A comprehensive review on genetic diversity and phylogenetic relationships among native Turkish cattle breeds based on microsatellite markers

Demir, Eymen; Karslı, Taki; Balcıoğlu, Murat Soner

doi:10.3906/vet-2006-107

Cited by 6 publications

(9 citation statements)

References 48 publications

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“…Additionally, GS via NGS data will facilitate selection practises in terms of accuracy and genetic gain in the future. As highlighted by Demir et al (2021), we highly recommend that NGS technologies should be adopted by scientists to succeed these goals in native Turkish cattle breeds in the future.…”

Section: Current Status Of Population Structure In Turkish Cattlementioning

confidence: 99%

“…The genetic structure of cattle breeds has been assessed via different molecular techniques such as microsatellites (Demir andBalcioğlu, 2019), mtDNA (Di Lorenzo et al, 2018) and SNP Arrays (Kukučková et al, 2017). These molecular tools are useful to genetically distinguish taurine cattle breeds from indicine ones (Edea et al, 2015;van der Westhuizen et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…However, their population size has been decreasing, since farmers prefer rearing high-yielding culture breeds such as Holstein Friesian. Besides, crossbreeding practices results in genetic dilution in native cattle populations (Demir et al, 2021). A decrease in effective population size has led to awareness among scientists to reveal genetic diversity and population structure of native Turkish cattle breeds to support conservation programs.…”

Section: Introductionmentioning

confidence: 99%

“…In 2019, three different studies (Table 1) were published to reveal the genetic diversity and population structure of Turkish cattle (Demir and Balcioğlu, 2019;Öner et al, 2019;Özşensoy et al, 2019). Recently, the genetic diversity and population structure of native Turkish cattle have been comprehensively reviewed by Demir et al (2021).…”

Section: Introductionmentioning

confidence: 99%

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Future Perspective of NGS Data for Evaluation of Population Genetic Structure in Turkish Cattle

Demir

2022

Acta fytotechn zootechn

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Licensed under a Creative Commons Attribution 4.0 International License Developments in sequencing and SNP chip technologies have enabled scientists to obtain high-density genomic data from different livestock species, including cattle. Moreover, many bioinformatics tools are available to analyse high-density genomic data. Via these tools, several statistical approaches such as Principal Component Analysis and clusterin-based analyses could be conducted to reveal the genetic structure of cattle populations. However, revealing the genetic structure and selection signatures of Turkish cattle breeds is a new area of research, since the previous studies are limited with a few microsatellite data. On the other hand, rearing in different geographical and environmental conditions for a long period could possibly lead to more genetic variation in native Turkish cattle breeds compared to high-yielding culture breeds. These variations obviously cannot be detected by limited number of microsatellite markers, while Next Generation Sequencing is promising for further population structure studies. Hence this review aims to summarise previous studies and give a perspective of Next Generation Sequencing possibilities to reveal the population structure of Turkish cattle for further studies.

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Section: Current Status Of Population Structure In Turkish Cattlementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Future Perspective of NGS Data for Evaluation of Population Genetic Structure in Turkish Cattle

Demir

2022

Acta fytotechn zootechn

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“…Therefore, the government initiated to import of globally widespread high-production (cosmopolitan) cattle breeds such as Holstein Friesian (HF), Brown Swiss (BS), Simmental (SIM), Jersey (JER), Hereford (HER) and Aberdeen Angus (ANG) from other countries between 1925 and 1970 (Koç, 2016). Compared to native Turkish cattle breeds, farmers have adopted cosmopolitan ones for their higher yield capacities (Demir et al, 2021). This preference E. Demir et al: Mitochondrial DNA diversity of D-loop region has decreased effective population size and genetic diversity among native Turkish cattle breeds (Demir and Balcioglu, 2019).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2023

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Abstract. 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 0.891, respectively, whereas the genetic differentiation derived from Wright's FST index was 0.174 across the breeds. A significant level of total variation (17.42 %) was observed among breeds in molecular variance analysis. Six main haplogroups (T, T1, T2, T3, Q and I2) were detected in Anatolian cattle populations, where T3 was the most frequent among breeds (43.55 %), whereas I2, an indicine specific haplogroup, was observed only in ZAV. At the breed level, phylogenetic analyses supported by 198 sequences of 17 cattle breeds and 3 outgroup species retrieved from the GenBank clustered native Turkish cattle breeds with the taurine group rather than the indicine one, as expected. However, indicine admixture at low frequency (8.89 %) was detected in the ZAV breed for the first time due to more likely gene flow from indicine cattle breeds raised in neighbour countries, particularly Iran. This finding should be further investigated in all native Turkish and indicine cattle breeds from nearby countries to clarify gene flow and indicine admixture in Anatolian cattle.

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

Demir,

Moravčíková,

Kaya

et al. 2023

Animal Genetics

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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. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross‐population extended haplotype homozygosity (XP‐EHH) and fixation index (FST) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP‐EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP‐EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3‐1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.

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A comprehensive review on genetic diversity and phylogenetic relationships among native Turkish cattle breeds based on microsatellite markers

Cited by 6 publications

References 48 publications

Future Perspective of NGS Data for Evaluation of Population Genetic Structure in Turkish Cattle

Future Perspective of NGS Data for Evaluation of Population Genetic Structure in Turkish Cattle

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

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

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