Phenomic and genomic landscape of Ethiopian village chickens

This study involves two village chicken populations sampled from Horro and Jarso regions of Western and Eastern Ethiopia respectively. This study maps the phenomic and genomic landscape of the two chicken populations using morphological markers and a high density (600K) SNP array. Although the two chicken populations tend to display nondescript morphological characteristics, they show a subtle variation except for rare morph variants that have been in most instances scored on Jarso chickens. Morphological analysis uncovers a vast array of intrapopulation variation. Genetic diversity and population structure analyses assign the two chicken populations to two distinct genepools representing their population of origin. A high intrapopulation genetic diversity is uncovered, which shows a broad genetic base (high genetic diversity) of the two chicken populations. We hypothesized that a clearly evident genetic divergence observed between the two chicken populations may be attributed to difference in demographic history, origin (routes of introduction to Africa), breeding history of the two chicken populations and demographic structure of subsistence farmers. Absence of gene flow owing to their distant geographic location and ecological variation may have also contributed to this divergence. A population structure analysis performed on a random subset of the two Ethiopian chicken populations along with village chickens sampled from other African countries, Asia and Latin America, commercial populations and the junglefowl species reveals a unique genetic structure of Ethiopian chickens, which implicates the need for further study on the genetic landscape of the latter. To infer the extent of inbreeding we performed a run of homozygosity analysis (ROH). Our analysis indicates that ROH is more intense in Jarso than Horro chickens and in macrochromosomes than microchromosomes. The extensive ROH mapped in some chickens implicates the need to restructure the existing traditional breeding practice of subsistence farmers. Our analysis confirms the commonness of ROH in genic regions. For the first time, we detect twenty three putative uniparental disomy in twenty two Ethiopian village chickens. Signature of selection analysis detects divergently selected genomic regions in the two chicken populations indicating a considerable divergent selection imposed on the two populations. Genes involving in melanogenesis pathway are among those subjected to a divergent selection. However, some overlapping regions were also mapped in the two chicken populations implicating the ubiquitous impact of natural selection on genes regulating vital biological processes. A genome-wide association study performed on pigmentation (earlobe, plumage and shank) traits and variants of crest, comb and a lightly feathered shank maps a number of putative loci that may underlie variations in these traits. Our GWAS analysis on pigmentation traits produced a long list of loci than that have been known to involve in the genetic control of pigmentation in the chicken, with most of these have been mapped in the mouse. We also refined further the causative variants underlying a lightly feathered shank mutation. Our GWAS analysis map a number of putative novel loci that may underlie the genetic control of the traits analysed and this has laid a foundation for subsequent work that would involve targeted sequencing and a candidate gene approach. This study is the first of its kind in Africa that uses a large number of samples and a high density SNP array to unlock phenomic and genomic landscape of the true type village chickens

Predation and theft: the standing threats of the scavenging chicken production system

Indigenous Village Chickens (IVCs) obtain most of their feed from a scavenging feed resource base. Free roaming makes IVCs express their instincts at will, which could enhance their welfare. Free-ranging has also endowed IVCs with excellent explorative behavior. However, predators might have also co-evolved, which necessitates special interference from smallholder farmers to reduce the adverse impact of predators. This study identified the main predators of IVCs and the evading strategies adopted by smallholder farmers. This cross-sectional study involved a general interview with 119 smallholder farmers. The prevalence of enset, Ensete ventricosum (Welw.) Cheesman, around the farmer's backyard can impose a significant threat because it shelters terrestrial predators. Smallholder farmers evade predators through patrolling, guarding dogs, fencing, confinement, and, in rare cases, killing. An unplanned conversation made with an informant revealed that men with some clerical ability but no priesthood title incantate on whole grains of black wheat. When the chicken is fed this grain, reportedly, the aerial predator becomes weak and cannot catch the chicken. The agroecological zone has a statistically significant impact on the proportions of predators encountered and the types of evading strategies adopted by smallholder farmers. This association entails the need for developing agroecology-based predator-evading methods. Predators' evading methods, however, need to be refined further to reduce the recurrent losses of chickens. The threats associated with predators' challenges must be thoroughly investigated to advance their evading strategies. Another problem that leads to the significant loss of family poultry is theft. In addition to the strategies used to avoid predators, which may also apply to controlling theft, the legal system must be well-organized to punish such misdeeds

The reaction of secondary school and university students toward COVID-19-induced lockdown

Background: The Coronavirus pandemic triggered a worldwide partial lockdown. The lockdown instigated the school’s shutdown making the students follow their courses in the virtual modalities while staying at home. Methods: The data were collected using an online survey using a semi-structured questionnaire. The study involved anonymous as well as voluntary 77 secondary schools (Grades 9th to 12th) and 132 university students (class standing 1st to 5th year). Results: The lockdown introduced excruciating experiences for most of the students; however, it also created unanticipated opportunities to learn new skills and develop insights on how to mitigate unforeseen crises while remaining reasonably productive. The steps taken to reduce exposure to the coronavirus infection showed a gender discrepancy. Accordingly, males were disproportionately taken risks regardless of the curfew imposed, while females were deeply concerned about the lockdown-induced break of social connections. Students who were attending public schools, presumably from low-income families were found to be more productive during the lockdown compared to their private school counterparts. This shows that, in some instances, the Coronavirus pandemic is a blessing in disguise. The lockdown created mixed feelings; accordingly, the students reported significantly varied responses towards it. This also introduced some inconsistencies in the response of the students. Perceptions about the lockdown and its impact in most instances significantly varied among students, which unlocked the opportunities to learn new lessons on how to manage unprecedented crises. Conclusion: Policymakers need to take into account gender and living standard while developing strategies to mitigate unprecedented challenges

The antiviral properties of edible medicinal plants: potential remedies against coronaviruses

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is an unparalleled challenge for the international community. Subsequently, an extraordinary effort has been made to contain SARS-CoV-2. However, this has been largely limited to behavioral changes and vaccination. To make the containment strategies effective, behavioral changes and vaccination need to be complemented with alternative prevention methods and curative treatments. This work reports the antiviral properties of some of the commonly known edible medicinal plants that can be used as potential remedies to suppress coronaviruses. A growing body of evidence substantiates that edible medicinal plants with antiviral properties that have been proven effective against sibling coronaviruses likely contain the spread of SARS-CoV-2, and they may also suppress the fatality of COVID-19 (coronavirus disease 2019). The secondary metabolites found in herbal medicines do not cause pathogens to develop drug resistance, which is a common problem in conventional medicines. The use of edible medicinal plants is much safer and causes less panic, thereby avoiding the fear associated with the use of herbal medicines. Right dosages and mixtures of edible medicinal plants need to be rigorously investigated to circumvent unanticipated side effects and chronic health risks

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

Background: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallusgallus and several inbred experimental lines using whole-genome sequence data. Results: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5% are common to 90% of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P<2.31−6), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P<0.05). Conclusions: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts

Phenomic and genomic landscape of Ethiopian village chickens

This study involves two village chicken populations sampled from Horro and Jarso regions of Western and Eastern Ethiopia respectively. This study maps the phenomic and genomic landscape of the two chicken populations using morphological markers and a high density (600K) SNP array. Although the two chicken populations tend to display nondescript morphological characteristics, they show a subtle variation except for rare morph variants that have been in most instances scored on Jarso chickens. Morphological analysis uncovers a vast array of intrapopulation variation. Genetic diversity and population structure analyses assign the two chicken populations to two distinct genepools representing their population of origin. A high intrapopulation genetic diversity is uncovered, which shows a broad genetic base (high genetic diversity) of the two chicken populations. We hypothesized that a clearly evident genetic divergence observed between the two chicken populations may be attributed to difference in demographic history, origin (routes of introduction to Africa), breeding history of the two chicken populations and demographic structure of subsistence farmers. Absence of gene flow owing to their distant geographic location and ecological variation may have also contributed to this divergence. A population structure analysis performed on a random subset of the two Ethiopian chicken populations along with village chickens sampled from other African countries, Asia and Latin America, commercial populations and the junglefowl species reveals a unique genetic structure of Ethiopian chickens, which implicates the need for further study on the genetic landscape of the latter. To infer the extent of inbreeding we performed a run of homozygosity analysis (ROH). Our analysis indicates that ROH is more intense in Jarso than Horro chickens and in macrochromosomes than microchromosomes. The extensive ROH mapped in some chickens implicates the need to restructure the existing traditional breeding practice of subsistence farmers. Our analysis confirms the commonness of ROH in genic regions. For the first time, we detect twenty three putative uniparental disomy in twenty two Ethiopian village chickens. Signature of selection analysis detects divergently selected genomic regions in the two chicken populations indicating a considerable divergent selection imposed on the two populations. Genes involving in melanogenesis pathway are among those subjected to a divergent selection. However, some overlapping regions were also mapped in the two chicken populations implicating the ubiquitous impact of natural selection on genes regulating vital biological processes. A genome-wide association study performed on pigmentation (earlobe, plumage and shank) traits and variants of crest, comb and a lightly feathered shank maps a number of putative loci that may underlie variations in these traits. Our GWAS analysis on pigmentation traits produced a long list of loci than that have been known to involve in the genetic control of pigmentation in the chicken, with most of these have been mapped in the mouse. We also refined further the causative variants underlying a lightly feathered shank mutation. Our GWAS analysis map a number of putative novel loci that may underlie the genetic control of the traits analysed and this has laid a foundation for subsequent work that would involve targeted sequencing and a candidate gene approach. This study is the first of its kind in Africa that uses a large number of samples and a high density SNP array to unlock phenomic and genomic landscape of the true type village chickens

Casein loci SNPs and haplotypes association with milk production traits of Norwegian Goats and their French Alpine Crosses

På grunn av deres kvantitative og kvalitative effekter på melkeproduksjonen og melkekomponenter, har kaseinloci vært og vil fortsatt være gjenstand for intens forskning. Vårt arbeid var også ment å studere haplotypestrukturer og –diversitet og additive og dominante effekter av kasein-SNPer og haplotyper på melkeproduksjonstrekk i norske geiter og deres franske alpinkryssinger (kryssinger). Vår analyse brukte 376 geiter (216 norske geiter og 160 kryssinger) som har fenotypiske registreringer på test dagen av melkeproduksjonen og genotypedata slik at en kunne beregne faste additive- og dominanseffekter av SNPer og haplotyper på studerte trekk. Analyse av koplingsulikevekt (LD) og haplotypekonstruksjon ble gjort med 38 SNP markører i alle kaseinloci for de to geitepopulasjoner. Våre resultater viste at det er omfattende koplingsulikevekt, spesielt for S1- og -kasein, men LD er relativt svak for kryssingene. Omfanget av LD varierer fra null til fullstendig mellom loci. Kopling innen locus var sterkere enn på tvers av loci. På grunn av omfattende LD var antallet plausible konstruerte haplotyper langt mindre enn forventet antall. Mangfoldet av plausible haplotyper er høyt for kryssingene særlig for - og -kasein. Derfor ble mer tagger-SNPer observert i kryssingene. Våre resultater fra analyse av SNPhaplotypenes additive- og dominans- fast effekt og av effektene av hele kaseinloci og individuelle kaseingener viste signifikante effekt på melkeproduksjonen og dens komponenter bortsett fra laktoseprosent. Derfor kan denne genetiske variasjonen blant haplotypene brukes i det genetiske forbedringsprogrammet for norske geiter gjennom haplotypeassistert seleksjon. Vi fant også signifikant effekt av noen kasein-SNPer på melkeproduksjonsegenskaper, spesielt for S2- og -kasein. Denne SNP-effekten er imidlertid lokalisert innenfor et segment av tilstøtende SNPer innen ett locus. SNP 14 delesjon (D) i exon12 i S1-kasein har betydelig additiv genetisk effekt på FFA og urea-innholdet i melk og det er en betydelig dominans effekt av AD-genotypen på SCC. Analysen av vårt materiale viste at frekvensen av D-allelet er redusert til 0,66, noe som viser at seleksjonsprogrammet virker mot dette allelet. Blant de studerte egenskaper hadde de norske geitene og kryssingene betydelige forskjeller bare for laktoseprosent. Men kryssingene er like gode som de norske geitene for resten av egenskapene, - noe som viser betydningen av dette kryssingsprogrammet utover det å skape genetisk variasjon. Derfor ville sammenlignende studier på renrasenivå være et alternativ for å dokumentere hvorvidt denne forskjellen skyldes heteroseeffekt eller skyldes reelle genetiske forskjeller mellon rasane. Due to their quantitative and qualitative implications on milk yield and its component traits, casein loci have been and would remain the subject of intense research. Our work was also intended to resolve haplotype structures and diversity, and to study the additive and dominance effects of casein SNPs and SNP haplotypes on milk production traits in the Norwegian goats and their French Alpine crosses (crosses). Our analysis used 376 does (216 Norwegian goats and 160 crosses) that have phenotypic records on test day milk yield and genotype data. Linkage disequilibrium (LD) resolution and haplotype construction were done using 38 SNP markers detected in the entire casein loci block of the two goat populations. Our result showed that, there was extensive LD, especially for S1- and -casein loci; however, the LD is relatively weak in the crosses. The extent of LD varies across the casein loci segment from nearly zero to almost complete LD. The intra-locus LD was stronger than the LD found for inter-loci. Due to extensive LD, the numbers of plausible haplotypes constructed were by far less than what were expected. The diversity of plausible haplotypes is high for the crosses especially for - and -casein. Therefore, more tagger SNPs were detected for the crosses. Our results from SNP halpotypes additive and dominance fixed effect analysis of the entire casein loci and of the individual casein genes showed significant effect on studied milk production traits except lactose percentage. Therefore, this genetic variation observed among haplotypes can be used in the genetic improvement program of Norwegian goats through haplotype assisted selection. We also found significant effect of some casein SNPs on milk production traits, especially for S2- and -casein SNPs. The SNP effect is, however, localized within a segment of adjacent SNPs even at locus level. SNP 14 deletion (D) of exon12 in S1-casein has significant additive genetic effect on FFA and urea content of the milk and a significant dominance effect of AD genotype on SCC. Our analysis showed that the frequency of D allele for Norwegian goats has reduced to 0.66, which showed that the selection program is against this allele. Among studied traits, the Norwegian goats and the crosses significantly differ for lactose percentage only. However, the crosses were as good as the Norwegian goats in the rest of the traits, which indicates the importance of this crossbreeding program beyond creating genetic variation. Therefore, comparative study at pure breed level would be a plausible option to substantiate whether this difference is due to heterotic effect or real genetic difference between breeds

COVID-19: socio-economic impacts and challenges in the working group

The COVID-19 pandemic has influenced the lives of the global community, consequently, many parts of people's lives have been jeopardized. Therefore, there is a need to curb the spread of coronavirus. Accordingly, countries are enforcing partial or full-fledged lockdown to restrict all sorts of socialization. However, studies reported that people have despised the ordinances. The study assessed the economic, societal, and psychological impacts of the pandemic and the practice of abiding by curfews by staying and working from home. One hundred thirty-three government, private, and self-employed workers have anonymously and voluntarily completed an online survey. The change in lifestyle associated with the pandemic influenced the working group economically, socially, emotionally, and spiritually. In addition to inflation in the prices of food and commodity, workers have spent unintended costs for the prevention of the COVID-19 such as hand sanitizer and facemask. Furthermore, staying home was unbearable for the majority of the respondents and led to stress, boredom, and confined feelings which forced them to leave their homes to liberate themselves. Nevertheless, flexibility in time management, reduced commuting, and being safe from COVID-19 made the lockdown advantageous for some of the respondents. Telecommuting is influenced by factors such as home suitability to work, availability of supplies, and the behavior of the workers. Home suitability to work and access to vital working facilities varied between government, private, and self-employed individuals. Government employees exceptionally lack appropriate homes and resources to work. Therefore, to minimize the impact of COVID-19 on people's life it is important to make timely adjustments to the enforced orders to make them more productive