Araştırma Makalesi
Microsatellite Diversity and Restriction Enzyme-based Polymorphisms of MHC Loci in Some Native Turkish Goats
Öz
Playing a key role in immunity and autoimmunity, Major Histocompatibility Complex (MHC) contains microsatellite regions and polymorphisms associated with resistance to several diseases and thermo-physiologic characteristics in farm animals. This study aims to reveal genetic diversity in four native Turkish goat populations via MHC related gene regions including MHC-linked microsatellite markers (BF1, BM1818, BM1258, SMHCC1 and DYMS1) and MHC Class II-DRB gene. A total of 120 unrelated animals belonging to Hair (HAI), Honamlı (HNM), Kabakulak (KBK) and Norduz (NRD) from different representative populations in Antalya and Van provinces were sampled and genotyped for molecular analysis. Based on MHC-linked microsatellite markers, number of alleles ranged from 8.20 (NRD) to 8.80 (HAI and KBK) across studied goat populations. Observed heterozygosity was between 0.68 (NRD) and 0.80 (KBK), whereas expected heterozygosity ranged from 0.74 (NRD) to 0.82 (KBK) in native Turkish goats. Inbreeding coefficients were 0.04, 0.13, -0.01 and 0.09 for HAI, HNM, KBK and NRD populations, respectively. A 284 bp length PCR products belonging to MHC Class II-DRB gene region were digested separately with PstI, TaqI, BsaHI and AluI restriction endonucleases to assess polymorphism status together with Hardy-Weinberg equilibrium in studied goat populations. P allele frequency ranged from 0.73 (KBK) to 0.95 (NRD), while p allele frequency was between 0.05 (NRD) and 0.27 (KBK) in PstI polymorphism. The highest and lowest frequency of T allele were detected in HNM (0.80) and KBK (0.49), respectively, whereas frequency of t allele was between 0.20 (HNM) and 0.51 (KBK) in TaqI polymorphism. G and A allele frequency were between 0.16 (HNM) - 0.39 (HAI) and 0.84 (HNM) – 0.61 (HAI), respectively in BsaHI polymorphism, while three different genotypes and two alleles, which were different from results reported in the literature, were observed in AluI polymorphism. In this study, high genetic diversity and low inbreeding were detected in native Turkish goats according to MHC-linked microsatellite markers. Similarly, native Turkish goats hold enough polymorphisms in MHC Class II-DRB gene which gives opportunity to support selection strategies against tuberculosis and heat stress in the future.
Anahtar Kelimeler
genetic diversity heat tolerance PCR-RFLP SSR tuberculosis resistance
Destekleyen Kurum
The Scientific Research Projects Coordination Unit of Akdeniz University
Proje Numarası
FYL-2018-4301
Teşekkür
This work was supported by The Scientific Research Projects Coordination Unit of Akdeniz University (Project Number: FYL-2018-4301).
Kaynakça
- Ağaoğlu Ö K & Ertuğrul O (2012). Assessment of genetic diversity, genetic relationship and bottleneck using microsatellites in some native Turkish goat breeds. Small Ruminant Research 105(1-3): 53-60
- Basiricò L, Morera P, Primi V, Lacetera N, Nardone A & Bernabucci U (2011). Cellular thermotolerance is associated with heat shock protein 70.1 genetic polymorphisms in Holstein lactating cows. Cell Stress Chaperone 16(4): 441-448
- Belkhir K, Borsa P, Goudet J & Bonhomme F (2004). GENETIX 4.05, logiciel sous Windows pour la ge´ne´tique des populations. Universite´ de Montpellier II, Montpellier, France
- Bulut Z, Kurar E, Ozsensoy Y, Altunok V & Nizamlioglu M (2016). Genetic diversity of eight domestic goat populations raised in Turkey. BioMed Research International 2016: 2830394
- Cecchi F, Russo C, Iamartino D, Galiero A, Turchi B, Fratini F, Degl’Innocenti S, Mazza R, Biffani S, Preziuso G & Cantile C (2017). Identification of candidate genes for paratuberculosis resistance in the native Italian Garfagnina goat breed. Tropical Animal Health and Production 49(6): 1135-1142
- Ceccobelli S, Lasagna E, Demir E, Rovelli G, Albertini E, Veronesi F, Sarti F M & Roselini D (2020). Molecular Identification of the “Facciuta Della Valnerina” Local Goat Population Reared in the Umbria Region, Italy. Animals 10: 601
- Earl D A & vonHoldt B M (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359– 361
- Eren M G, Balcioğlu M S & Demir E (2019). Detection of complex vertebral malformation in Holstein cattle reared in Antalya using allele-spesific PCR. Mediterranean Agricultural Sciences 32(3): 443-446
- Glaubitz J C (2004). CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4(2): 309–310
- Goudet J (1995). FSTAT (Version 1.2): A computer program to calculate F-Statistics. Journal of Hereditary 86(6): 485-486
- Gowane G R, Akram N, Misra S S, Prakash V & Kumar A (2018). Genetic diversity of Cahi DRB and DQB genes of caprine MHC class II in Sirohi goat. Journal of Genetics 97(2): 483-492
- Guang-Xin E, Yong-Fu H, Yong-Ju Z, Yue-Hui M, Ri-Su N, Jia-Hua Z, Hui-Jiang G & Xin W (2015). Genetic variability of ten Chinese indigenous goats using MHC-linked microsatellite markers. Veterinary Immunolgy and Immunopathology 167(3-4): 196–199
- Gül S, Yilmaz O, Gündüz Z, Keskin M, Cemal I, Ata N & Önel S E (2020). The genetic structure of the goat breeds belonging to Northwest part of Fertile Crescent. Small Ruminant Research 182: 22-28
- Humblet M F, Boschiroli M L & Saegerman C (2009) Classification of worldwide bovine tuberculosis risk factors in cattle: a stratified approach. Veterinary Research 40(5): 1-24
- Kalinowski S T & Taper M L (2006): Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics 7(6): 991-995
- Kannaki T R, Reddy M R, Raja Ravindra K S & Chatterjee R N (2017). Genetic diversity analysis of the major histocompatibility complex region in Indian native chicken breeds and pureline chickens using the LEI0258 microsatellite marker. Indian Journal of Animal Research 51(6): 998-1001
- Karsli T, Demir E, Fidan H G, Aslan M, Argun Karsli B, Arik İ Z, Sahin Semerci E, Karabag K & Balcioglu M S (2020). Determination of genetic variability, population structure and genetic differentiation of indigenous Turkish goat breeds based on SSR loci. Small Ruminant Research 190: 106147
- Kim E S, Sonstegard T S, da Silva M V G B, Gasbarre L C & Tassell C P V (2015). Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC. PLoS One, 10(3): e0119380
- Kopelman N M, Mayzel J, Jakobsson M, Rosenberg N A & Mayrose I (2015): CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15(5): 1179-1191
- Liu Y, Li D, Li H, Zhou X & Wang G (2011). A novel SNP of the ATP1A1 gene is associated with heat tolerance traits in dairy cows. Molecular Biology Reports 38(1): 83-88
- Miller S A, Dykes D D & Polesky H F R N (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 16(3): 1215
- Petlane M, Noor R R & Maheswari R R A (2012). The Genetic diversity of TLR4 MHC-DRB genes in dairy goats using PCR-RFLP technique. Media Peternakan 35(2): 91-95
- Pisoni G, Moroni P, Genini S, Stella A, Boettcher P J, Cremonesi P, Scaccabarozzi L, Giuffra E & Castiglioni B (2010). Differentially expressed genes associated with Staphylococcus mastitis in dairy goats. Veterinary Immunology and Immunopathology 135(3-4): 208-217
- Pritchard J K, Stephens M & Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155(2): 945-95
- Radostits O M, Gay C C, Hinchcliff K W & Constable P D (2007). A textbook of the diseases of cattle, horses, sheep, pigs and goats. Veterinary Medicine 10: 2045-2050
- Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U & Lasagna E (2020). The genetics of phenotypic plasticity in livestock in the era of climate change: a review. Italian Journal of Animal Science, 19(1): 997-1014
- Salles P A, Santos S C, Rondina D & Weller M (2011). Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers. Journal of Veterinary Science 12(2): 127-132
- Shen H, Han G, Jia B, Jiang S & Du Y (2014). MHC-DRB1/DQB1 gene polymorphism and its association with resistance/susceptibility to cystic Echinococcosis in Chinese merino sheep. Journal of Parasitology Research 2014: 272601
- Singh P K, Singh S V, Singh M K, Saxena V K, Horin P, Singh A V & Sohal J S (2012). Effect of genetic variation in the MHC Class II DRB region on resistance and susceptibility to Johne’s disease in endangered Indian Jamunapari goats. International Journal of Immunogenetics 39(4): 314–320
- Vaccari G, Di Bari M A, Morelli L, Nonno R, Chiappini B, Antonucci G, Marcon S, Esposito E, Fazzi P, Palazzini N, Troiano P, Petrella A, Di Guardiola G & Agrimi U (2006). Identification of an allelic variant of the goat PrP gene associated with resistance to scrapie. Journal of General Virology 87(5): 1395-1402
- Yakubu A, Salako A E, De Donato M, Peters S O, Takeet M I, Wheto M, Okpeku M & Imumorin I G (2017). Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats. Tropical Animal Health Production 49(2): 323–336
- Yeh F C, Yang R C, Boyle T B J, Ye Z H & Mao J X (1997). POPGENE, The user-friendly shareware for population genetic analysis, Molecular Biology and Biotechnology Centre, University of Alberta, Canada.
Yıl 2022,
Cilt: 28 Sayı: 4, 626 - 634, 17.10.2022
Öz
Proje Numarası
FYL-2018-4301
Kaynakça
- Ağaoğlu Ö K & Ertuğrul O (2012). Assessment of genetic diversity, genetic relationship and bottleneck using microsatellites in some native Turkish goat breeds. Small Ruminant Research 105(1-3): 53-60
- Basiricò L, Morera P, Primi V, Lacetera N, Nardone A & Bernabucci U (2011). Cellular thermotolerance is associated with heat shock protein 70.1 genetic polymorphisms in Holstein lactating cows. Cell Stress Chaperone 16(4): 441-448
- Belkhir K, Borsa P, Goudet J & Bonhomme F (2004). GENETIX 4.05, logiciel sous Windows pour la ge´ne´tique des populations. Universite´ de Montpellier II, Montpellier, France
- Bulut Z, Kurar E, Ozsensoy Y, Altunok V & Nizamlioglu M (2016). Genetic diversity of eight domestic goat populations raised in Turkey. BioMed Research International 2016: 2830394
- Cecchi F, Russo C, Iamartino D, Galiero A, Turchi B, Fratini F, Degl’Innocenti S, Mazza R, Biffani S, Preziuso G & Cantile C (2017). Identification of candidate genes for paratuberculosis resistance in the native Italian Garfagnina goat breed. Tropical Animal Health and Production 49(6): 1135-1142
- Ceccobelli S, Lasagna E, Demir E, Rovelli G, Albertini E, Veronesi F, Sarti F M & Roselini D (2020). Molecular Identification of the “Facciuta Della Valnerina” Local Goat Population Reared in the Umbria Region, Italy. Animals 10: 601
- Earl D A & vonHoldt B M (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359– 361
- Eren M G, Balcioğlu M S & Demir E (2019). Detection of complex vertebral malformation in Holstein cattle reared in Antalya using allele-spesific PCR. Mediterranean Agricultural Sciences 32(3): 443-446
- Glaubitz J C (2004). CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes 4(2): 309–310
- Goudet J (1995). FSTAT (Version 1.2): A computer program to calculate F-Statistics. Journal of Hereditary 86(6): 485-486
- Gowane G R, Akram N, Misra S S, Prakash V & Kumar A (2018). Genetic diversity of Cahi DRB and DQB genes of caprine MHC class II in Sirohi goat. Journal of Genetics 97(2): 483-492
- Guang-Xin E, Yong-Fu H, Yong-Ju Z, Yue-Hui M, Ri-Su N, Jia-Hua Z, Hui-Jiang G & Xin W (2015). Genetic variability of ten Chinese indigenous goats using MHC-linked microsatellite markers. Veterinary Immunolgy and Immunopathology 167(3-4): 196–199
- Gül S, Yilmaz O, Gündüz Z, Keskin M, Cemal I, Ata N & Önel S E (2020). The genetic structure of the goat breeds belonging to Northwest part of Fertile Crescent. Small Ruminant Research 182: 22-28
- Humblet M F, Boschiroli M L & Saegerman C (2009) Classification of worldwide bovine tuberculosis risk factors in cattle: a stratified approach. Veterinary Research 40(5): 1-24
- Kalinowski S T & Taper M L (2006): Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics 7(6): 991-995
- Kannaki T R, Reddy M R, Raja Ravindra K S & Chatterjee R N (2017). Genetic diversity analysis of the major histocompatibility complex region in Indian native chicken breeds and pureline chickens using the LEI0258 microsatellite marker. Indian Journal of Animal Research 51(6): 998-1001
- Karsli T, Demir E, Fidan H G, Aslan M, Argun Karsli B, Arik İ Z, Sahin Semerci E, Karabag K & Balcioglu M S (2020). Determination of genetic variability, population structure and genetic differentiation of indigenous Turkish goat breeds based on SSR loci. Small Ruminant Research 190: 106147
- Kim E S, Sonstegard T S, da Silva M V G B, Gasbarre L C & Tassell C P V (2015). Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC. PLoS One, 10(3): e0119380
- Kopelman N M, Mayzel J, Jakobsson M, Rosenberg N A & Mayrose I (2015): CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15(5): 1179-1191
- Liu Y, Li D, Li H, Zhou X & Wang G (2011). A novel SNP of the ATP1A1 gene is associated with heat tolerance traits in dairy cows. Molecular Biology Reports 38(1): 83-88
- Miller S A, Dykes D D & Polesky H F R N (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 16(3): 1215
- Petlane M, Noor R R & Maheswari R R A (2012). The Genetic diversity of TLR4 MHC-DRB genes in dairy goats using PCR-RFLP technique. Media Peternakan 35(2): 91-95
- Pisoni G, Moroni P, Genini S, Stella A, Boettcher P J, Cremonesi P, Scaccabarozzi L, Giuffra E & Castiglioni B (2010). Differentially expressed genes associated with Staphylococcus mastitis in dairy goats. Veterinary Immunology and Immunopathology 135(3-4): 208-217
- Pritchard J K, Stephens M & Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155(2): 945-95
- Radostits O M, Gay C C, Hinchcliff K W & Constable P D (2007). A textbook of the diseases of cattle, horses, sheep, pigs and goats. Veterinary Medicine 10: 2045-2050
- Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U & Lasagna E (2020). The genetics of phenotypic plasticity in livestock in the era of climate change: a review. Italian Journal of Animal Science, 19(1): 997-1014
- Salles P A, Santos S C, Rondina D & Weller M (2011). Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers. Journal of Veterinary Science 12(2): 127-132
- Shen H, Han G, Jia B, Jiang S & Du Y (2014). MHC-DRB1/DQB1 gene polymorphism and its association with resistance/susceptibility to cystic Echinococcosis in Chinese merino sheep. Journal of Parasitology Research 2014: 272601
- Singh P K, Singh S V, Singh M K, Saxena V K, Horin P, Singh A V & Sohal J S (2012). Effect of genetic variation in the MHC Class II DRB region on resistance and susceptibility to Johne’s disease in endangered Indian Jamunapari goats. International Journal of Immunogenetics 39(4): 314–320
- Vaccari G, Di Bari M A, Morelli L, Nonno R, Chiappini B, Antonucci G, Marcon S, Esposito E, Fazzi P, Palazzini N, Troiano P, Petrella A, Di Guardiola G & Agrimi U (2006). Identification of an allelic variant of the goat PrP gene associated with resistance to scrapie. Journal of General Virology 87(5): 1395-1402
- Yakubu A, Salako A E, De Donato M, Peters S O, Takeet M I, Wheto M, Okpeku M & Imumorin I G (2017). Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats. Tropical Animal Health Production 49(2): 323–336
- Yeh F C, Yang R C, Boyle T B J, Ye Z H & Mao J X (1997). POPGENE, The user-friendly shareware for population genetic analysis, Molecular Biology and Biotechnology Centre, University of Alberta, Canada.
Toplam 32 adet kaynakça vardır.
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Mühendislik |
| Bölüm | Makaleler |
| Yazarlar | |
| Proje Numarası | FYL-2018-4301 |
| Yayımlanma Tarihi | 17 Ekim 2022 |
| Gönderilme Tarihi | 3 Haziran 2021 |
| Kabul Tarihi | 13 Kasım 2021 |
| Yayımlandığı Sayı | Yıl 2022 Cilt: 28 Sayı: 4 |
Cited By
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