Indigenous Goat Selection and Breeding Practices in Pastoral areas of West Guji zone, Southern Oromia, Ethiopia

Placing relevant breeding objectives and identification of indigenous breeding practices is crucial to integrating modern development in animal breeding into purposeful industry programs. Hence, the objective of this study was to identify selection criteria and indigenous breeding practices of the goat in Abaya and Galan district southern Oromia, part of Ethiopia. Data were collected from 180 households through interview schedules and focus group discussions. The effective population size and inbreeding rate of the community were calculated using ΔF = 1/2Ne. Conformation, growth rate, coat color for buck and conformation, twining ability, age at sexual maturity, kidding interval, and color for females are selection criteria for replacement of stock in the study area. In both districts, farmers have relatively similar production and breeding objectives. Conformation is hub selection criteria for replacement of breeding flock. The study area has liable by inbreeding 0.22 in Abaya and 0.29 in Galan. Goat in the study area is prolific twinning birth (72.22%). Trait preferences of farmers in goats were conformation, growth rate, twinning, and kidding interval. Hence adopting a community-based goat breeding program that is suited to study areas which aimed at improving preferred traits is relevant.

Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

Identification of genetic diversity of Bali cattle in Bali and Nusa Penida Island with microsatellite DNA

Bali cattle is one of Indonesia’s biodiversity with some superiority. Bali cattle scattered in various region, built centered in Bali Island. Polymorphism is very important to keep a population. Microsatellite is one of easiest methods to identify genetic diversity. The aim of this research was to identify genetic polymorphism loci Bali cattle from SPS115, ETH225, and INRA37 in Bali island and Nusa Penida island with microsatellite DNA labeling system. SPS115, ETH225 and INRA37 had been analyzed from total sample of 48 Bali cattle in Bali Island and 47 in Nusa Penida Island. The results of sequent were analyzed by GenAlEx 6.41. The results of this research showed that SPS115, ETH225 and INRA37 are of higher diversity. The highest heterozygosity was found in loci ETH225 in Bali island. The highest PIC was found in loci INRA37 in Nusa Penida Island. The inbreeding rate of Bali cattle was up to 14.1%. Bali cattle in Bali island and Nusa Penida island were different.

Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability.

Influence of the degree of homozygosity of STR-loci on the fertility of thoroughbred horses

Purpose: to study the effect of the level of homozygosity and inbreeding on the fecundity of thoroughbred mares.Materials and methods. A total of 3662 heads of breeding sows from leading stud farms of the Russian Federation were selected for the analysis. The influence of the homozygosity level on 17 microsatellite DNA loci on the main indices of reproduction of thoroughbred mares, such as the safe yield of foals and the number of fetal years, was analyzed in the article. All mares in the experimental sample had at least three years of breeding use. Individual fecundity rates and the number of homozygous loci in the STR profile were calculated for each horse.Results. The highest live foal yields (75.92%) had sows with homozygosity levels of 62.78-69.02%, and the lowest foal yields (45.73%) were recorded in mares with the highest homozygosity levels (75.28-76.92%). The maximum foal yield (65.85%) was determined in sows with an inbreeding rate of 4.1% or more, with a productive longevity of 6.26 fetal years on average. Analysis of the data showed that the level of inbreeding had almost no effect on the yield of live foals (R=0.010 at P>0.05), but had a negative correlation with the number of fruiting years (R=-0.092 at P<0.005).Conclusion. Estimation of homozygosity level of thoroughbred horses is especially relevant, as this breed has been perfected by purebred breeding method only for more than thirty years. In the thoroughbred horse breed, it is necessary to create a system of maintaining heterozygosity as well as the diversity of genotypes through the organization of breeding work.

Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species.Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window-based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses.Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The Canadian inbreeding rate appears to be higher, presumably due to isolation of subpopulations, than the inbreeding rate of the Iowa population.Conclusions This study was the first to document that brood stock Muskellunge from Iowa showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected. Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, but apparent isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. Finally, these results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

Study on the Gembrong Goat Inbreeding in Tumbu Village, Indonesia

Gembrong goat is an Indonesian breed originating from Bali Province that is very rare, having a high level of inbreeding. The inbreeding coefficient (Fis), inbreeding rate (IR), and inbreeding probability (PI) values of Gembrong goat were estimated in Tumbu village, Bali province, Indonesia. Previous studies provide data on the pedigree records of goats in 2015. According to research, the Fis value of Gembrong goats at Tumbu village was 0.413, putting them in the high category (Fx > 0.125). The IR value in the Gembrong population at Tumbu village was 0.025, putting it in the high group (IR > 0.020). The PI value in the F1 Gembrong population was 0.184, which was in the low category (PI 0.50). In conclusion, the elevated Fis and IR values in Gembrong goats were caused by a small population size. In the future, the Gembrong goat recording system will be critical for reducing inbreeding.

An Analysis of the Genetic Relationships and Inbreeding in Tatra Shepherd Dogs Depending on the Type of Breeding

The aim of the study was the analysis of the structure of the population, relationship coefficients, and inbreeding trends in terms of: sex, breeding system, and inbreeding degree of Tatra Shepherd dogs. The breed's inbreeding rate was 6.34%, and for a standardised 4-generation population was 6.68%. The highest inbreeding rate was found in "non-champion-dogs" and in "Polish dog" groups consisting of males and females. The limit value FX was exceeded for 25.65% of Tatra dogs, and the critical value was exceeded for 11.52%. An increasing ancestor loss coefficient (AVK) was found, which may result in an increased number of inbred animals. In particular, this referred to female dogs in the nCH, PL, and Z groups, whereas a significant increase of AVK was observed in the group of male dogs from foreign kennels. The resulting COR values were 55.58% for males and 55.44% for females.

Population Structure Analysis of Javan Rhinoceros at Ujung Kulon National Park, West Java

<p>Javan rhino (Rhinoceros sondaicus) is one of the rare animals with critically endangered status. The Ujung Kulon National Park (UKNP) is one of javan rhino habitat in Indonesia. Every year the monitoring program for javan rhino in UKNP was performed to identify the animals. This research was aimed to analyze the population structure of javan rhino based on the records data from 2011 to 2019 in UKNP. Research showed that the natural increase (NI) and birth rate (BR) values were 17.34% (moderate) and 67.33% (high) respectively. The net return rate (NRR) value was 15.38% (male) and 14.28% (female). The NRR value in the present study was lower than 100% and caused by less number of animals in a population for 30 years of breeding length. Despite this, the inbreeding rate of javan rhino at UKNP in 2019 was 0.01 (low). It was concluded that the natural increase of javan rhino at UKNP showed a good parameter but the population number needs to be increased.</p>

Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse

The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an “ideal type” that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height.