Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq.

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure.

Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye.

Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method.

Genome-wide genetic variation and population structure of native and cosmopolitan cattle breeds reared in Türkiye.

This is the first comprehensive study to reveal genetic variation and population structure at genome level in six Anatolian (Anatolian Black, East Anatolian Red, South Anatolian Red, South Anatolian Yellow, Turkish Grey Steppe, and Zavot) and two cosmopolitan (Brown Swiss and Holstein Friesian) cattle breeds reared in Türkiye. Being 20 samples from each population, a total of 160 blood samples retrieved from representative herds were utilized to generate genomic libraries by ddRADseq method. Genomic libraries sequenced by Illumina HiSeq X Ten instrument revealed a total of 211,119 bi-allelic SNPs with high call rate.

Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds.

This study aimed to reveal the genetic variability of mitochondrial DNA (mtDNA) displacement-loop (D-loop) region in 62 animals belonging to three native Turkish cattle breeds, namely Anatolian Black (AB), East Anatolian Red (EAR) and Zavot (ZAV), and to conduct phylogenetic relationship analyses to obtain deeper information on their genetic origin and breeding history by comparison of 6 taurine and 11 indicine breeds, together with 66 polymorphic sites, a total of 31 haplotypes, of which 15, 10 and 6 were detected in AB, EAR and ZAV, respectively. Mean nucleotide and haplotype diversity were 0.01 and 0.

Direct and indirect contributions of molecular genetics to farm animal welfare: a review.

Since domestication, farm animals have played a key role to increase the prosperity of humankind, while animal welfare (AW) is debated even today. This paper aims to comprehensively review the contributions of developing molecular genetics to farm animal welfare (FAW) and to raise awareness among both scientists and farmers about AW. Welfare is a complex trait affected by genetic structure and environmental factors.

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data.

Background: During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established.

Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color.

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes.

Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites.

Conservation and breeding programmes of livestock species depend on determination of genetic diversity. Today in livestock species, microsatellite markers are commonly used to reveal population structure and genetic diversity in both breeds and varieties. In this study, population structure, genetic diversity, and differentiation among four native Turkish sheep breeds including Güney Karaman, Kangal, Norduz, and Karakas were assessed by using 21 microsatellite loci.

Genetic characterization and population structure of six brown layer pure lines using microsatellite markers.

Objective: The first stage in both breeding and programs for the conservation of genetic resources are the identification of genetic diversity in the relevant population. The aim of the present study is to identify genetic diversity of six brown layer pure chicken lines (Rhode Island Red [RIRI, RIRII], Barred Rock [BARI, BARII], Columbian Rock [COL], and line 54 [L-54]) with microsatellite markers. Furthermore, the study aims to employ its findings to discuss the possibilities for the conservation and sustainable use of these lines that have been bred as closed populations for a long time.

Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin.

Background: Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius).