Analysing the genetic diversity of three sheep breeds in Turkey and nearby countries using 50 K SNPs data.

This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population's genetic characteristics and conservation requirements.

Analysing the genetic diversity and population structure of five native Turkish cattle breeds using SNP data.

The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035-0.071) and Asian breeds (Fst = 0.025-0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.

Assessment of the association of the MOGAT1 and MOGAT3 gene with growth traits in different growth stages in Holstein calves.

The members of the monoacylglycerol acyltransferase (MOGAT) family are essential candidate genes that influence economic traits associated with triglyceride synthesis, dietary fat absorption, and storage in livestock. In addition, the MOGAT gene family may also play an essential function in human polygenic diseases, like type 2 diabetes and obesity. The present study was conducted on Holstein calves to find the association between MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A and growth traits. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was performed for genotyping the MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A genes' locus using the TaqI, MspI, and BsuRI restriction enzyme. The allele frequency of A and G of the MOGAT1 locus was 0.79 and 0.21, respectively, while the genotype frequency was 0.65, 0.28, and 0.07 for AA, AG, and GG, respectively. While the allele and genotype frequencies of the MOGAT3/g.A229G locus were 00.57( A 1 ), 0.43( G 1 ), 0.35( A 1 A 1 ), 0.45( A 1 G 1 ), and 0.20( G 1 G 1 ), the allele and genotype frequencies of the MOGAT3/g.G1627A locus were 0.49( A 2 ), 0.51( G 2 ), 0.25( A 2 A 2 ), 0.49( A 2 G 2 ), and 0.26( G 2 G 2 ). Chi-square analysis showed that MOGAT3/g.G1627A distribution was at the Hardy-Weinberg disequilibrium ( p   <  0.05), and MOGAT1 and MOGAT3/g.A229G distribution was at the Hardy-Weinberg equilibrium ( p   >  0.05). In total, two statistical methods (general linear model (GLM) and PROC MIXED) were used to identify an association between gene locus and growth traits. An association analysis showed a statistically significant difference between the MOGAT1 and body weight, body length, and chest circumference, MOGAT3/g.A229G with average daily gain (ADG) and withers height, and MOGAT3/g.G1627A with body weight and body length ( p   <  0.05). The results confirmed that the MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A locus are strong candidate genes that could be considered molecular markers for growth traits in cattle breeding.

Estimation of the associations between GH and DGAT1 genes and growth traits by using decision tree in Awassi sheep.

GH and DGAT1 are candidate genes associated with growth traits in sheep breeds. This study aims to determine the association between growth traits and GH and DGAT1 gene polymorphism using three statistical methods in Awassi sheep. The polymorphism was detected by the PCR-RFLP method. Three genotypes (AA, AB and BB) were observed for GH gene locus with allele and genotype frequency 0.70(A) and 0.30(B); 0.60(AA), 0.20(AB) and 0.20(BB). Three genotypes (CC, CT and TT) were found for DGAT1 gene locus with allele and genotype frequency 0.58(C) and 0.42(T); 0.47(CC), 0.23(CT) and 0.30(TT). The genes were in agreement with Hardy-Weinberg equilibrium (p > 0.05). CHAID, CRT and GLM were used to identify the association between growth traits and gene polymorphism. The results showed an association between GH locus and body weight and tail length. Also, found an association between DGAT1 locus and tail length. The three methods showed similar results in determining the association between genes and growth traits. Thus, the CHAID and CRT methods can evaluate the association between genes and growth traits.

Relationships between FAMACHA© scores and parasite incidence in sheep and goats.

One of the most important activities in animal raising is parasite control. Since parasites share what animals eat on one hand, they have disease-causing effects on the other hand, they are parasites that must be fought. In fact, they can be responsible for the decrease in yield and can also cause death. Haemonchus contortus parasite from the Trichostrongylidae family is a blood parasite that causes anemia in sheep and goats. In this study, using the FAMACHA© card, which is widely used in the determination of anemia caused by Haemonchus contortus in the world, the color of the conjunctiva was scored in Akkaraman sheep and Hair goats raised in the Sizma district of Konya, and the relations between the score and the parasite type and density were determined. Accordingly, while no animals with 1 and 5 scores were observed in sheep, the numbers of animals with scores of 2, 3, and 4 were determined as 7.84%, 40.2%, and 52.96%, respectively. Parasite eggs belonging to the Trichostrongylidae family were observed in 96.07% of the sheep. On the other hand, no animal with score 1 or 2 was observed in goats. The numbers of animals with 3, 4, and 5 scores were determined as 6.12%, 54.08%, and 39.80%, respectively. Eimeria, the most common parasite species, was found in 68.18% of the goats and parasite eggs from the Trichostrongylidae family were observed in 17.05%. As a result, it was concluded that the card in question was a practical, easily available, and cheap tool in the detection of anemia by using the relationships between FAMACHA© card scoring and parasite loads.

Estimate of the Association of IGF-I and IGFALS Genes with Growth Traits in Hamdani Sheep

Abstract IGF-I and IGFALS play a vital stimulator role in skeletal growth, cell differentiation, metabolism, and other physiological processes. A total of 65 (male and female) animals were used in the study. Animals were measured for growth traits at birth weight, weaning weight, and weights at 6 months. The average daily gain (ADG) was calculated from birth to weaning (ADG1) and from birth to 6th month (ADG2). PCR-RFLP analysis was used to detect IGF-I polymorphism at the 5' regulatory region and IGFALS at Exon 1. Three genotypes (AA, AB and BB) were observed for IGF-I/BfoI locus with allele and genotype frequency 0.79(A) and 0.21(B); 0.71(AA), 0.15(AB) and 0.14(BB). Also, three genotypes (AA, AB and BB) were found for IGFALS/HinfI site with allele and genotype frequency as 0.22(A) and 0.78(B); 0.11(AA), 0.23(AB) and 0.66(BB). The genes were in agreement with Hardy-Weinberg equilibrium (p>0.05). Association analysis suggested that IGF-I and IGFALS significantly affected the growth traits (P<0.05). In terms of birth weight, The AA genotypes of IGF-I were higher than AB and BB. The AB genotype in terms of IGF-I had higher ADG2 compared with other genotypes. The AA genotype of the IGFALS gene was higher in terms of birth weight than other genotypes. In addition, the BB genotype was higher ADG1 than AA and BB. It is suggested that polymorphism of the IGF-I and IGFALS genes may be a potential molecular marker for growth traits in Hamdani sheep.

Association between MYLK4 gene polymorphism and growth traits at different age stages in Anatolian black cattle.

This study aims to find the association between MYLK4 gene polymorphism and growth traits at different ages, such as birth, 3rd-month, 6th-month and 12th-month ages in Anatolian black cattle. PCR-RFLP method was used to detect the polymorphism for MYLK4 gene in at G61595A locus. Allele and genotype frequencies were A: 0.34, G: 0.66 and AA: 0.17, AG: 0.34 and GG: 0.49. The chi-square χ2 test showed an agreement to Hardy-Weinberg equilibrium (p > .01). GLM and RRM models were used to estimate the association between MYLK4 gene polymorphism and growth traits. The results of the statistical analysis indicated an association between MYLK4 gene polymorphism and growth traits at different stage ages in Anatolian black cattle. Therefore, the G61595A mutation of MYLK4 gene can be used as a genetic marker for the selection of growth and development traits in the cattle breeding programs.