Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep.

Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle.

BACKGROUND: Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. RESULT: In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. CONCLUSIONS: Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies.

Crossed beaks in a local Swiss chicken breed.

BACKGROUND: Crossed beaks have been reported to occur in Appenzeller Barthuhn, a local Swiss chicken breed. The assumed causes for this beak deformity which are also seen in other bird species including domestic chickens, range from environmental influences to genetic factors. The aim of this project was to characterize the prevalence, the phenotype, and the underlying genetics of crossed beaks in Appenzeller Barthuhn chickens. RESULTS: The estimated prevalence of 7% crossed beaks in Appenzeller Barthuhn was significantly higher compared to two other local Swiss chicken breeds. A breeding trial showed significantly higher prevalence of offspring with deformed beaks from mating of affected parents compared to mating of non-affected parents. Examination of 77 Appenzeller Barthuhn chickens with crossed beaks showed a variable phenotype presentation. The deviation of the beak from the median plane through the head ranged from 1° to 61°. In more than 60% of the cases, the upper and lower beak were bent in the same direction, whereas the remaining cases showed different forms of crossed beaks. Computed tomographic scans and bone maceration of the head of two chickens with crossed beaks revealed that the maxilla and the mandibula were affected, while other parts of the skull appeared to be normal. The gene LOC426217, a member of the keratin family, was postulated as a candidate gene for beak deformity in domestic chickens. Sequencing of the coding region revealed two significantly associated synonymous variants for crossed beaks in Appenzeller Barthuhn chickens. A genome-wide association study and a comparative analysis of runs of homozygosity based on high-density SNP array genotyping data of 53 cases and 102 controls showed no evidence of association. CONCLUSIONS: The findings suggest a hereditary cause of crossed beaks in Appenzeller Barthuhn chickens. However, the observed variation in the phenotype, together with the inconclusive molecular genetic results indicates the need for additional research to unravel the genetic architecture of this beak deformity.

Assessment of performance and egg quality in laying hens of Spanish indigenous breed Black Castellana as compared with a selected white egg-layer strain.

Indigenous animal genetic resources should be preserved because of their well adaptation to the environment, their tolerance to low food availability and their sociocultural importance. The characterization of the quality of the products generated by heritage breeds may bring more arguments to encourage the raising of these animals. This study aimed at evaluating the egg performance and quality of Spanish indigenous Black Castellana (BC) breed as compared with a selected strain (Lohmann LSL-Classic). Four groups of 30 hens were arranged: 1) Lohmann hens fed a control diet; 2) BC hens fed the control diet; 3) Lohmann hens fed a diet including linseed at 70 g/kg (omega-3 diet); 4) BC hens fed the omega-3 diet. Egg production was higher by 12.3% for Lohmann hens but, since BC eggs were heavier by 15.4%, no effect of genetics was found on daily egg mass. Feed intake was higher by 5.0% for BC hens. Nonetheless, no difference was detected for feed conversion ratio. Eggshell was thicker by 6.78% in Lohmann eggs. Haugh units did not differ among freshly laid and stored eggs in Lohmann hens, whereas Haugh units decreased in stored BC eggs (80.5 vs. 76.7 vs. 72.3 at 0, 14, and 30 d of storage). Yolks of BC eggs contained less fat (57.5 vs. 60.8% DM), more protein (32.8 vs. 31.9% DM) and more cholecalciferol (1.25 vs. 1.22 µg/g DM), and showed lower proportion of saturated fatty acids (29.0 vs. 37.0%) and higher proportions of monounsaturated (45.7 vs. 39.6%) and polyunsaturated (25.2 vs. 23.4%) fatty acids. Feeding the omega-3 diet reduced the yolk proportions of saturated (32.5 vs. 33.5%) and monounsaturated (42.0 vs. 43.3%) fatty acids and increased those of polyunsaturated (25.4 vs. 23.2%) and ω-3 (7.05 vs. 2.42%) fatty acids. No effect due to genetics or diet was found on yolk color score or on yolk content in cholesterol, cobalamin, retinol and γ-tocopherol. This study represents the first exhaustive characterization of eggs from Spanish indigenous Black Castellana breed.

Fecal Microbiota and Diet Composition of Buryatian Horses Grazing Warm- and Cold-Season Grass Pastures.

The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistological fecal studies of horse diet composition on steppe pasture. The alpha diversity analysis showed horses had a more abundant and diverse gut microbiota in summer. There were significant effects on the beta diversity of microbial families, which were clustered by the warm and cold season in a principal coordinate analysis (PCoA), with 45% of the variation explained by two principal coordinates. This clustering by season was further confirmed by the significant differences observed in the relative abundances of microbial families and genera. The obtained results can serve as an experimental substantiation for further study of the impact of pasture grasses, which have a pharmacological effect, on the diversity of the gut microbiome and horse health.

Genomics of Dwarfism in Italian Local Chicken Breeds.

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as "dwarf", namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.

Characterization of the fecal microbiota of Pampa Rocha pigs, a genetic resource endemic to eastern Uruguay.

Pampa Rocha (PR) is a breed of pig that emerged in eastern Uruguay during the 18th century. They represent an important resource for non-intensive production using purebred or crossbred animals. However, productive activities have been oriented towards intensive production using commercial breeds, abandoning, except by some academic and educational institutions, the promotion of this creole breed. Thus, a population of few animals is still maintained, which could be in danger of disappearing. This work focuses on the fecal microbiota of these animals, which is related to the animal genetic background but also to their grazing capacity and resistance to weather. The structure and diversity of bacterial communities in the intestines of four PR adult females and of other breeds, including crosses, reared under non-grazing conditions, were analyzed and compared. Results obtained indicate that PR fecal microbiota is clearly different from those of other animals analyzed. Some sequences, corresponding to particular groups apparently related to the consumption of fiber, were strongly associated with PR pigs.

Phenotypic Analysis of Growth and Morphological Traits in Miniature Breeds of Japanese Indigenous Chickens.

Japanese indigenous chickens include approximately 50 breeds exhibiting various morphological traits, such as a long tail. These genetic resources will be important for revealing the genetic basis of morphological traits in the future. However, little is known about the phenotypic characteristics of each breed during the growth stages. To understand age-dependent changes in growth and morphological traits, we investigated tail length, tail number, body weight, and shank length at several time points using three genetically distinct Japanese indigenous chicken breeds. A total of 155 birds from the Tosa-jidori, Chabo, and Minohikichabo breeds were used for trait measurements from 1 to 36 weeks of age to reveal breed and sex effects. Significant sex differences through the growth stages were observed for all traits except for tail number. Although there were no clear breed differences in tail length traits at the 6- and 20-week stages, Minohikichabo ultimately had a significantly longer tail due to extended tail feather growth at later stages (28 and 36 weeks). By measuring two tail length variables (central and maximum), it was revealed that the shape of the tail feathers varies with the growth stage. Minohikichabo's tail number was higher than that of Tosajidori and Chabo at earlier ages (8 and 16 weeks), which leads to an elegant visual in Minohikichabo. Tosa-jidori's body weight was higher than that of Chabo and Minohikichabo, whereas the shank lengths of Chabo and Minohikichabo were shorter than those of Tosa-jidori. These differences in body weight and shank length were consistent from the early to late growth stages. These results revealed the age-dependency of growth and morphological trait breed characteristics.

Isolation, identification, and pathogenicity of a ALV-K strain from Chinese indigenous chicken breed.

Subgroup K avian leukosis virus (ALV-K) is a new subgroup of avian leukosis virus (ALV) first identified in Chinese indigenous chickens in recent years. In this study, an ALV-K strain was isolated from Luhua chicken in Shandong province, China, and designated SD20LH01. The full-length genomic sequence of SD20LH01 was 7491 bp, which had the highest homology with ALV-K reference strains GDFX0601, GDFX0602 and GDFX0603. The nucleotide homology of env gene of SD20LH01 with reference strains of subgroup A, B, C, D, E, and J was ranged from 57.1 to 93.2%, while 94.1 to 99.4% with other ALV-K reference strains. The nucleotide difference of SD20LH01 mainly clustered with gp85 gene and U3 sequence when compared with the reference strain of ALV-K. In order to investigate the pathogenicity of SD20LH01, SPF chicken embryos were infected by yolk sac inoculation, and 1-day-old chickens were infected by intraperitoneal inoculation of SD20LH01. The results showed that yolk sac inoculation of SD20LH01 could induce persistent viremia, growth retardation and reduce the immune response to NDV and AIV-H9 vaccines. However, intraperitoneal inoculation in 1-day-old chickens could only induce a low level of viremia. In addition, no tumors were found in infected chickens during the animal experiments. This study enriched the genomic sequence data of ALV-K isolated in Chinese indigenous chickens, and laid a foundation for further study on the pathogenesis and prevention of ALV-K.

Evaluation of non-linear growth curve models in the Vietnamese indigenous Mia chicken.

Understanding of animal growth is important for the improvement of management and feeding practices; however, little is known about the growth curve in Vietnamese indigenous chicken. This study was performed to determine the most appropriate models for describing the growth curve of Vietnamese Mia chicken. The study evaluated the performances of the Logistic, Gompertz, Richards, and Bridges models of body weights in 224 Mia chickens. Models were fitted using minpack.lm package in R software and Akaike's information criterion and Bayesian information criterion were used for model comparison. Based on these criteria, the Gompertz and Bridges were the best models for males and females, respectively. Estimated asymmetric weights (α) were ranged from 2,241.91 ± 14.74 (g) (Logistic) to 2,623.86 ± 30.23 (g) (Gompertz) for males and from 1,537.36 ± 10.97 (g) (Logistic) and 1,958.36 ± 72.92 (g) (Bridges) for females, respectively. The age at the inflection point was estimated from 9.32 to 10.5 weeks and from 8.51 to 9.86 weeks for males and females, respectively. In conclusion, the Gompertz model is the most suitable model for describing the growth curve of Mia chicken. The parameters obtained from growth models could help define feeding programs to meet nutritional needs from hatching to the age of maximum growth, reproduction programs, and marketing strategies.

A retrospective study reveals the Porcine circovirus-2f genotype predominant in the indigenous pig population of North-eastern India.

Porcine circovirus-2 (PCV2) is a widespread virus and presents sub-clinically in most of the swineherd. Globally, eight genotypes of PCV2 have been identified that is PCV2a to 2h. To determine the region-wide genotype distribution of PCV2 infection, with additional reference to indigenous breeds, a total of 1314 pig's clinical samples from the eight states of North-eastern India between 2011 and 2014; were analyzed. The overall prevalence rate of PCV2 in this region was 28.2% (370/1314) by PCR. The state-wise PCR based PCV2 prevalence rate was: Tripura (20.8%), Nagaland (25.0%), Meghalaya (25.8%), Assam (32.1%), Sikkim (32.6%), Manipur (33.3%), Mizoram (36.7%) and Arunachal Pradesh (42.3%). Subsequently, a total of 29 complete genomes of PCV2 were amplified and sequenced from these PCV2 positive samples. The phylogenetic tree represents that the 29 PCV2 isolates of this study were divided into four distinct genetic groups; PCV2a, PCV2b, PCV2d, and PCV2f. Among these, 14 PCV2 strains were classified as PCV2f, 13 classified as PCV2d, and one isolate of each classified as PCV2a and PCV2b. All the 14 PCV2f strains appeared from indigenous pigs of this region. Based on the date of collection, the present study further describes that the PCV2f genotypes circulate in the indigenous pigs' population back in 2011. The amino acid residues and the atomic coordinate structure (3D model) of PCV2f capsid protein represents similarity to PCV2d capsid protein support the efficacy of the existing PCV2 vaccine against the PCV2f. The observation of this study helps to understand the genotype distribution of PCV2 and stands as a reference for future molecular epidemiological studies in North-eastern India.

Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis.

As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h2) was 0.33 for height and 0.28 for weight trait in Jindo. At p-value < 5 × 10-5, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, HHIP, LCORL and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR and PTPN2, IGFI and RASAL2 for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (p < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog's population.

Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria.

Poultry are the most widely distributed type of livestock in Nigeria. Indigenous chickens are extremely common throughout the country. Indeed, approximately 83 million chickens are raised in extensive systems and 60 million in semi-intensive systems. To provide the first comprehensive overview of the maternal lineages in Southwest Nigeria, we analyzed 96 mitochondrial DNA control region sequences from 2 indigenous chicken ecotypes: Fulani and Yoruba. All samples belonged to the most frequent haplogroup (E) in Africa and Europe and showed noticeably low haplotype diversity. Although only 11 different haplotypes were detected, with 2 of them never found before in Nigeria, the presence of unique sequences among our indigenous samples testified to their status as an important genetic resource to be preserved. Furthermore, a total of 7,868 published sequences were included in the comparative analysis, which revealed an east-west geographic pattern of haplogroup distribution and led to the conclusion that the gene flow from Southeastern Asia mainly involved one mitochondrial clade. Moreover, owing to the extensive genetic intermixing among Nigerian chickens, conservation efforts are required to safeguard the extant mitochondrial variability in these indigenous ecotypes and establish future improvement and selection programs.

Differences in the Detailed Milk Mineral Composition of Italian Local and Saanen Goat Breeds.

Very little information about local breed goat milk is available, which is relevant for biodiversity preservation and local cheese production. This study aimed to evaluate the effect of breed and week of lactation on milk mineral profile of five Italian local breeds (Garganica, Girgentana, Jonica, Maltese and Mediterranean Red) and a cosmopolitan breed (Saanen). Sixty goats (10 per breed) from an experimental farm were enrolled in the study and sampled every 2 weeks for milk gross composition analysis. In addition, an individual milk sample was collected monthly from 42 goats (seven goats per breed) for mineral determination through inductively coupled plasma optical emission spectrometry. Data were analysed using a mixed linear model with repeated measures, including breed and week of lactation as fixed effects. Week of lactation affected mineral contents, except for B, being lower in early than late lactation, whereas, breed affected only P, Mg and Zn. Mediterranean Red and Jonica breeds' milk was richer in P than Maltese, and in Zn than Maltese, Girgentana and Saanen breeds. For Mg, only Saanen differed from Maltese. Such information might be useful for the valorisation of goat milk produced by autochthonous breeds.