Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle

peer-reviewedThe genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR)  2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds

Addressing post-harvest losses during traditional banana fermentation for increased food security in Southwest Uganda

Postharvest losses (PHL) destroy 20-60% of the food production in East Africa, exacerbating already severe regional food insecurity. Fermenting perishable foods such as fruits may reduce PHL while providing nutritional enrichment, improving shelf-life and food quality, and addressing seasonality in food supply. Fermented banana products have been refined and diversified in Uganda over generations to make the greatest use of available food resources, but still parts of the raw material are being lost during processing. This study aimed at exploring existing traditional methods and efficiency of fermentation of Musa (AAA-EAHB) 'Mbidde' in southwestern Uganda. The study gathered information through participatory explorations (working with brewers) on banana juice (lightly fermented beer with <1% alcohol content [n=20 brewers]), tonto (turbid beer with ~4% alcohol [n=20]), and amarwa (smoky spirit with ~ 40% alcohol [n=20]). Brewers mentioned several losses of material during harvest and processing. Harvesting bananas requires felling the plant causing ripe fruit damage, particularly during harvest for processing banana juice (loss from fresh bananas=6.4%±8.8%) or amarwa (loss=9.3%±9.5%). Second, losses occur when brewers squeeze juice from the raw banana pulp using stems of Imperata cylindrica, which is then discarded or fed to animals together with the adherent fruit pulp (losses from raw banana juice=50.6%±0.2%; from tonto 39.2%±21.4% and amarwa 47.6%±12.5%). Other causes of PHL during processing are excessive peeling for tonto processing (loss of banana flesh=18.6%±5.8%) and losses of intermediate products during distillation of amarwa (loss=75.9%±1.3%). Total losses of banana products during processing were rare and caused by sabotage (mostly by children), mistakes in the brewing process (e.g. addition of too much water), using bananas of wrong ripening stage, and equipment failure (e.g., burst or leaking drums in distillation equipment). Other non-PHL challenges include Banana Xanthomonas Wilt (BXW) and bad weather (up to 50% losses in the field). Despite the general efficiency of traditional fermentation practices, significant portions of fruit are still lost. Reduction in PHL can complement, both culturally and nutritionally, the role that fermented banana products play in Ugandan food systems and contribute to regional food security. Collaborative mechanisms for PHL reduction should target the cited sources of PHL

Food Insecurity as a Barrier to Sustained Antiretroviral Therapy Adherence in Uganda

Background: Food insecurity is emerging as an important barrier to antiretroviral (ARV) adherence in sub-Saharan Africa and elsewhere, but little is known about the mechanisms through which food insecurity leads to ARV non-adherence and treatment interruptions. Methodology: We conducted in-depth, open-ended interviews with 47 individuals (30 women, 17 men) living with HIV/AIDS recruited from AIDS treatment programs in Mbarara and Kampala, Uganda to understand how food insecurity interferes with ARV therapy regimens. Interviews were transcribed, coded for key themes, and analyzed using grounded theory. Findings: Food insecurity was common and an important barrier to accessing medical care and ARV adherence. Five mechanisms emerged for how food insecurity can contribute to ARV non-adherence and treatment interruptions or to postponing ARV initiation: 1) ARVs increased appetite and led to intolerable hunger in the absence of food; 2) Side effects of ARVs were exacerbated in the absence of food; 3) Participants believed they should skip doses or not start on ARVs at all if they could not afford the added nutritional burden; 4) Competing demands between costs of food and medical expenses led people either to default from treatment, or to give up food and wages to get medications; 5) While working for food for long days in the fields, participants sometimes forgot medication doses. Despite these obstacles, many participants still reported high ARV adherence and exceptional motivation to continue therapy. Conclusions: While reports from sub-Saharan Africa show excellent adherence to ARVs, concerns remain that these successes are not sustainable in the presence of widespread poverty and food insecurity. We provide further evidence on how food insecurity can compromise sustained ARV therapy in a resource-limited setting. Addressing food insecurity as part of emerging ARV treatment programs is critical for their long-term success

Suitability of existing Musa morphological descriptors to characterize East African highland ‘matooke’ bananas

Article purchased; Published online: 18 Sept 2017Morphological traits are commonly used for characterizing plant genetic resources. Germplasm characterization should be based on distinctly identifiable, stable and heritable traits that are expressed consistently and are easy to distinguish by the human eye. Characterization and documentation of a representative sample of East African highland bananas (Lujugira–Mutika subgroup) was carried out following an internationally accepted standard protocol for bananas. Eleven cultivars were characterized using an existing set of minimum descriptors (31 qualitative and quantitative traits) with the aim of determining stable descriptors and the ability of these descriptors to distinguish among East African highland banana cultivars. There was variation in stability of these descriptors within cultivars and across the 11 cultivars. Only 10 (32%) out of 31 descriptors studied were stable in the 11 cultivars. However, they had similar scores and therefore are not suitable to distinguish between cultivars within this group. Nonetheless, these 10 descriptors may be useful for distinguishing the East African highland bananas as a group from other groups of bananas. A few descriptors were unique to the cultivar ‘Tereza’ and may be used to distinguish this cultivar from other ‘matooke’ cultivars. None of the quantitative descriptors were stable

Genome wide association study of passive immunity and disease traits in beef-suckler and dairy calves on Irish farms

peer reviewedCalves with lower concentrations of immunoglobulin G (IgG) in their blood, have a greater risk of developing diseases. There is a lack of knowledge on genetic markers known to be associated with immunological variability or disease resistance. Therefore, the objective of this study was to identify SNP markers associated with passive immunity measures (serum IgG, serum protein, albumin, globulin and total protein concentrations, total solids Brix percentage, zinc sulphate turbidity units) and disease (pneumonia, diarrhoea, crude illness) traits in Irish commercial beef-suckler and dairy calves through genome wide association studies (GWAS). Genotyping was performed on DNA samples from beef-suckler (n = 698) and dairy (n = 1178) calves, using the IDBv3 chip. Heritability of passive immunity associated traits (range 0.02–0.22) and the disease traits (range 0.03–0.20) were low-to-moderate. Twenty-five and fifteen SNPs approached genome wide significance (P < 5 × 10−5) for the passive immunity and the disease traits, respectively. One SNP “ARS-BFGL-BAC-27914” reached Bonferroni genome wide significance (P < 1.15 × 10−6) for an association with serum IgG concentration in beef calves. Further work will evaluate these SNPs in larger cattle populations and assess their contribution to genomic selection breeding strategies, aimed towards producing more disease resistant livestock.Department of Agriculture, Food and the Marine, Irelan

Phenotypic diversity and chemical properties of pawpaw fruit quality in Ugandan germplasm

Pawpaw (Carica pawpaw L.) fruit production and utilisation have been on the increase in Uganda. However, challenges related to identification of phenotypes with inherent characteristics for improvement of fruit shelf life have limited identification of better varieties. The objective of this study was to evaluate the phenotypic diversity and shelf life determinants of Uganda\u2019s pawpaw accessions and their variations based on selected quality parameters. Nineteen accessions were collected as seeds from different markets of Uganda, germinated and planted in Namulonge-Wakiso district, central Uganda. The accessions were significantly (P&lt;0.05) variable in terms of fruit weight parameters, with dry matter ranging from 14 - 19% and fruit weight of up to 3.9 kg; while pulp weight was up to 3.2 kg per fruit. Pulp firmness parameters were also significantly variable (P&lt;0.05) and highly correlated with shelf life of the fruit, which ranged from 7 - 13 days depending on the accession. Fruit pulp pH ranged from 4.4-5.6; while titratable acidity of the fruit ranged from 0.03-0.08%. The accessions were clustered in four main clusters depending on the fruit firmness properties, fruit shelf life, fruit weight, pH and titratable acidity as definitive parameters. These accessions were distinguished based on morphological parameters, and henceforth defined for nutritional and economic uses. Accessions with high fruit firmness (&gt;5 kg F) such as 16/20\u2019 16/16, 16/17 and 18/1; and external pulp thickness (&gt;2 cm) such as 16/16, 16/17 and 18/1 had improved fruit shelf life and are recommended for marketability and processing.La production et l\u2019utilisation de fruits de papaye (Carica pawpaw L.) ont augment\ue9 en Ouganda. Cependant, les d\ue9fis li\ue9s \ue0 l\u2019identification des ph\ue9notypes ayant des caract\ue9ristiques inh\ue9rentes \ue0 l\u2019am\ue9lioration de la dur\ue9e de conservation des fruits ont limit\ue9 l\u2019identification des meilleures vari\ue9t\ue9s. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer la diversit\ue9 ph\ue9notypique et les d\ue9terminants de la dur\ue9e de conservation des accessions de papaye en Ouganda et leurs variations en fonction de certains param\ue8tres de qualit\ue9. Dix-neuf accessions ont \ue9t\ue9 collect\ue9es sous forme de semences sur diff\ue9rents march\ue9s de l\u2019Ouganda, germ\ue9es et plant\ue9es dans le Namulonge, district de Wakiso, \ue0 l\u2018 Ouganda centrale. Les accessions \ue9taient significativement variables (P &lt;0,05) en termes de param\ue8tres de poids des fruits, avec une mati\ue8re s\ue8che allant de 14 \ue0 19% et un poids des fruits allant jusqu\u2019\ue0 3,9 kg; tandis que le poids de la pulpe atteignait 3,2 kg par fruit. Les param\ue8tres de fermet\ue9 de la pulpe \ue9taient \ue9galement significativement variables (P &lt;0,05) et fortement corr\ue9l\ue9s \ue0 la dur\ue9e de conservation du fruit, qui allait de 7 \ue0 13 jours selon l\u2019accession. Le pH de la pulpe de fruit variait de 4,4 \ue0 5,6; tandis que l\u2019acidit\ue9 titrable du fruit variait de 0,03 \ue0 0,08%. Les accessions ont \ue9t\ue9 regroup\ue9es en quatre groupes principaux selon les propri\ue9t\ue9s de fermet\ue9 du fruit, la dur\ue9e de conservation du fruit, le poids du fruit, le pH et l\u2019acidit\ue9 titrable comme param\ue8tres d\ue9finitifs. Ces accessions ont \ue9t\ue9 distingu\ue9es sur la base de param\ue8tres morphologiques, et d\ue9finies \ue0 la base des usages nutritionnels et \ue9conomiques. Les accessions \ue0 forte fermet\ue9 du fruit (&gt; 5 kg F) telles que 16/20 \u201916/16, 16/17 et 18/1; et une \ue9paisseur de pulpe externe (&gt; 2 cm) telle que 16/16, 16/17 et 18/1 avaient une dur\ue9e de conservation am\ue9lior\ue9e des fruits, et elles sont recommand\ue9es pour la commercialisation et la transformation

Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes

peer-reviewedAverage daily gain (ADG) and daily dry matter intake (DMI) are key determinants of beef industry profitability. These traits together with metabolic body weight (MWT) are combined as component traits to calculate residual feed intake (RFI), a common measure of feed efficiency in beef cattle. Recently, there have been significant efforts towards molecular genetic characterization of RFI through transcriptomic studies in different breeds and tissues. However, molecular mechanisms of RFI component traits still remain predominately unexplored. Therefore, in the current study, we investigated the hepatic transcriptomic profiles and their associations with ADG, DMI, and MWT in Angus, Charolais, and Kinsella Composite (KC) populations through global RNAseq analyses. In each population and for each trait, 12 steers with extreme phenotypes (n = 6 low and n = 6 high) were analyzed for differential gene expression. These animals were from 20 beef steers of each Angus, Charolais, and KC breed population that were initially selected for a transcriptome study of RFI. At a false discovery rate 1.5, we identified 123, 102, and 78 differentially expressed (DE) genes between high- and lowADG animals of Angus, Charolais, and KC populations, respectively. For DMI, 108, 180, and 156 DE genes were identified between high- and low-DMI from Angus, Charolais, and KC populations, respectively, while for MWT, 80, 82, and 84 genes were differentially expressed between high- and low-MWT animals in Angus, Charolais, and KC populations, respectively. The identified DE genes were largely breed specific (81.7% for ADG, 82.7% for DMI, and 83% for MWT), but were largely involved in the same biological functions across the breeds. Among the most enriched biological functions included metabolism of major nutrients (lipids, carbohydrates, amino acids, vitamins, and minerals), small molecule biochemistry, cellular movement, cell morphology, and cell-to-cell signaling and interaction. Notably, we identified multiple DE genes that are involved in cholesterol biosynthesis, and immune response pathways for the 3 studied traits. Thus, our findings present potential molecular genetic mechanisms and candidate genes that influence feed intake, growth, and MWT of beef cattle