A general trend was however observed for all quality parameters assessed for the various pretreatment methods as: V + US + OD > US + OD > US.

Application of non-thermal pretreatment techniques on agricultural products prior to drying: a review.

BACKGROUND: Most agricultural crops contain high moisture content (80-95% wet basis (wb)) which makes them very susceptible to microbial damage leading to shorter shelf-life and high postharvest losses. The high perishability of these agricultural products requires preservation techniques to prolong their shelf-lives. Drying remains an important component of processing in this regard. Therefore, any pretreatment methods for drying agricultural product that decreases the moisture content and minimizes drying time by conserving the quality of the crop product is of prime significance. This article is a comprehensive review of recent developments of non-thermal pretreatment (NTP) methods. A summary of their significance, emerging and innovative methods of this technology together with its applications and limitations are discussed. This article further examines the environmental impact of NTP techniques. RESULTS: NTP techniques, such as high pressure, ultrasound, pulsed electric field and osmotic dehydration methods are essential operations for pre-dehydration of agricultural products prior to drying. These techniques can avoid the deleterious effects of heat on nutritive value, colour and flavour of agricultural products compared to thermal pretreatments. They also enhance the inactivation of the enzymes, improve energy efficiency and mass transfer, reduce processing time, preserve bioactive compounds, improve drying kinetics and drying rate, minimize enzymatic browning, and enhance product quality. CONCLUSION: These findings will provide a better understanding of different NTP methods and also make available more information for selecting pretreatment techniques for drying of agricultural products. © 2020 Society of Chemical Industry.

Impact of health education intervention on knowledge and perception of cervical cancer and screening for women in Ghana.

BACKGROUND: The burden of cervical cancer continues to rise in developing economies. Women in the sub-Saharan African region have higher chances of developing cervical cancer due to a greater prevalence of related risk factors. The purpose of this study was to determine the effect of health education intervention on cervical cancer and screening perceptions of women in the Komenda, Edina, Eguafo, and Abirem (K.E.E.A) District in the Central Region of Ghana. METHODS: A non-equivalent control-group design was used to select church women; 396 in the intervention group and 386 in the control group, aged 11 to 70 years in the K.E.E.A District in the Central Region of Ghana. Data was collected via a validated structured interview schedule and analysed using the paired - and independent-samples t-tests, Kruskal-Wallis test, and Mann-Whitney U test. RESULTS: A comparison of the mean differences between the pre-post-test scores for the intervention and control groups showed a statistically significant difference for knowledge of cervical cancer (t = 6.22, df = 780, p = 0.001), knowledge of cervical cancer screening (t = 5.96, df = 780, p = 0.001), perceived seriousness (t = 3.36, df = 780, p = 0.001), perceived benefits (t = 9.19, df = 780, p = 0.001), and perceived barriers (t = 3.19, df = 780, p = 0.001). However, perceived susceptibility for the intervention group reduced, evidenced by a decrease in the mean (mean = - 0.12) compared to the control group (mean = 0.93) and this was statistically significant (t = 2.72, df = 780, p = 0.007). CONCLUSIONS: Health education interventions are critical in improving knowledge and perceptions, and increasing self-efficacy of women about cervical cancer and screening.