Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya

Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats

Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.

Mitochondrial DNA D-Loop Polymorphisms among the Galla Goats Reveals Multiple Maternal Origins with Implication on the Functional Diversity of the HSP70 Gene

Despite much attention given to the history of goat evolution in Kenya, information on the origin, demographic history, dispersal route, and genetic diversity of Galla goats remains unclear. Here, we examined the genetic background, diversity, demographic history, and population genetic variation of Galla goats using mtDNA D-loop and HSP70 single-nucleotide polymorphism markers. The results revealed 90 segregating sites and 68 haplotypes in a 600-bp mtDNA D-loop sequence. The overall mean mitochondrial haplotype diversity was 0.993. The haplotype diversities ranged between 0.8939 ± 0.0777 and 1.0000 ± 0.0221 in all populations supporting high genetic diversity. Mitochondrial phylogenetic analysis revealed three Galla goat haplogroups (A, G, and D), supporting multiple maternal ancestries, of which haplogroup A was the most predominant. Analysis of molecular variance (AMOVA) showed considerable variation within populations at 94.39%, evidence of high genetic diversity. Bimodal mismatch distribution patterns were observed while most populations recorded negative results for Tajima and Fu's Fs neutrality tests supporting population expansion. Genetic variation among populations was also confirmed using HSP70 gene fragment sequences, where six polymorphic sites which defined 21 haplotypes were discovered. Analysis of molecular variance revealed a significant FST index value of 0.134 and a high FIS index value of 0.746, an indication of inbreeding. This information will pave the way for conservation strategies and informed breeding to improve Galla or other goat breeds for climate-smart agriculture.

Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo

This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d‐loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (F_ST) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p‐value <.05) values for Fu's Fs (−20.418) and Tajima's (−2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long‐term conservation of indigenous goats in DRC.

Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations

The Small East African (SEA) goat are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (H d = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats

Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.

Genetic diversity analysis among Indian goat breeds based on mitochondrial DNA

India ranks second in goat population with 34 genetically recognized and registered breeds. Information on their diversity and origin and ancestry is little known. Hence, the mtDNA based genetic diversity analysis of Indian goats; targeting mitochondrial HVR1 region from 21 Indian breeds belonging to different geographical regions was undertaken. A total of 124 haplotypes were identified and haplotype diversity estimate ranged from 0.67 to 1.0 with an average value of 0.99. The average nucleotide diversity was minimum (0.02) in Kanniadu and maximum in Surti breeds. Analysis of molecular variance revealed 5.16% variation among the breeds and 94.84% within breeds indicating weak phylogeographic structure. Neighbor-joining tree analysis revealed that the maximum number of individuals of Indian goats fall under A and few in B and C lineages. Principal component analyses of the Indian goat breeds revealed that Kanniadu goats clustered distantly from rest of the breeds of the country. Mantel test revealed a significant correlation between FST and geographical distance (r=0.29) among the goat breeds. The mismatch distribution analysis of the Indian goat breeds revealed bimodal distribution patterns. The analysis revealed that Kanniadu is highly distinct from the rest of the breeds.

Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats

Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.

Mitochondrial DNA variation and phylogeography of native Mongolian goats

OBJECTIVE

Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA.

METHODS

In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses.

RESULTS

Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats.

CONCLUSION

In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest H_O (0.335±0.13) and H_E (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest H_O (0.401±0.12) and H_E (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high F_IS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average F_ST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA

The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.

Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d-loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (Ne) predating domestication, they also have experienced a decline in Ne at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio-cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.

Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis

The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population F_ST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times.

New insights into mitogenomic phylogeny and copy number in eight indigenous sheep populations based on the ATP synthase and cytochrome c oxidase genes

The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.