Investigation of genetic diversity and selection signatures in Czech cattle genetic resources revealed by genome-wide analysis

Kyselová, J; Gurgul, Artur; Jasielczuk, Igor; Bugno‐Poniewierska, Monika; Mátlová, V.; Pikousová, Jitka; Mušková, Michala; Jochová, Kateřina; Tichý, Ladislav; Sztankóová, Z.; Sakowski, T.

doi:10.1016/j.livsci.2022.104825

Cited by 2 publications

(7 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The Fis was near zero in most Turkish breeds, except for a moderately positive Fis of 0.05 in ASY, potentially indicating limited recent inbreeding. The negative Fis values in TUR (−0.02) and SAN (−0.01) may reflect outbreeding practices (Kyselová et al., 2022). The ROH analysis provided a detailed view, with many short ROH segments found across Turkish breeds indicating ancient shared ancestry.…”

Section: Discussionmentioning

confidence: 99%

“…Assessing selection signatures through runs of homozygosity, integrated haplotype scores, and Fst outlier analyses can reveal targets of both natural and artificial selection in Turkish breeds (Masharing et al., 2023; Wang et al., 2018). Exploring functional annotations of breed‐specific variants can uncover adaptive diversity (Kyselová et al., 2022). Epigenetic factors affecting gene expression merit investigation as additional molecular mechanisms underlying phenotypic diversity and adaptation (Edea et al., 2015).…”

Section: Discussionmentioning

confidence: 99%

“…However, the moderately long ROHs in ASY and EAR suggest the possibility of some recent inbreeding, potentially from geographical isolation or closing herd books. However, lower FROH values compared to highly specialized breeds signify that Turkish cattle likely did not undergo extreme selective pressure (Edea et al., 2013; Kyselová et al., 2022). Extremely long ROHs were rare, providing confidence that severe inbreeding is uncommon in these breeds.…”

Section: Discussionmentioning

confidence: 99%

“…Exploring functional annotations of breed-specific variants can uncover adaptive diversity (Kyselová et al, 2022). Epigenetic factors affecting gene expression merit investigation as additional molecular mechanisms underlying phenotypic diversity and adaptation (Edea et al, 2015).…”

Section: Future Research Directionsmentioning

confidence: 99%

See 3 more Smart Citations

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

Bayraktar,

Cebeci,

Gökçe

2024

Reprod Domestic Animals

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Future Research Directionsmentioning

confidence: 99%

See 2 more Smart Citations

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

Bayraktar,

Cebeci,

Gökçe

2024

Reprod Domestic Animals

View full text Add to dashboard Cite

show abstract

“…To identify regions of the genome that could explain the differences between groups, the rolling average of the F ST values was calculated for a window of 10 SNPs to account for the locus-by-locus random variation in each autosome [ 37 ].…”

Section: Methodsmentioning

confidence: 99%

Exploring the Effects of Robertsonian Translocation 1/29 (Rob (1;29)) on Genetic Diversity in Minor Breeds of Spanish Berrenda Cattle via Genome-Wide Analysis

González-Cano,

González-Martínez,

Ramón

et al. 2024

Animals

View full text Add to dashboard Cite

Most of the previous studies on the genetic variability in Spanish “Berrenda” breeds have been carried out using DNA microsatellites. The present work aimed to estimate the genetic diversity, population structure, and potential genetic differences among individuals of both Berrenda breeds and groups based on the presence of the Robertsonian chromosomal translocation, rob (1;29). A total of 373 samples from animals belonging to the two breeds, including 169 cases diagnosed as rob (1;29)-positive, were genotyped using an SNP50K chip. The genetic diversity at the breed level did not show significant differences, but it was significantly lower in those subpopulations containing the rob (1;29). Runs of homozygosity identified a region of homozygosity on chromosome 6, where the KIT (KIT proto-oncogene, receptor tyrosine kinase) gene, which determines the typical spotted coat pattern in both breeds, is located. The four subpopulations considered showed minor genetic differences. The regions of the genome that most determined the differences between the breeds were observed on chromosomes 4, 6, 18, and 22. The presence of this Robertsonian translocation did not result in sub-structuring within each of the breeds considered. To improve the reproductive performance of Berrenda breeds, it would be necessary to implement strategies considering the involvement of potential breeding stock carrying rob (1;29).

show abstract

Investigation of genetic diversity and selection signatures in Czech cattle genetic resources revealed by genome-wide analysis

Cited by 2 publications

References 31 publications

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

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

Exploring the Effects of Robertsonian Translocation 1/29 (Rob (1;29)) on Genetic Diversity in Minor Breeds of Spanish Berrenda Cattle via Genome-Wide Analysis

Contact Info

Product

Resources

About