Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world?

Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Introduction

The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.

Methods

In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.

Results and discussion

We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

Review of sheep breeding and genetic research in Türkiye

The livestock industry in Türkiye is vital to the country's agricultural sector and economy. In particular, sheep products are an important source of income and livelihood for many Turkish smallholder farmers in semi-arid and highland areas. Türkiye is one of the largest sheep producers in the world and its sheep production system is heavily dependent on indigenous breeds. Given the importance of the sheep industry in Türkiye, a systematic literature review on sheep breeding and genetic improvement in the country is needed for the development and optimization of sheep breeding programs using modern approaches, such as genomic selection. Therefore, we conducted a comprehensive literature review on the current characteristics of sheep populations and farms based on the most up-to-date census data and breeding and genetic studies obtained from scientific articles. The number of sheep has increased in recent years, mainly due to the state's policy of supporting livestock farming and the increase in consumer demand for sheep dairy products with high nutritional and health benefits. Most of the genetic studies on indigenous Turkish sheep have been limited to specific traits and breeds. The use of genomics was found to be incipient, with genomic analysis applied to only two major breeds for heritability or genome-wide association studies. The scope of heritability and genome-wide association studies should be expanded to include traits and breeds that have received little or no attention. It is also worth revisiting genetic diversity studies using genome-wide single nucleotide polymorphism markers. Although there was no report of genomic selection in Turkish sheep to date, genomics could contribute to overcoming the difficulties of implementing traditional pedigree-based breeding programs that require accurate pedigree recording. As indigenous sheep breeds are better adapted to the local environmental conditions, the proper use of breeding strategies will contribute to increased income, food security, and reduced environmental footprint in a sustainable manner.

Genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep using parametric models and artificial neural networks

This study aimed to assess the predictive ability of parametric models and artificial neural network method for genomic prediction of the following indicator traits of resistance to gastrointestinal nematodes in Santa Inês sheep: packed cell volume (PCV), fecal egg count (FEC), and Famacha© method (FAM). After quality control, the number of genotyped animals was 551 (PCV), 548 (FEC), and 565 (FAM), and 41,676 SNP. The average prediction accuracy (ACC) calculated by Pearson correlation between observed and predicted values and mean squared errors (MSE) were obtained using genomic best unbiased linear predictor (GBLUP), BayesA, BayesB, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayesian regularized artificial neural network (three and four hidden neurons, BRANN_3 and BRANN_4, respectively) in a 5-fold cross-validation technique. The average ACC varied from moderate to high according to the trait and models, ranging between 0.418 and 0.546 (PCV), between 0.646 and 0.793 (FEC), and between 0.414 and 0.519 (FAM). Parametric models presented nearly the same ACC and MSE for the studied traits and provided better accuracies than BRANN. The GBLUP, BayesA, BayesB and BLASSO models provided better accuracies than the BRANN_3 method, increasing by around 23% for PCV, and 18.5% for FEC. In conclusion, parametric models are suitable for genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep. Due to the small differences in accuracy found between them, the use of the GBLUP model is recommended due to its lower computational costs.

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs-for group of traits withers height, rump height, body length, 2 SNPs-for withers height and rump height, 1 SNP-for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.

SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep

Rambouillet sheep are commonly raised in extensive grazing systems in the US, mainly for wool and meat production. Genomic evaluations in US sheep breeds, including Rambouillet, are still incipient. Therefore, we aimed to evaluate the feasibility of performing genomic prediction of breeding values for various traits in Rambouillet sheep based on single nucleotide polymorphisms (SNP) or haplotypes (fitted as pseudo-SNP) under a single-step GBLUP approach. A total of 28,834 records for birth weight (BWT), 23,306 for postweaning weight (PWT), 5,832 for yearling weight (YWT), 9,880 for yearling fibre diameter (YFD), 11,872 for yearling greasy fleece weight (YGFW), and 15,984 for number of lambs born (NLB) were used in this study. Seven hundred forty-one individuals were genotyped using a moderate (50 K; n = 677) or high (600 K; n = 64) density SNP panel, in which 32 K SNP in common between the two SNP panels (after genotypic quality control) were used for further analyses. Single-step genomic predictions using SNP (H-BLUP) or haplotypes (HAP-BLUP) from blocks with different linkage disequilibrium (LD) thresholds (0.15, 0.35, 0.50, 0.65, and 0.80) were evaluated. We also considered different blending parameters when constructing the genomic relationship matrix used to predict the genomic-enhanced estimated breeding values (GEBV), with alpha equal to 0.95 or 0.50. The GEBV were compared to the estimated breeding values (EBV) obtained from traditional pedigree-based evaluations (A-BLUP). The mean theoretical accuracy ranged from 0.499 (A-BLUP for PWT) to 0.795 (HAP-BLUP using haplotypes from blocks with LD threshold of 0.35 and alpha equal to 0.95 for YFD). The prediction accuracies ranged from 0.143 (A-BLUP for PWT) to 0.330 (A-BLUP for YGFW) while the prediction bias ranged from -0.104 (H-BLUP for PWT) to 0.087 (HAP-BLUP using haplotypes from blocks with LD threshold of 0.15 and alpha equal to 0.95 for YGFW). The GEBV dispersion ranged from 0.428 (A-BLUP for PWT) to 1.035 (A-BLUP for YGFW). Similar results were observed for H-BLUP or HAP-BLUP, independently of the LD threshold to create the haplotypes, alpha value, or trait analysed. Using genomic information (fitting individual SNP or haplotypes) provided similar or higher prediction and theoretical accuracies and reduced the dispersion of the GEBV for body weight, wool, and reproductive traits in Rambouillet sheep. However, there were no clear improvements in the prediction bias when compared to pedigree-based predictions. The next step will be to enlarge the training populations for this breed to increase the benefits of genomic predictions.

Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review

Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.

Status quo of genetic improvement in local goats: a review

This review aims to summarize and synthesize the fragmented information available on the genetic improvement of local goats (criollo, indigenous, native) on the American and other continents, where populations with these goats have an important role in food security and the economy of rural communities, as well as in conservation of biodiversity and productivity improvement. Topics such as the current state of goat production globally, conservation programs, resistance to parasites and diseases, use of phenotypical characteristics and genomic information, and molecular markers for genetic improvement are addressed. The main challenges, opportunities, and limitations described in recent literature concerning local goats in the immediate future are discussed.

Effects of Lactobacillus rhamnosus and Enterococcus faecalis Supplementation as Direct-Fed Microbials on Rumen Microbiota of Boer and Speckled Goat Breeds

The effects on rumen microbial communities of direct-fed probiotics, Lactobacillus rhamnosus and Enterococcus faecalis, singly and in combination as feed supplements to both the Boer and Speckled goats were studied using the Illumina Miseq platform targeting the V3-V4 region of the 16S rRNA microbial genes from sampled rumen fluid. Thirty-six goats of both the Boer and Speckled were divided into five experimental groups: (T1) = diet + Lactobacillus rhamnosus; (T2) = diet + Enterococcus faecalis; (T3) = diet + Lactobacillus rhamnosus + Enterococcus faecalis; (T4, positive control) = diet + antibiotic and (T5, negative control) = diet without antibiotics and without probiotics. Our results revealed that Bacteroidetes, Firmicutes, TM7, Proteobacteria, and Euryarchaeota dominate the bacterial communities. In our observations, Lactobacillus rhamnosus and Enterococcus faecalis supplements reduced the archaeal population of Methanomassiliicocca in the T1, T2 and T3 groups, and caused an increase in the T4 group. Chlamydiae were present only in the T5 group, suggesting that probiotic and antibiotic inhibit the growth of pathogens in the rumen. We inferred, based on our results, that Lactobacillus rhamnosus and Enterococcus faecalis favour the survival of beneficial microbial communities in the goats’ rumen. This may lead to an overall improved feed efficacy and growth rate.

Small Ruminants and Its Use in Regenerative Medicine: Recent Works and Future Perspectives

Simple Summary

Small ruminants such as sheep and goats have been increasingly used as animal models due to their dimensions, physiology and anatomy identical to those of humans. Their low costs, ease of accommodation, great longevity and easy handling make them advantageous animals to be used in a wide range of research work. Although there is already a lot of scientific literature describing these species, their use still lacks some standardization. The purpose of this review is to summarize the general principles related to the use of small ruminants as animal models for scientific research.

Abstract

Medical and translational scientific research requires the use of animal models as an initial approach to the study of new therapies and treatments, but when the objective is an exploration of translational potentialities, classical models fail to adequately mimic problems in humans. Among the larger animal models that have been explored more intensely in recent decades, small ruminants, namely sheep and goats, have emerged as excellent options. The main advantages associated to the use of these animals in research works are related to their anatomy and dimensions, larger than conventional laboratory animals, but very similar to those of humans in most physiological systems, in addition to their low maintenance and feeding costs, tendency to be docile, long life expectancies and few ethical complications raised in society. The most obvious disadvantages are the significant differences in some systems such as the gastrointestinal, and the reduced amount of data that limits the comparison between works and the validation of the characterization essays. Despite everything, recently these species have been increasingly used as animal models for diseases in different systems, and the results obtained open doors for their more frequent and advantageous use in the future. The purpose of this review is to summarize the general principles related to the use of small ruminants as animal models, with a focus on regenerative medicine, to group the most relevant works and results published recently and to highlight the potentials for the near future in medical research.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BACKGROUND

Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits.

RESULTS

SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117).

CONCLUSIONS

Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

The potential for vaccines against scour worms of small ruminants

This review addresses the research landscape regarding vaccines against scour worms, particularly Trichostrongylus spp. and Teladorsagia circumcincta. The inability of past research to deliver scour-worm vaccines with reliable and reproducible efficacy has been due in part to gaps in knowledge concerning: (i) host-parasite interactions leading to development of type-2 immunity, (ii) definition of an optimal suite of parasite antigens, and (iii) rational formulation and administration to induce protective immunity against gastrointestinal nematodes (GIN) at the site of infestation. Recent 'omics' developments enable more systematic analyses. GIN genomes are reaching completion, facilitating "reverse vaccinology" approaches that have been used successfully for the Rhipicephalus australis vaccine for cattle tick, while methods for gene silencing and editing in GIN enable identification and validation of potential vaccine antigens. We envisage that any efficacious scour worm vaccine(s) would be adopted similarly to "Barbervax™" within integrated parasite management schemes. Vaccines would therefore effectively parallel the use of resistant animals, and reduce the frequency of drenching and pasture contamination. These aspects of integration, efficacy and operation require updated models and validation in the field. The conclusion of this review outlines an approach to facilitate an integrated research program.

Ancestral Haplotype Mapping for GWAS and Detection of Signatures of Selection in Admixed Dairy Cattle of Kenya

Understanding the genetic structure of adaptation and productivity in challenging environments is necessary for designing breeding programs that suit such conditions. Crossbred dairy cattle in East Africa resulting from over 60 years of crossing exotic dairy breeds with indigenous cattle plus inter se matings form a highly variable admixed population. This population has been subject to natural selection in response to environmental stresses, such as harsh climate, low-quality feeds, poor management, and strong disease challenge. Here, we combine two complementary sets of analyses, genome-wide association (GWA) and signatures of selection (SoS), to identify genomic regions that contribute to variation in milk yield and/or contribute to adaptation in admixed dairy cattle of Kenya. Our GWA separates SNP effects due to ancestral origin of alleles from effects due to within-population linkage disequilibrium. The results indicate that many genomic regions contributed to the high milk production potential of modern dairy breeds with no region having an exceptional effect. For SoS, we used two haplotype-based tests to compare haplotype length variation within admixed and between admixed and East African Shorthorn Zebu cattle populations. The integrated haplotype score (iHS) analysis identified 16 candidate regions for positive selection in the admixed cattle while the between population Rsb test detected 24 divergently selected regions in the admixed cattle compared to East African Shorthorn Zebu. We compare the results from GWA and SoS in an attempt to validate the most significant SoS results. Only four candidate regions for SoS intersect with GWA regions using a low stringency test. The identified SoS candidate regions harbored genes in several enriched annotation clusters and overlapped with previously found QTLs and associations for different traits in cattle. If validated, the GWA and SoS results indicate potential for SNP-based genomic selection for genetic improvement of smallholder crossbred cattle.

Genetic Parameters for Growth and Kid Survival of Indigenous Goat under Smallholding System of Burundi

The goal of this study was to estimate genetic parameters for the growth, conformation, and survival of goat kids raised in smallholder farming systems in Burundi. To do this, measurements were taken on live weight, thoracic perimeter, length, and height at birth (n = 1538 animals), at 3 months (n = 1270 animals), at 6 months (n = 992 animals), at 9 months (n = 787 animals), and at 12 months (n = 705 animals). Kids were born between 2016 and 2019, from 645 dams and 106 bucks. Three bivariate animal models were used to estimate genetic parameters of body weight and conformation measurements as potential indicators of this weight. According to the measure, heritability was estimated between 15 and 17% and genetic correlations between 65 and 79%. An accelerated failure time animal model was used to estimate the heritability of survival for kids under one year, adjusted for birth weight. Goat survival was significantly prolonged by 0.64 days per kilogram of birth weight. The estimated heritability for this trait was 2%. Overall, these results suggest that a selection program could be implemented to improve animal growth, either directly on weight or indirectly on conformational traits. At the same time, efforts need to be made to improve rearing conditions to increase the survival of kids.

Leveraging Available Resources and Stakeholder Involvement for Improved Productivity of African Livestock in the Era of Genomic Breeding

The African continent is home to diverse populations of livestock breeds adapted to harsh environmental conditions with more than 70% under traditional systems of management. Animal productivity is less than optimal in most cases and is faced with numerous challenges including limited access to adequate nutrition and disease management, poor institutional capacities and lack of adequate government policies and funding to develop the livestock sector. Africa is home to about 1.3 billion people and with increasing demand for animal proteins by an ever growing human population, the current state of livestock productivity creates a significant yield gap for animal products. Although a greater section of the population, especially those living in rural areas depend largely on livestock for their livelihoods; the potential of the sector remains underutilized and therefore unable to contribute significantly to economic development and social wellbeing of the people. With current advances in livestock management practices, breeding technologies and health management, and with inclusion of all stakeholders, African livestock populations can be sustainably developed to close the animal protein gap that exists in the continent. In particular, advances in gene technologies, and application of genomic breeding in many Western countries has resulted in tremendous gains in traits like milk production with the potential that, implementation of genomic selection and other improved practices (nutrition, healthcare, etc.) can lead to rapid improvement in traits of economic importance in African livestock populations. The African livestock populations in the context of this review are limited to cattle, goat, pig, poultry, and sheep, which are mainly exploited for meat, milk, and eggs. This review examines the current state of livestock productivity in Africa, the main challenges faced by the sector, the role of various stakeholders and discusses in-depth strategies that can enable the application of genomic technologies for rapid improvement of livestock traits of economic importance.

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest H_O (0.335±0.13) and H_E (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest H_O (0.401±0.12) and H_E (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high F_IS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average F_ST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

Effects of genomic selection for intramuscular fat content in breast muscle in Chinese local chickens

Improvements in living standards have resulted in consumers having higher expectations for chicken meat quality. This is particularly true in Asia, where there is high consumer preference for local breeds. Nothing is presently known about the effectiveness of using genomic selection (GS) strategies in chickens to genetically improve meat quality traits that cannot be measured in living potential parents. In this study, 724 Beijing-You chickens were used as a training population; all were genotyped using Illumina 60K SNP chips, and intramuscular fat content in breast muscle (IMFbr ) was measured. Birds in the GS line were selected based on genomic estimated breeding values, IMFbr being the sole trait. Genetic progress in one generation was compared to that from conventional family-based selection, and both were evaluated against random-bred controls. Results showed that relative to the random-bred controls, IMF percentage was improved 9.62% using GS, comparable to the 10.38% improvement using family-based selection. We quantified the effectiveness of GS when applied to a meat quality trait with low heritability in chickens. We plan to introduce custom SNP chips, appropriate for native chicken breeds in China, to assist in applying GS in local breeding and accelerate genetic gain.