The D-loop region, which is 1212 bp long in domestic goats, was amplified using D-loop region primers and a 598 bp long segment thereof. As a result of gene sequence analysis and editing, 481 bp of sequence information was obtained for all samples. The gene sequence information and DNA polymorphism features were determined in goats (Table 1). In goats, 97 polymorphic sequences and 19 haplotypes were detected in the D-loop region. Haplotype and nucleotide diversity (HD and ND) in goats were 1.000±0.0039 and 0.0375±0.00209, respectively. Of the goat haplotypes identified, the rooted UPGMA tree formed downstream of the D-loop region is shown in Graph 1, the N-J tree is shown in Graph 2 and the rootless N-J tree is shown in Graph 3.
In this study, ninety-seven polymorphic regions and 19 haplotypes were detected in the D-loop region of goats. Haplotype and nucleotide differences of 1.000±0.0039 and 0.0375±0.00209, respectively, were calculated in goats. Haplotype distances between Mahalli goats were calculated between 0.003 and 0.087. The genetic distance between Mahalli goats and other domestic goat breeds (Kathari, Kilis and Abaza goats) ranged from 0.016 to 0.027 (Table 2). The lowest genetic distance was calculated to be 0.019 between Mahalli goats and Hair goats and the highest genetic distance was 0.027 in Ankara goats. When the phylogenetic trees were examined, complete clustering between the identified goat haplotypes could not be detected because the bootstrap test values were low (<50%). Genetic distances between Mahalli goat haplotypes were found to range from 0.003 to 0.087. In addition, the genetic distances between the indigenous goat breeds in Turkey ranged from 0.016 to 0.027 (Table 2).
Based on the reference sequences of the D-loop gene determined for goat lines A, B, C, D, F and G and the sequences of the haplotypes identified in this study (19 haplotypes),
Naderi et al., (2007) determined the haplogroups of the Mahalli goat haplotypes. It was also found that all goat haplotypes belonged to lineage A (100%).
In addition, the majority of goats (93.51%) belonged to the A line and were common worldwide, whereas other lines were extremely rare. In this study, the A lineage was also detected to a high degree. In addition, multidimensional evaluations were performed by comparing the D-loop region sequences of the available goat haplotypes with the sequence information of domestic goats from different regions of Turkey. In this context,
Naderi et al., (2008) found the existence of B, C, D and F strains in Turkish goats, including goats in different regions of Turkey, in addition to previous studies. Similarly,
Akis et al., (2014) found that haplogroup A is the dominant haplogroup in Anatolian goat breeds. Haplogroup D was observed only in Kilis and Angora goats. Lineage G was found in Ankara and Anatolian Black goat breeds. The Anatolian goat breeds show high genetic diversity and weak phylogeographic structure. Moreover, regarding the Anatolian peninsula,
Akis et al., (2014) figured out that haplogroup A is the dominant haplogroup in Anatolian goat breeds. Anatolian goat breeds show high genetic diversity and weak phylogeographic relationships. When considering domestic goats, it should also be noted that the results in terms of mtDNA polymorphism and phylogenetic characters are different when other regions of the world are considered geographically.
Zhong et al., (2013) determined Hd and π in Chinese rural goats to be between 0.782±0.079 and 1.000±0.020 and 0.009± 0.001 and 0.045±0.006, respectively. Based on phylogenetic analysis, five haplogroups were identified (A, B1, B2, C and D). Haplogroups A, B1 and B2 were dominant in most breeds, in contrast to C and D, which were found only in northern and northwestern Chinise breeds. Furthermore, in the study by
Awotunde et al., (2015), mean Hd and π values of 0.982±0.005 and 0.02350±0.00213, respectively, were calculated for two popular Nigerian goat breeds, West African Dwarf and Red Sokoto and for an exotic breed imported from South Africa, Kalahari Red. Phylogenetic analyzes revealed the existence of two mtDNA strains (A and B), with lineage A predominant. In addition,
Ganbold et al., (2020) calculated Hd and π in Mongolian goats to be 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four lineages (A, B, C and D), with lineage A predominating (90.8%). However, less genetic differentiation was observed in Kazakh, Chinese and Arabian goats (Turkish and Baladi breeds) than in Mongolian goats.
Genetic differences and phylogenetic relationships have been demonstrated based on the sequences of the goat mtDNA control region in different geographical regions, especially in the Asian continent where the goat population is dense. The phylogenetic tree of Chinese domestic goats shows that goats are divided into four mtDNA lineages (A, B, C, D)
(Chen et al., 2005; Liu et al., 2006; Fan et al., 2007; Wang et al., 2008; Liu et al., 2009; Wu et al., 2009).
However, haplotype differences in Tibetan, North and South Chinese goats were reported by
Chen et al., (2005) between 0.712±0.091-0.980±0.0243,
Liu et al., (2006) between 0.9333-1.000,
Hao et al., (2008) 0.988±0.003,
Wang et al., (2008) 0.943-1.000,
Liu et al., (2009) as 0.989±0.001 and
Wu et al., (2009) between 0.9111±0.0773-0.9872±0.0354.
In addition,
Joshi et al., (2004) showed that Indian goats are divided into four lineages (lineages A, B, C and D).
Odahara et al., (2006) have also shown that Korean goats belong to haplogroup A. Similarly,
Sardina et al., (2006) calculated the mean haplotype difference in Sicilian goats (Girgentana, Maltese, Derivata di Siria) as 0.969±0.007 and the mean nucleotide difference as 0.02359±0.00450. In the phylogenetic tree constructed with the mtDNA sequences of the Sicilian goats and the published sequences of domestic goats from India and Pakistan, it appeared that the majority of the haplotypes belong to the A lineage.
As for the European continent,
Azor et al., (2005) reported that there is a weak phylogenetic relationship between the Spanish goats (Pirenáica, Moncaína, Blanca Andaluza, Negra Serana, Azpi-Gorri, Blanca Celtibérica) and the Iberian Peninsula goats. They showed that in the phylogenetic tree the individuals of a breed are not grouped in a single cluster.
However,
Amills et al., (2009) found nucleotide and haplotype differences of 0.020±0.00081 and 0.963±0.0012 in North and South American goats, respectively. They found that South and Central American goats formed a cluster together with Spanish and Portuguese breeds, whereas Bolivia, Chile, Canary Islands and Argentine goats formed distinct clusters in the phylogenetic tree constructed from the sequences of European, Iberian, Atlantic and South and Central American goats. However, all South and Central American goats were assigned to the A lineage, while other lineages were not observed.
As can be seen from the above, many phylogenetic studies have found that lineage A is predominant or unique in goats, with high haplotype diversity and low nucleotide diversity. However, similar results have been found in Mahalli goats.
Kamalakkannan et al., (2018) studied haplotype diversity in domestic goats in southern India and found that goats in this region belong to haplogroups A, B and D. A study by
Tabata et al., (2019) examined Kazakh goats and assigned them to four haplogroups: A, C and D, with haplogroup A being the predominant haplogroup with 97%. It is clear that the genetics of Kazakh goats is highly associated with haplogroup A. Moreover,
Deniskova et al., (2020) found in their study that most of the indigenous goat breeds in Russia belong to haplogroup A. As
Mannen et al., (2020) also found in their study of indigenous goat breeds in Indonesia, most Kacang and Marica breeds belong to haplogroup B, suggesting that haplogroup B is widespread in goat populations around the world.
In the study by
Nguluma et al., (2021), indigenous goat populations in Tanzania were found to have high haplotype and nucleotide diversity, with the majority of haplotypes belonging to haplogroup A, consistent with the global genetic pattern of maternal origin in goat breeds. It was reported that Baenyi
Simon et al., (2022) conducted a study of three indigenous goat populations in the Democratic Republic of Congo and found that these goat populations were predominantly of haplogroup A.
In addition,
Gorkhali et al., (2022) studied the genetic diversity of indigenous Nepalese goat breeds, including Khari, Chyangra, Terai and Sinhal. The result of their study was that these breeds have high haplotype diversity divided into four haplogroups (A-D). The complex mtDNA diversity and structure found in indigenous Nepalese goats is explained by gene flow through ancient trade and the current ‘free’ movement of goats between geographic regions in India and China.
Finally,
Guo et al., (2022) investigated the genetic diversity and phylogeny of mitochondrial DNA (mtDNA) of goats worldwide. In this comprehensive study, the sequences of the hypervariable region of the mtDNA D_loop of a total of 4,165 individuals from 196 different breeds were analyzed. As a result of the analysis, it was found that the nucleotide diversity (Pi) was 0.03471 and the haplotype diversity (Hd) was 0.9983. Based on the results of phylogenetic analysis, 98.92% of goat haplotypes were classified into six different clusters consistent with the known classification of mitochondrial haplogroups for goats. It is estimated that 86% of these clusters belong to haplogroup A. Phylogenetic analysis of domestic goats and wild goats also suggests that Capra aegagrus was the most likely wild ancestor and played a role in the domestication of the ancestors of haplogroups A, B, C and F. The work of
Guo et al., (2022) provides valuable insights into understanding the genetic diversity, phylogeny and domestication history of goats.
On the other hand, studies on genetic diversity in goats have also been carried out using microsatellite and single nucleotide polymorhisms (SNP) markers instead of mitochondrial DNA. Some examples of genetic diversity studies conducted with microsatellite markers are
Rajkumar and Santpal (2020) and
Verma et al., (2022) in Indian goats and
Pan et al., (2023) in Chinese goats, while
Mukhina et al., (2022) used SNP markers in Mogolian goats.
Taken together, these studies contribute to our understanding of the genetic diversity of goat populations around the world. Different haplogroups are a reflection of geography and historical events and this knowledge is critical to the conservation and management of goat breeds.
