Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation

Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes

Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations’ ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda–Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda–Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions

Gut Microbiota Diversity of Local Egyptian Cattle Managed in Different Ecosystems

The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host’s environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups (p = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified Firmicutes and Actinobacteriota as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of Firmicutes and Euryarchaeota and a lower abundance of Actinobacteriota in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the Methanobacteriaceae family and the Methanobrevibacter genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including Bacillus, DNF00809, Kandleria, Lachnospiraceae_NK3A20_group, Methanobrevibacter, Mogibacterium, Olsenella, Paeniclostridium, Romboutsia, Turicibacter, and UCG-005. These significant differences in microbiota composition may impact the animal’s adaptation to varied environment

Commercialisation of Alternative Livestock Feeds Could Save Fish Stocks in Lake Victoria

Increasing livestock production in East Africa requires increased use of fish meal as a source of protein, some of which comes from the Silver Cyprinid (Rastrineobola argentea) in Lake Victoria, which could result in its over-exploitation and affect the survival of other organisms in the lake. The crude protein content of cockroaches (38-76% CP depending on the age) and of other insects is similar to that of fish meal (61.24% CP) and could be a substitute for it, if these insects can be domesticated and used as animal feeds. Non-conventional feeds such as cockroaches, houseflies, termites, earthworms and carabid beetles are used on a small scale by farmers in Uganda who would be willing to use them more if they could be produced on a large scale. There is therefore a need to promote large scale insect breeding so that these alternative protein sources can be integrated into farming systems.Keywords: Alternative protein sources, Fishmeal, Insects, Poultr

Influence of school garden learning approach on academic development of global service-learners

Students need to develop cross-cultural awareness and understanding, which has led educational institutions to create high-impact global programs to enhance their academic learning. Global service-learning, a U.S.-based pedagogy, interconnects service-learning, study abroad, and international education programs. A service-learning program in [Country] was founded on the school garden approach which was conceptualized based on the emphasis by the Food and Agricultural Organization in 2004. NGO1, [State University], and [Country University] adopted school gardens as a feasible approach to fulfill the service-learning curricular objectives and meet NGO1’s goal of solving undernutrition in schools using garden products in school lunches. This study sought to determine the influence of service-learning program activities on alumni’s academic development. Alumni (n = 274) from 2006-2019 completed a self-administered questionnaire through Qualtrics where 94.2% responded. A principal components analysis (PCA) was employed, aligning activities into three components. The first component loaded school gardening, bi-national team projects, arrival orientations, farmer field visits, and school teaching assistance, depicting alumni’s community engagement in reciprocal learning. Component two loaded journaling/logbooks, critical reflections, and presentations, depicting alumni’s reflexive actions resulting in cognitive development through documenting and confronting their assumptions about their service-learning activities. Component three loaded co-curricular, tours and travels, and social parties, portraying alumni’s social life that provided opportunities to learn about distinct cultures. Pre-departure orientations loaded well on [State University] alumni’s PCA which mitigated culture shocks while in [Country]. Alumni could benefit overall from more instructor-led cognitive development activities whereby they could both learn from and question their activities.This article is published as Ikendi, S., Retallick, M. S., Nonnecke, G. R., & Kugonza, D. R. (2023). Influence of school garden learning approach on academic development of global service-learners. Journal of Agricultural Education, 64(4). Retrieved from https://jae-online.org/index.php/jae/article/view/167. Posted with permission

Lowland grazing and Marburg virus disease (MVD) outbreak in Kween district, Eastern Uganda

Abstract Background Uganda is one of the few countries in Africa that has been experiencing outbreaks of viral hemorrhagic fevers such as Ebola, Marburg and Crimean-Congo Hemorrhagic fevers. In 2017 Uganda experienced a Marburg Virus Disease (MVD) outbreak with case fatality rate of 100% in Kween district. Although hunting for wild meat was linked to the MVD outbreak in Kween district, less was reported on the land use changes, especially the changing animal grazing practices in Kween district. Methods Through Makerere University One Health graduate fellowship program with attachment to Uganda Red Cross Society, a study was conducted among the agricultural communities to elucidate the risk behaviors in Kween district that can be linked to the 2017 Marburg disease outbreak. Results Results show that although a few elderly participants ascribed fatal causes (disobedience to gods, ancestors, and evil spirits) to the MVD outbreak during FGDs, majority of participants linked MVD to settling in caves (inhabited by Fruit Bats) during wet season as upper belts are extensively used for crop production leaving little space for animal grazing. Members also noted side activities like hunting for wild meat during this grazing period that could have predisposed them to Marburg Virus. Conclusions There is need to integrate One Health concepts within agricultural extension service provision in Uganda so as to enhance the management of such infectious diseases

Commonalities in Global Service-Learning Activities on Alumni Academic Development

Students need to develop cross-cultural awareness and understanding, which has led higher educational institutions (HEI) to create high-impact global programs including service-learning to enhance their academic learning. Service-learning has been part of the history of HEIs in the U.S. more than in any other region of the world (Bringle & Hatcher, 2011; Ma et al., 2019). In the U.S., service-learning and its relevance to HEIs in advancing knowledge to students were described by Eyler and Giles (1999). This scholarly book resulted from the urgency to respond to the growing number of practitioners whose outcome was not founded. The required servicelearning component as part of students’ courses and graduation has grown over time in the U.S. (Jones et al., 2008; Moely & Ilustre, 2011). Service-learning is relevant at the peak age of 18-23 years (Wilsey, 2013) when students are undergoing formative development, often enrolled in HEIs which are responsible for assisting in their development of cross-cultural competencies. Due to efforts to increase global competencies, HEIs have gone further to internationalize their high-impact programs. As a U.S. pedagogy, international service-learning was conceptualized as an interconnection between service-learning, study abroad, and international education (Bringle & Hatcher, 2011). Service-learning brings a study abroad program and international education into an experiential learning model for students to learn in the international community. In this study, the service-learning program was held in Uganda and included three partner organizations. The partnership is among Makerere University (MAK), Iowa State University (ISU), and non-government organizations including Volunteer Efforts for Development Concerns (2004-2014) and Iowa State University Uganda Program (ISU-UP) in 2014 to date (Butler & Acker., 2015; Ikendi & Retallick, 2023a; 2023b). ISU-UP implements development programs of the Center for Sustainable Rural Livelihoods (CSRL) based in the College of Agriculture and Life Sciences at ISU. Service-learning is an academic program of the college led by an Associate Director of the CSRL program who is also an ISU faculty member. The servicelearning program was conceptualized in 2005 out of the participatory needs assessment between the stakeholders of MAK and ISU Colleges of Agriculture and national and local entities and communities in Uganda (Nonnecke et al., 2015).This presentation is published as Ikendi, S., Retallick, M. S., Nonnecke, G. R., Kugonza, D. R, Miller, G. S, Owusu, F., Cooper, T. N., Lubaale, G., Commonalities in Global Service-Learning Activities on Alumni Academic Development. Presented at Western Region Research Conference American Association for Agricultural Education. Sept 2023. Logan, UT. https://aaea.wildapricot.org/page-18453. Posted with permission

Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation