Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation

Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences

Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.

Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages

More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D- loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.

Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes

Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.

Evaluation of Maternal Genetic Background of Two Hungarian Autochthonous Sheep Breeds Coming from Different Geographical Directions

The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (KST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background.

Comparison of mtDNA control region among descendant breeds of the extinct Zaupel sheep revealed haplogroup C and D in Central Europe

The consideration of the descendance is indispensable in the preservation of endangered animal breeds. The authors compared mitochondrial DNA (mtDNA) control region sequence in three descendant breeds of the extinct Zaupel sheep, firstly. Their investigation was carried out in order to prove the common origin of Waldschaf (Austria), Bovec sheep (Slovenia) and Cikta (Hungary). A total of 118 biological samples were taken from non-related representatives of the three breeds between 2015 and 2017. A newly designed primer pair was also used to amplify the segment (1180 bp) to be tested. The total number of haplotypes in the whole study population was 49. The majority of which fell into haplogroup B. The significant negative value of the Fu's Fs statistic (Fs statistic = -3.296, p = 0.013) based on haplotype frequencies demonstrated a moderate foreign gene flow. As a novel observation haplogroups C and D appeared in Cikta and Bovec sheep, respectively. The Tajima D-test value in the entire study population was -0.914 (p > 0.10), meaning that the separation of the three descendant breeds did not cause genetic drift, these are collectively in genetic equilibrium. The genetic information confirmed the common origin of the breeds known from the breed history.

Characterization of the complete mitochondrial genome of the Qiaoke sheep (Ovis aries)

Qiaoke sheep (Ovis aries) is a local sheep breed in Gansu province, China. It is a kind of Tibetan sheep that used for both meat and wool after long-term breeding. In this paper, the complete mitochondrial genome of Qiaoke sheep was sequenced. The total length of the mitochondrial genome is 16616 bp, and the base composition is 33.65% A, 13.14% G, 25.88% C and 27.33% T. The genome has a total of 37 genes, including 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes and a control region (D-loop region). This complete sequence would enlarge useful genomic information for further studies.

Detecting signatures of selection within the Tibetan sheep mitochondrial genome

Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of π = 0.05215, while the lowest π value was detected in the tRNAs region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in 12S rRNA were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.

Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation

NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies.

Characterization of the complete mitochondrial genome sequence of Ujumuqin sheep (Ovis aries)

Sheep is one of the most important and widespread domestic animals. Nevertheless, the origins of most sheep breeds are poorly understood, specifically the fat-tailed sheep that maternally originates from a specific group. Here, we reported the whole mitochondrial DNA of Ujumuqin sheep (Ovis aries), derived from one of the oldest fat-tailed sheep breed-Mongolian sheep in China. It harbors 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a D-Loop region. The mitogenome is 16 617 bp in length, with a homology of 50% between the mitogenome of Ujumuqin sheep and that of Texel sheep. The unveiling of the mitochondrial DNA sequence of Ujumuqin sheep will have a significant role to play in the further studies on sheep evolution and domestication.

The complete mitochondrial genome of Xinong Saanen dairy goat (Capra hircus)

Xinong Saanen dairy goat (Capra hircus), a breed distributed widely and adapted highly in China, has the characteristics of high milk production and high litter size. Our research revealed that the complete mitochondrial genome of Xinong Saanen dairy goat was 16,639 bp in length. The contents of A, C, G and T in the mitochondrial genome were 33.6%, 26.0%, 13.1% and 27.3%, respectively. It had a typical mitogenome structure, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. Most of the PCGs have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. These results provide essential information for phylogeographic history and population genetic structure, genetic diversity of domestic goats and mitochondrial genome editing based on the goat model.

The complete mitochondrial genome of Shaannan White goat (Capra hircus)

The Shaannan White goat (Capra hircus), a breed native to China, has the characteristics of high fecundity and white fur. In this study, we sequenced the complete mitochondrial genome and found its length to be 16,641 bp with the base composition of 33.5% A, 26.1% C, 13.1% G and 27.3% T. It has a typical mitogenome structure, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and a non-coding control region. Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 genes start with ATA. These results provide important reference sequence for future phylogenetic studies.

The complete mitochondrial genome of Xiangdong black goat (Capra hircus)

Xiangdong black goat (Capra hircus) is a native breed of Hunan province in China. It is the first time that the complete mitochondrial genome sequence of Xiangdong black goat is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,641 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 conntrol region (D-loop region). The total base composition of Lantang pig mitochondrial genome is 33.53% A, 13.12% G, 27.25% T and 26.09% C, in the order A > T > C > G. The complete mitochondrial genome of Xiangdong black goat provides an important data in genetic mechanism and the evolution genomes.

Complete sequence and characterization of mitochondrial genome of Jianyang Daer goat (Capra hircus)

This study has presented the complete mitogenome of Jianyang Daer goat (Capra hircus), a crossbreed known for its high growth rate and good-meat quality in China. The mitogenome was 16,643 bp in length, including 33.54% A, 26.07% C, 13.10% G and 27.29% T. It contained a non-coding control region, 2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. Two kinds of inititiation codon and four types of termination codon were identified. Moreover, most of the genes were encoded on H-strand. These information will be useful for further investigation on the genetic divergence among Chinese domestic goats.

The complete mitochondrial genome of Leizhou goat Capra hircus (Bovidae; Caprinae)

Leizhou goat (Capra hircus) is one of the famous native goat breed in China. In this study, the 16,651 bp complete nucleotide sequence of Leizhou goat mitochondrial genome was sequenced for the first time. It contained 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes.

The complete mitochondrial genome of Chinese tibetan goat (Capra hircus)

The Tibetan goat (Capra hircus), a breed native to China, is adapted to cold and hypoxia. Here, we describe the complete mitochondrial genome sequence of Tibetan goat. The mitochondrial genome is 16,640 bp in length, with a base composition of 33.6% A, 26.0% C, 13.1% G and 27.3% T. It has a typical mitogenome structure, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and a non-coding control region (D-loop region). Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. This genomic data provides a strating point for future phylogenetics studies.

The complete mitochondrial genome of Bos taurus coreanae (Korean native cattle)

Korean native cattle is one of the famous native breeds in Korean. In the present work, we report the complete mitochondrial genome sequence of Korean native cattle for the first time. The total length of the mitogenome was 16,339 bp with the base composition of 33.4% for A, 27.2% for T, 26.0% for C, and 13.4% for G, and an A-T (60.6%)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of cattle. The complete mitochondrial genome sequence of Korean native cattle would serve as an important data set of the germplasm resources for further study.