Genomic Diversity Using Copy Number Variations in Worldwide Chicken Populations

Recently, many studies in livestock have focused on the identification of Copy Number Variants (CNVs) using high-density Single Nucleotide Polymorphism (SNP) arrays, but few have focused on studying chicken ecotypes coming from many locations. CNVs are polymorphisms, which may influence phenotype and are an important source of genetic variation in populations. The aim of this study was to explore the genetic difference and structure, using a high density SNP chip in 936 individuals from seven different countries (Brazil, Italy, Egypt, Mexico, Rwanda, Sri Lanka and Uganda). The DNA was genotyped with the Affymetrix Axiom®600k Chicken Genotyping Array and processed with stringent quality controls to obtain 559,201 SNPs in 915 individuals. The Log R Ratio (LRR) and the B Allele Frequency of SNPs were used to perform the CNV calling with PennCNV software based on a Hidden Markov Model analysis and the LRR was used to perform CNV detection with SVS Golden Helix software.After filtering, a total of 19,027 CNVs were detected with the SVS software, while 9,065 CNVs were identified with the Penn CNV software. The CNVs were summarized in 7,001 Copy Number Variant Regions (CNVRs) and 4,414 CNVRs, using the software BedTool.The consensus analysis across the CNVRs allowed the identification of 2,820 consensus CNVR, of which 1,721 were gain, 637 loss and 462 complex, for a total length of 53 Mb corresponding to the 5 % of the GalGal5 chicken autosomes. Only the consensus CNV regions obtained from both detections were considered for further analysis.The intersection analysis performed between the chicken gene database (Gallus_gallus-5.0) and the 1,927 consensus CNVRs allowed the identification (within or partial overlap) of a total of 2,354 unique genes with an official gene ID.  The CNVRs identified here represent the first comprehensive mapping in several worldwide populations, using a high-density SNP chip

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

Development of a weigh-band for pigs in Uganda (Data on weights and body measurements of Ugandan pigs)

Knowledge of the body weight in pigs is important in informing management decisions and, often, negotiating a sale price. In the smallholder pig system in Uganda the smallholder pig keepers usually do not know the body weights of their animals nor have access to scales. To overcome this, we propose to collect body measurement of pigs with the following objectives: 1. Determine the best predictive equation for weight from body measurement for (a) all animals, and (b) subsets of animals (e.g., grouped by weight, age, sex) 2. Estimate the loss in predictive accuracy in only using one variable for all animals and subsets of animals (testing this as one predictive variable makes a weigh-band a viable option) 3. Should one variable not be viable explore the options for making a farming friendly tool for predicting weight (weigh band, table, app etc.) 4. Synthesis and reporting of results including sharing with local partners 5. Production and dissemination of weight bands (or alternative tool) to participating farmers. Exploration of options for a distributor of these (e.g.private sector partner) The dataset is provided along with the ODK tool used to collect the data (the dictionary for coded variables can be found on the Choices sheet

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

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.This article is published as Elbeltagy, Ahmed R., Francesca Bertolini, Damarius S. Fleming, Angelica Van Goor, Chris M. Ashwell, Carl Joseph Schmidt, Donald R. Kugonza, Susan J. Lamont, and Max F. Rothschild. "Natural Selection Footprints among African Chicken Breeds and Village Ecotypes." Frontiers in Genetics 10 (2019): 376. doi: 10.3389/fgene.2019.00376.</p