Abstract
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. The aims of this study were ı) to estimate genetic diversity and phylogenetic relationships via 5 different MHC-linked microsatellite markers (BF1, BM1818, BM1258, SMHCC1 and DYMS1) and ıı) to assess restriction ezyme-based (PstI, TaqI, BsaHI and AluI) polymorphisms of MHC Class II-DRB gene in native Turkish goats. 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 unexpected genotype patterns 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. Additionally, presence of genotypes previously reported to be associated with tuberculosis resistance and heat tolerance were observed in native Turkish goat populations. Nevertheless, association analysis between these genotypes and tuberculosis resistance and heat tolerance should be confirmed in native Turkish goats.
Highlights
In Turkey, goat raising is practised by smallholder farmers across the country in order to obtain specific products such as milk, meat, cashmere and angora
This paper aims i) to reveal current genetic diversity by Major Histocompatibility Complex (MHC)-linked microsatellite markers and ii) to obtain preliminary results of enzyme-based polymorphisms of MHC Class II-DRB gene which may be further analysed for association studies for heat tolerance and tuberculosis resistance in native Turkish goats
3.1 Genetic diversity among native Turkish goat populations based on MHC-linked microsatellite markers A total of 65 alleles ranging from 11 (BM1258) to 15 (DYMS1) per marker were detected in all population (Table 2)
Summary
In Turkey, goat raising is practised by smallholder farmers across the country in order to obtain specific products such as milk, meat, cashmere and angora. Large part of goat population (more than 90%) is Hair (HAI) goat, it possesses different varieties [Kabakulak (KBK), Pavga and Çandır] adapted to different environmental conditions (Karsli et al 2020). There are differences between HAI and its varieties in terms of body size, fertility and milk yield (Erduran & Kırbas 2010). A recent study based on 20 microsatellite loci demonstrated that KBK is genetically different from HAI (Karsli et al 2020). Norduz (NRD) possess the lowest body size and live weight among native Turkish goats and is raised in limited region of Van province and villages close to Iran border (Kirk et al 2004)
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