Polymorphism detection of DGAT1 and Lep genes in Anatolian water buffalo (Bubalus bubalis) populations in Turkey

Acyl-CoA: diacylglycerol-acyltransferase 1 (DGAT1) enzyme plays a key role in controlling the synthesis rate triglyceride from diacylglycerol. Leptin (LP, OB, obese) is an important hormone that synthesizes mostly from adipose tissue and regulates glucose metabolism and homeostasis. DGAT1 and Lep genes are closely related to reproduction, growth, milk yield and composition in water buffalo breeds. This study aimed to identify genetic variation in the DGAT1 and Lep gene regions in 150 water buffalo individuals from five different provinces of Turkey using DNA sequencing. A total of 38 nucleotide variations and indels have identified 761 bp long partial intron 2 and exon 3 and 5' UTR regions of the Lep gene in Anatolian water buffalo populations; 422 bp long partial exon 7-9 and exon 8 regions of DGAT1 gene were amplified and two mutations were defined in the point of 155 and 275 nucleotide that is three genotypes for S allele and Y allele of DGAT1 gene in intron 7 in Anatolian buffalo populations, respectively. These SNPs may have an effect on reproduction, growth, milk yield and composition in water buffalo populations and may prove to be useful for water buffalo breeding.Scientific Research Projects Coordination Unit of Namik Kemal University [NKUBAP.00.24.AR.14.32]; Republic of Turkey Ministry of Agriculture and Forestry General Directorate of Agricultural Research and Policies [TAGEM 13/AR-GE/29]This research was supported by the Scientific Research Projects Coordination Unit of Namik Kemal University, under project number NKUBAP.00.24.AR.14.32, and the Republic of Turkey Ministry of Agriculture and Forestry General Directorate of Agricultural Research and Policies, under project number TAGEM 13/AR-GE/29

Identification of novel single nucleotide polymorphisms in the growth hormone (GH) gene in Anatolian water buffalo (Bubalus bubalis) populations in Turkey

This study was conducted to investigate the growth hormone (GH; somatotropin-like) gene polymorphisms in 150 water buffalo (Bubalus bubalis) from different regions of Turkey. 404 bp long partial intron 4, exon 5, 3’ UTR regions of the GH gene (also called GH/AluI locus) and 347 bp long exon-intron 3 and partial exon 4 regions of the GH gene (also called GH/MspI locus) were amplified, and their PCR products analyzed via DNA sequencing method. Seven genotypes due to twenty single nucleotide polymorphisms (SNP) and one deletion/insertion were identified in a 347 bp long region of the GH/MspI locus. A missense mutation from glycine to glutamate amino acid and four silent mutations in the serine, threonine, and asparagine amino acids were determined in the exon 3 region of the GH gene. Four genotypes due to eight SNP were identified in a 404 bp long region of the GH/AluI locus. A missense mutation from lysine to arginine amino acid and six silent mutations in Leucine, aspartate, histidine, lysine, arginine, and cysteine amino acids were revealed in the exon 5 region of the GH gene. The partial DNA sequence of the GH gene in water buffalos was reported, and these sequences were deposited at the NCBI Genbank database with the accession numbers MN266903-MN266909 and MN530973-MN530976. These SNP may have an effect on economic (such as body composition) and carcass traits, reproduction, and milk yield and content in water buffalo populations and may prove to be useful for water buffalo breeding. © 2020 All Rights ReservedAR.14.32, NKUBAP.00.24; Tarimsal Araştirmalar ve Politikalar Genel Müdürlüğü, Türkiye Cumhuriyeti Tarim Ve Orman Bakanliği: TAGEM ??AR -GE/ ??This research was supported by the Scientific Research Projects Coordination Unit of Nam?k Kemal University, under project number NKUBAP.00.24.AR.14.32, and the Republic of Turkey Ministry of Agriculture and Forestry General Directorate of Agricultural Research and Policies, under project number TAGEM 13/AR-GE/29.This research was supported by the Scienti ?ic Research Projects Coordination Unit of Namık Kemal University, under project number NKUBAP. ??????AR. ?????? and the Republic of Turkey Ministry of Agriculture and Forestry General Directorate of Agricultural Research and Policies, under project number TAGEM ??AR -GE/ ??

Genetic relationships of Thrace and Yigilca honey bee populations based on microsatellite structure

Thrace and Yigilca honey bees, two important honey bee ecotypes in apicultural activity of Turkey, are the subject of genetic conservation effort. In this study, the genetic structure and diversity of honey bee populations from Thrace and Yigilca were investigated using 27 microsatellites. Except Kirklareli and Yigilca (Fst: 0.14), it was observed lower genetic divergence between the populations based on the value of pairwise Fst. Although Thrace populations (Edirne, Tekirdag and Kirklareli) were not fully separated from each other, Yigilca population was significantly separated from Kirklareli and separated slightly from the rest of other populations. The calculated gene diversity of the populations ranged from 0.44 in Kirklareli to 0.56 in Edirne and Tekirdag. Despite the high genetic diversity within the populations, the significant heterozygous deficiency found in Kirklareli may be due to repeated and controlled swarming of the selected colonies by beekeepers. These factors could have contributed the observed genotypic homogenization within Kirklareli honey bee population. Our results demonstrate that genetic differantiation of Thrace and Yigilca populations is still conserved, but gene flow is not prevented by the current management strategies, creating urgent demand for an improved conservation management of honey bee populations.Duzce UniversityDuzce University [20100501038]The research was supported by Duzce University Scientific Research fund through A research project (DUBAP Project no:20100501038). We thank beekeepers for providing the honey bee samples and their cooperation. We also thank Davud Gur for his support during the collection of some of the samples for this study

Identification of novel genetic variants for KAP1.1, KAP1.3 and K33 genes in some of indigenous goat breeds of Turkey

The animal fibres such as mohair, cashmere and cashgora have a complex structure and affected by genetic variation of keratin associated protein genes as KAP 1.1 (Keratin Associated Protein 1.1, formerly known as B2A), KAP1.3 (Keratin Associated Protein 1.3, formerly known as B2C) and K33 (Keratin Intermediate Filaments Type I, formerly known as KRT1.2). Keratin-associated proteins play a significant role in identifying structural and mechanical properties of the hair and wool fibres. This study was conducted to detect genetic variation at the KAP1.1, KAP1.3 and K33 genes in indigenous Turkish goat populations using DNA sequencing method. The DNA of 100 individuals selected from 5 different native goat breeds (Hair, Honamli, Kilis, Norduz, and Angora) that reared different regions of Turkey were used as materials. A total of 59 nucleotide variations and indels (insertion/deletion) of KAP1.1 gene, 15 nucleotide variations and indels of KAP1.3 gene, 16 nucleotide variations of K33 gene were determined in the studied samples. These nucleotide variations and indels have been causing changes in the number and sequence of amino acids. It is necessary to determine the relationships with mohair yield, quality and polymorphisms that are determined in KAP1.1, KAP1.3 and KRT1.2 genes

Genetic variation and relationships among Turkish water buffalo populations

P>The genetic variation and relationships among six Turkish water buffalo populations, typical of different regions, were assessed using a set of 26 heterologous (bovine) microsatellite markers. Between seven and 17 different alleles were identified per microsatellite in a total of 254 alleles. The average number of alleles across all loci in all the analysed populations was found to be 12.57. The expected mean heterozygosity (H-e) per population ranged between 0.5 and 0.58. Significant departures from Hardy-Weinberg equilibrium were observed for 44 locus-population combinations. Population differentiation was analysed by estimation of the F-st index (values ranging from 0.053 to 0.123) among populations. A principal component analysis of variation revealed the Merzifon population to show the highest differentiation compared with the others. In addition, some individuals of the Danamandira population appeared clearly separated, while the Afyon, Coskun, Pazar and Thural populations represented a single cluster. The assignment of individuals to their source populations, performed using the Bayesian clustering approach implemented in the structure 2.2 software, supports a high differentiation of Merzifon and Danamandira populations. The results of this study are useful for the development of conservation strategies for the Turkish buffalo

Growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) gene polymorphisms in Turkish native cattle breeds

The aim of this study was to determine the genetic diversity of 4 native Turkish cattle breeds, based on the growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) genes. In order to study the polymorphisms in these genes, the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method was performed. A 329-bp fragment and a 223-bp fragment of GH, a 156-bp fragment of PRL, and a 411-bp fragment of DGAT1, thus 4 loci of 3 genes, were amplified via PCR. These fragments were then restricted with the enzymes MspI, Alu1, RsaI, and CfrI, respectively. In this study, 2 types of alleles, (+) and (-) for the GH-MspI, L and V for the GH-Alu1, A and B for the PRL, and K and A for the DGAT1 loci, were observed. The results of the present study will contribute to the polymorphism data on the world's cattle breeds. Furthermore, the above-mentioned allele frequencies of Turkish native breeds are evaluated in relation to their genetic relatedness, and to infer their milk production properties on the basis of the available literature. In turn, these results can be utilized for future breeding programs of dairy cattle in Turkey

Phylogenetic relationships of Turkish indigenous donkey populations determined by mitochondrial DNA D-loop region

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD ) and nucleotide diversity (?D ), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.Türkiye Bilimsel ve Teknolojik Araştirma Kurumu, TÜBITAK: 215O555This research was funded by TUBITAK (The Scientific and Technological Research Council of Turkey), grant number 215O555, project leader Fulya ?zdil. The authors would like to kindly thank to Selen Yatkin who provide help during the sample collection. We are also grateful to all farmers and pastoralists for allowing us to use their animal to collect blood samples for free. Many thanks to our lab team ?eref M?cahit Topalo?lu and Ayla Fidan for helping laboratory experiment. The authors want to thank four anonymous reviewers for comments on this work

Genetic characterization of native donkey (Equus asinus) populations of Turkey using microsatellite markers

This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty‐two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi‐locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations. © 2020 by the authors. Licensee MDPI, Basel, Switzerland

Determination of the morphometric characteristics of donkey (Equus asinus) populations reared in Turkey

This research aims to determine the morphometric characteristics of the donkey (Equus asinus) populations reared in Turkey. For this purpose, live weights and body measurements were collected from 500 donkeys. The donkeys were grouped according to the factors of color, age, sex, and province and the live weights (LW) (kg), withers heights (WH), rump heights (RH), body lengths (BL), chest circumferences (CC), chest depths (CD), front shank circumferences (FSC), head lengths (HL) and ear lengths (EL) (cm) of the donkeys were measured. In the study, the males were found to have higher values of live weight, withers height, rump height, and chest depth than the females (p < 0.05). Significant differences in the live weights of the donkeys were seen by province, age, color, and sex (p < 0.01 and p < 0.05). Significant differences were found among the age groups as well (p < 0.01). Accordingly, the least squares means of the animals aged 1???3 years, 4???5 years, 6???8 years, and 9 years and over for live weight were measured as 112.10 ?? 3.11 kg, 141.54 ?? 2.76 kg, 153.98 ?? 2.42 kg, and 152.95 ?? 2.34 kg, respectively. The least squares mean of live weights were also determined as significant between the female and male animals (138.08 ?? 1.96 kg) and (142.21 ?? 2.25 kg), respectively (p 0.05). The highest correlation coefficient was calculated between live weight and body length among the donkeys (r = 0.83). Furthermore, the classical method (CM) and the fixed object photo (FOP) method were compared for photographed animals in the study. No difference in WH, RH, CD or HL was seen between the two methods (p 0.05). In conclusion, the morphometric characteristics of the donkeys were determined and it was shown that the populations were not distinguished clearly from each other and that this was fundamentally due to the transitions among the donkey populations for long years

"Türkiye ve Pakistan yerli koyun ırklarında prion protein geni polimorfizmleri taranması"

TÜBİTAK TOVAG01.01.2012Koyun ve keçilerin inkübasyon süresi uzun, ölümcül, merkezi sinir sistemini etkileyen (nörodejeneratif) bir hastalığı olan skrapi; birçok memeli türünü etkileyen bulaşıcı süngerimsi ensefalopatilerden (Transmissible Spongyform Encephalopathy -TSE) yani prion protein hastalıklarından biridir. Koyunda üç ekzon ve iki introndan oluşan prion protein geninde üçüncü ekzon bölgesinde halen 50’den fazla nokta mutasyonu polimorfizmi (TNP) gözlenmiştir. Ancak, skrapiye direnç / hassasiyeti belirleyen prion protein gen bölgesindeki mutasyonların 136, 141, 154 ve 171. kodonlarına dayalı genotiplerin olduğu bildirilmektedir. Avrupa-Asya yelpazesinde birikmiş verilerin çoğunlukla Avrupa’dan olduğu dikkat çekicidir. Halbuki arkeolojik ve genetik veriler Orta Doğu’nun koyun evcilleştirme merkezi olduğunu göstermektedir. Ancak, yapılan çalışmalar incelendiğinde bu bölgeden verilerin daha sınırlı olduğu görülmektedir. Bu çalışmada, skrapi vakasının rapor edilmediği Türkiye yerli koyun ırklarında prion protein gen polimorfizminin 15 farklı populasyonda incelemesi yapılmıştır. Çalışmada prion protein gen bölgesinin 3’üncü ekzon bölgesine ait 745 bç (baz çifti) uzunluğundaki bölgesi 655 bireyde sekanslanarak çalışılmıştır. Elde edilen veriler, Türkiye’de skrapiyi önlemeden sorumlu otoriteler, hayvan yetiştirme birlikleri ve üniversitelerin araştırma birimlerince kullanılması açısından yararlıdır. Ayrıca veriler, Dünya’daki PrP protein polimorfizm verilerinin coğrafi dağılımındaki büyük boşluğu önemli ölçüde doldurmuştur. Çalışmada elde edilen detaylı veriler fonksiyonu tam olarak bilinmeyen PrP protein bölgesinin hangi evrimsel güçler etkisinde olabileceği ile ilgili bilgilere katkılarda bulunmaktadır.Scrapie is an infectious fatal disease of sheep and it is a member of Transmissible Spongiform Encephalopathies (TSE) (or a prion disease) and affects the central nervous system. Susceptibility to scrapie is associated with polymorphisms in sheep prion protein (PrP) gene, based on their genotypes at codons 136, 141, 154 and 171. In Europe-Asia spectrum, accumulated data is mostly from Europe. Whereas, archeological and genetic evidences indicated that Middle East is the heart of sheep domestication and all of the sheep breeds must have went out from this region. Yet, data from this region is preliminary. The main purpose of the study is to collect an extensive data,covering 14 breeds 15 different populations represented by 655 individuals where each of which are sequenced for 745 base pairs of PrP 3rd exon region. It will be a data where individuals were from Turkey from which scrapie incidence was not reported. This data is important and useful for the authorities responsible from the risk management of scrapie in Turkey, for animal breeders association and for research units of universities. At the same time, it will, considerably, fill the big gap which is present in the data of geographic distribution of PrP polymorphisms in the world. The detailed data obtained by the study will contribute to the understanding of evolutionary mechanisms operating on the PrP gene of which the function is unknown