Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.

Chinese Domestic Ducks Evolved from Mallard Duck (Anas platyrhynchos) and Spot-Billed Duck (A. zonorhyncha)

China has a rich genetic resource in its 34 domestic duck breeds. In order to detect the genetic diversity and explore the origin of these indigenous duck populations, the mitochondrial DNA (mtDNA) control region was sequenced and analyzed for 208 individual ducks, including 22 domestic breeds, wild Mallards ducks, Eastern spot-billed ducks, White Muscovy ducks, and Black Muscovy ducks. The haplotype diversity (Hd) was 0.653 and the average nucleotide diversity (Pi) was 0.005, indicating moderate genetic diversity. Sixty haplotypes were detected, and the maximum-likelihood (ML) phylogenetic tree and median-joining (MJ) network were generated from the sequence analyses. In this study, haplotypes from the Mallard duck (Anas platyrhynchos) were detected in most of the Chinese domestic duck breeds. In addition, the Eastern spot-billed duck (A. zonorhyncha) H8 haplotype was detected in two duck breeds. Only two haplotypes were found in Muscovy ducks, suggesting low genetic diversity within this population. The sequence and haplotype analyses revealed that both A. platyrhynchos and A. zonorhyncha contributed to the evolution of domestic ducks in China.

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.

High-resolution genomic analysis of four local Vietnamese chicken breeds

In Vietnam, local chicken breeds account for over 70% of the national poultry population. Although these breeds are abundant, their productivity is low and their use is threatened by the extensive importation of foreign productive breeds. In this context, conservation programmes targeting several emblematic breeds have been established. The goal of these programmes was to characterize endangered breeds and maintain a pool of characteristic birds for preserving their genetic heritage. To contribute to these programmes, we comprehensively characterized four Vietnamese local chicken breeds (Dong Tao, Ho, Mia and Mong) at the genomic level using high-density single-nucleotide polymorphism (SNP) genotyping. Despite originating in geographically close areas, Dong Tao and Ho were evidently different from each other as well as from Mong and Mia, which shared a more recent common ancestor. The genomic inbreeding coefficient revealed high homozygosity amongst the four breeds (10%-20%). The observation of clear differentiation at the genomic level supported the presence of distinct breeds; nonetheless, the occurrence of crossbred birds in a presumably purebred sample demonstrated the need to apply genomic tools to unambiguously assign the birds to the correct breed. Moreover, the occurrence of substantial inbreeding and the presence of subgroups in certain breeds warranted attention to create future nuclei for use in the conservation of these local breeds.

An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds

Simple Summary

The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity.

Abstract

Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.

Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (F_ST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD<0.5 and LD<0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the Russian White RG population, pruning was substantial for Dataset I, and F_ST values were only positive when LD<0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the Russian White RG population with the smallest r² values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates.

Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

Following chicken domestication, diversified chicken breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making chickens an ideal genetic research model. To better understand the genetic structure of chicken breeds under different selection pressures, we genotyped various chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and ROH analyses. The gamecock breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local chickens had lower genetic variation than the Chinese local breeds, which could be attributed to the shorter history of the European breed. ROH were present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild chickens). These ROH islands were involved in egg production, growth and silky feathers and other traits. Moreover, we estimated the effective sex ratio of these breeds to demonstrate the change in the ratio of the two sexes. We found that commercial chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, RJF comprised a greater proportion of males than females. Our results show the population genetics of chickens under selection pressures, and can aid in the development of better conservation strategies for different chicken breeds.

Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).

On the Extent of Linkage Disequilibrium in the Genome of Farm Animals

Given the importance of linkage disequilibrium (LD) in gene mapping and evolutionary inferences, I characterize in this review the pattern of LD and discuss the influence of human intervention during domestication, breed establishment, and subsequent genetic improvement on shaping the genome of livestock species. To this end, I summarize data on the profile of LD based on array genotypes vs. sequencing data in cattle and chicken, two major livestock species, and compare to the human case. This comparison provides insights into the real dimension of the pairwise allelic correlation and haplo-block structuring. The dependency of LD on allelic frequency is pictured and a recently introduced metric for moderating it is outlined. In the context of the contact farm animals had with human, the impact of genetic forces including admixture, mutation, recombination rate, selection, and effective population size on LD is discussed. The review further highlights the interplay of LD with runs of homozygosity and concludes with the operational implications of the widely used association and selection mapping studies in relation to LD.

Authentication of poultry products at the breed level using genetic markers

The Oravka tawny is a Slovak national breed of chicken. This breed has combined utility, which means it is valuable for both its meat and eggs. The Oravka tawny is linked to a specific region, Orava, and therefore these products could be protected by European geographical indication. The labeling and sale of chicken meat by the traditional breed of origin are widely used to promote quality and attract those products in the marketplace. For that use, we created the system and method of authentication that can reliably distinguish between the Oravka tawny, other chicken breeds, and other of Oravka”™s colorful characters. In our research, we analyzed 153 chicken feathers from the Oravka breed as well as from breeds used in the process of breeding the Oravka to their current state. They were divided into nine populations. To separate those populations, we used seven microsatellite markers recommended by FAO (Food and Agriculture Organization) and other authors. To create separate clusters of individual breeds, we used DAPC (discriminant analysis of principal components) analysis.

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.

Important candidate genes for abdominal fat content identified by linkage disequilibrium and fixation index information

Selection for rapid growth in chickens has always been accompanied by increased fat deposition and excessive fat deposition, especially abdominal fat, cannot only decrease feed efficiency but also cause many diseases. Finding the candidate genes associated with abdominal fat deposition is essential for breeding. To identify these candidate genes, we applied linkage disequilibrium and selection signature analysis using chicken 60 k single nucleotide polymorphism (SNP) chips in two broiler lines divergently selected for abdominal fat content for 11 generations. After quality control, 46,033 SNPs were left for analysis. Using these SNPs, we found that r2 was 0.06 to 0.14 in the lean line and 0.07 to 0.13 in the fat line for all 28 chromosomes (except GGA16). Pairwise SNP distances <25 kb showed a mean r2 = 0.33 in the lean line and r2 = 0.32 in the fat line. The fixation index (FST) analysis was carried out and 46 SNPs with the top 0.1% of the FST value was detected as the loci with selection signatures. Besides FST, hapFLK was also used to detect selection signatures for abdominal fat content. A total of 11 genes, including transient receptor potential cation channel subfamily C member 4, estrogen related receptor gamma, fibroblast growth factor 13, G-protein-signaling modulator 2, RAR related orphan receptor A, phospholipase A2 group X, mitochondrial ribosomal protein L28, metadherin, calcitonin receptor like receptor, serine/threonine kinase 39, and nuclear factor I A, were detected as the important candidate genes for abdominal fat deposition based on their basic functions. The results of the present study may benefit the understanding of genetic mechanism of abdominal fat deposition in chicken.

Rural household chicken management and challenges in the Upper River Region of the Gambia

Systematic assessment and documentation of extensive livestock production systems are necessary to design or review breeding programs, extension services, and policies. This study therefore examined management practices and challenges concerning village chicken production in the Upper River Region of the Gambia. The data gathered with 45-variable semi-structured questionnaires were analyzed based on the household head's education status and gender. Illiteracy level was high, and only 38% indicated that they attended certain schools. There was a significant relationship (p < 0.05) and phi coefficient of 0.35 between household heads' education status and record keeping. None of the examined management practices had a statistically significant relationship (p > 0.05) with household heads' gender. Children (10-14 years) were mostly responsible for providing care to the chickens. Foundation and replacement stocks were mainly acquired through purchase (78%). Many households (74%) indicated supplementary feeding of their flocks but only 34% provided separate houses apart from the household dwellings. Newcastle (68%) was the most common disease. Sick birds were recognized by restlessness (34%) and diarrhea (28%). External parasites were mainly controlled through local practices (52%) while the most common way to dispose dead birds was to throw them away (88%). Up to 90% indicated no formal training on disease management and access to extension agents was also low (20%). Control of chicken movement was occasionally done to protect birds from predators (60%) and then, to avoid contagious diseases (38%). Individual farmers and their associations need to be supported by stakeholders to access relevant information and uptake improved management techniques.

Whole genomic prediction of growth and carcass traits in a Chinese quality chicken population

By incorporating high-density markers into breeding value prediction models, the whole genomic prediction (WGP) method can effectively accelerate genetic improvement in livestock breeding. However, the performance of WGP varies across species and populations and is affected by the underlying genetic architecture. In particular, very little is known about the performance of WGP for many chicken breeds. Here we estimate the genetic parameters and evaluate the performance of WGP for 18 growth and carcass traits in a Chinese quality chicken population. In total, 435 chickens were systematically phenotyped and genotyped using a 600K genotyping array. Two variance component estimation scenarios, 3 breeding value prediction methods, and 2 validation procedures were compared. The results showed that the heritability of these 18 traits was medium to high (ranging from 0.28 to 0.60) and that deviations existed between the heritability estimated from pedigrees and markers. Compared with conventional breeding methods, WGP could potentially increase the selection accuracy by 20% or more depending on the prediction model used, the trait under consideration, and the genetic connectedness between the training and validation individuals. Our results showed the potential of implementing genomic selection in small breeding herds.