Identification of mitochondrial DNA substitutions related to meat quality in Japanese Black cattle

Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia

Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism.

The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies

Simple Summary

The western honeybee, Apis mellifera, is a globally distributed bee species with many recognised subspecies, one of which is Apis mellifera carnica, the Carniolan honeybee. Apis m. carnica is native to southern Central Europe and parts of the Balkans, with the locus classicus in Slovenia. It is also widely popular with beekeepers in parts of Central and Northern Europe and other parts of the world, including the USA, Canada, and even New Zealand. In Slovenia, A. m. carnica is protected, with measures to conserve the subspecies’ autochthonous domestic population in place. Such efforts depend heavily upon genomic and phylogenetic information. In this study, we sequenced and annotated the mitochondrial genome of a specimen from Slovenia and compared the obtained data with a previously published sample of the A. m. carnica from Austria and the closely related Italian honeybee A. m. ligustica. We found several features unique to the new mitochondrial genome. We also phylogenetically analyzed the relationship between our sequence and the selected available A. mellifera mitochondrial sequences. The acquired position of the sequenced A. m. carnica from Slovenia on the phylogenetic tree brings new evidence for close relationships among C and O lineages and reflects their recent historical matrilinear ancestry.

Abstract

The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.

The ND1 and CYTB genes polymorphisms associated with in vitro early embryo development of Sanjabi sheep

This study aimed to investigate the association between polymorphisms of ND1 and CYTB genes and in vitro early embryo development of Sanjabi sheep. Blood and ovarian samples were collected from a local slaughterhouse. The cumulus-oocyte complexes with a diameter greater than 3 mm were aspirated from follicles, and in vitro maturation (IVM) and in vitro culture (IVC) rates of them were recorded. A respective 1200 bp and 980 bp fragments of ND1 and CYTB genes were genotyped using a modified single strand conformation polymorphism (SSCP) method. The results of this study revealed that four different patterns, named as A, B, C, and D were observed for both ND1 and CYTB genes. The ND1 gene polymorphisms had significant effects on the IVM and IVC rate (p < 0.05). The pattern C of the ND1 gene significantly increased the IVM rate compared to the patterns A, B and D. For the IVC, the highest and lowest means were related to the C and B patterns, respectively. The CYTB gene polymorphisms also had significant effects on IVC (p < 0.01), but the IVM did not affected (p = 0.07). Here, the pattern D had the highest and the pattern C had the lowest means for both IVM and IVC rates.

Mitochondrial DNA Diversity in Large White Pigs in Russia

The Large White pig is the most commonly raised commercial pig breed in the world. The aim of this work was to investigate D-loop mtDNA in Large White pigs (n = 402) of various selections bred in the Russian Federation from 2000 to 2019. The general sample consisted of three groups: Old (n = 78) (Russian selection, 2000-2010); Imp (n = 123) (imported to Russia in 2008-2014); New (n = 201) (2015-2019). The synthesized score (Fz) was calculated by analyzing the main PCA (principal component analysis components). An affiliation to Asian or European haplogroups was determined according to the NCBI (National Center for Biotechnology Information). In the study, we defined 46 polymorphic sites and 42 haplotypes. Significant distinctions between groups Old, Imp and New in frequencies of haplotypes and haplogroups were established. The distribution of Asian and European haplotypes in the groups was Old: 50%/50%, Imp: 43%/57%, New: 75%/25%, respectively. The variety of haplotypes and haplogroups in the pigs of the group New is related to the farms in which they breed. Haplotype frequencies significantly differ between the clusters Old_Center, Old_Siberia and Old_South. This study will provide information on the genetic diversity of Large White breed pigs. The results will be useful for the conservation and sustainable use of these resources.

Relationship between mitochondrial DNA haplogroup and litter size in the pig

Mitochondrial DNA (mtDNA) has been widely associated with complex traits in farm animals. The present study evaluated the effects of mtDNA on litter size in pigs. Mitogenome sequencing of 1017 sows distinguished 232 variations, including 229 single nucleotide polymorphisms and three indels, which constituted 11 haplotypes and further clustered into two haplogroups that differed significantly (P&lt;0.05) in litter size. In order to explain the associations between the effect of haplogroup on litter size and different maternal origins, extant mitogenome sequences were used for phylogenetic or principal component analyses. The results of these analyses led to the identification of two groups, representing Chinese and European origins. The haplotypes corresponding to high litter size were all in the Chinese cluster, whereas haplotypes corresponding to low litter size were all in the European cluster. The results of this study suggest that the effect of haplogroup on litter size in the pig could be caused by diverse maternal origins, and that mtDNA haplogroup may be a marker for genetic selection for pig litter size.

The association of mitochondrial DNA haplotypes and phenotypic traits in pigs

Background

The mitochondrial genome (mtDNA) is an emerging determiner of phenotypic traits and disease. mtDNA is inherited in a strict maternal fashion from the population of mitochondria present in the egg at fertilisation. Individuals are assigned to mtDNA haplotypes and those with sequences that cluster closely have common origins and their migration patterns can be mapped. Previously, we identified five mtDNA haplotypes in the commercial breeding lines of Australian pigs, which defined their common origins, and showed how these mtDNA haplotypes influenced litter size and reproductive function in terms of egg and embryo quality and fertilisation efficiency.

Results

We have determined whether mtDNA haplotypes influence other phenotypic traits. These include fat density; muscle depth; fat to leanness ratios; lifetime daily gain; teat quality; muscle score; front and rear leg assessments; percentage offspring weaned; weaning to oestrus intervals; gilt age at selection; and gestational length. In all, we assessed 5687 pigs of which 2762 were females and 2925 were males. We assessed all animals together and then by gender. We further assessed by gender based on whether a sire had joined with females from only one haplotype or from more than one haplotype. We determined that fat density, muscle depth, fat to leanness ratios, lifetime daily gain and teat quality were influenced by mtDNA haplotype and that there were gender specific effects on teat quality.

Conclusions

Our data illustrate that mtDNA haplotypes are associated with a number of important phenotypic traits indicative of economic breeding values in breeding pigs with gender-specific differences. Interestingly, there are ‘trade offs’ whereby some mtDNA haplotypes perform better for one selection criterion, such as muscle depth, but less so for another, for example teat quality, indicating that pig mtDNA haplotypes are afforded an advantage in one respect but a disadvantage in another.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0629-4) contains supplementary material, which is available to authorized users.

Cattle phenotypes can disguise their maternal ancestry

Background

Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments.

Results

A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P < 0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos taurus phenotype.

Conclusions

The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0523-5) contains supplementary material, which is available to authorized users.

Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids

In farm animals, mitochondrial DNA mutations exist widely across breeds and individuals. In order to identify differences among mtDNA haplotypes, two porcine transmitochondrial cybrids were generated by fusion of a Lantang pig cell line devoid of mitochondrial DNA with enucleated cytoplasm from either a Large White pig or a Xiang pig harboring potentially divergent mitochondrial haplotypes. These cybrid cells were subjected to mitochondrial genome sequencing, copy number detecting and analysis of biochemical traits including succinate dehydrogenase (SDH) activity, ATP content and susceptibility to reactive oxygen species (ROS). The Lantang and Xiang mitochondrial genomes were highly homologous with only 18 polymorphic sites, and differed radically from the Large White with 201 and 198 mutations respectively. The Large White and Xiang cybrids exhibited similar mtDNA copy numbers and different values among biochemical traits, generated greater ROS production (P < 0.05) and less SDH activity (P < 0.05) and a lesser ATP content (P < 0.05). The results show that functional differences exist between cybrid cells which differ in mitochondrial genomic background. In conclusion, transmitochondrial cybrids provide the first direct evidence on pig biochemical traits linking different mitochondrial genome haplotypes.

Study on heteroplasmic variation and the effect of chicken mitochondrial ND2

NADH dehydrogenase subunit 2 gene (ND2) is one of the mitochondrial DNA (mtDNA) protein coding genes, which is a subunit of NADH dehydrogenase. The main purpose of this study was to investigate the variation/heteroplasmic sites of chicken ND2, and thus to evaluate the association with chicken growth traits, carcass traits, and serum biochemical indexes. Seventeen variants were detected in the ND2 gene by Sanger sequencing, which constructed 15 haplotypes; the haplotype diversity (hd) was 0.7692. Mt.A5703T and mt.T5727G in the ND2 gene had been detected as the heteroplasmic sites via the created restriction site restriction fragment length polymorphism (CRS-PCR-RFLP) method. Moreover, the study on distribution of two heteroplasmic variants in the Gushi chicken F2 resource population revealed that the heteroplasmic ratio of mt.A5703T and mt.T5727G was 9% and 40%, respectively. It showed that there was obvious heteroplasmic difference between two sites. Association analysis of the variation/heteroplasmy with the related traits in Gushi chicken F2 population showed that the mt.A5703T and mt.T5727G were significantly associated with the pectoral muscle fat content and the duodenum length, but no significance was found with body weight (BW). It was the first time to indicate that heteroplasmic variation had significant effect on growth traits, carcass parameters, and meat quality traits, which showed the potential importance of related variation.

Polymorphisms of mitochondrial ATPase 8/6 genes and association with milk production traits in Holstein cows

The maternal effect has been widely proposed to affect the production traits in domestic animals. However, the sequence polymorphisms of mitochondrial DNA (mtDNA) and association with milk production traits in Holstein cows have remained unclear. In this study, we investigated the single nucleotide polymorphisms (SNPs) of mtDNA ATPase 8/6 genes and association with four milk production traits of interest in 303 Holstein cows. A total of 18 SNPs were detected among the 842 bp fragment of ATPase 8/6 genes, which determined six haplotypes of B. taurus (H1-H4) and B. indicus (H5-H6). The mixed model analysis revealed that there was significant association between haplotype and 305-day milk yield (MY). The highest MY was observed in haplotype H4. However, we did not detect statistically significant differences among haplotypes for the traits of milk fat (MF), milk protein (MP), and somatic cell count (SC). The overall haplotype diversity and nucleotide diversity of ATPase 8/6 genes were 0.563 ± 0.030 and 0.00609 ± 0.00043, respectively. The results suggested that mitochondrial ATPase 8/6 genes could be potentially used as molecular marker to genetically improve milk production in Holstein cows.

Comparison of liver mitochondrial proteins derived from newborn cloned calves and from cloned adult cattle by two-dimensional differential gel electrophoresis

Aberrant reprogramming of donor somatic cell nuclei may result in many severe problems in animal cloning. The inability to establish functional interactions between donor nucleus and recipient mitochondria is also likely responsible for such a developmental deficiency. However, detailed knowledge of protein expression during somatic cell nuclear transfer (SCNT) in cattle is lacking. In the present study, variations in mitochondrial protein levels between SCNT-derived and control cattle, and from calves derived by artificial insemination were investigated. Mitochondrial fractions were prepared from frozen liver samples and subjected to two-dimensional (2-D) fluorescence differential gel electrophoresis (DIGE) using CyDye™ dyes. Protein expression changes were confirmed with a volume ratio greater than 2.0 (P < 0.05). 2D-DIGE analysis revealed differential expression of three proteins for SCNT cattle (n = 4) and seven proteins for SCNT calves (n = 6) compared to controls (P < 0.05). Different protein patterning was observed among SCNT animals even if animals were generated from the same donor cell source. No differences were detected in two of the SCNT cattle. Moreover, there was no novel protein identified in any of the SCNT cattle or calves. In conclusion, variation in mitochondrial protein expression concentrations was observed in non-viable, neonatal SCNT calves and among SCNT individuals. This result implicates mitochondrial-related gene expression in early developmental loss of SCNT embryos. Comparative proteomic analysis represents an important tool for further studies on SCNT animals.

Phylogenetic analysis and comparison between cow and buffalo (including Egyptian buffaloes) mitochondrial displacement-loop regions

Mitochondrial DNA (mtDNA) analysis has been used extensively for phylogenetic analysis studies and systematics. The displacement loop (D-loop) region inside the mtDNA is a non-coding part whose analysis can indicate variations between closely related populations. This paper reports for the first time the characterization and analysis of the complete sequence of the D-loop region from Egyptian buffaloes and analysis in conjunction with previously published Indian and European Bubalus bubalis and Bos sub-tribe sequences. In the entire D-loop of the Egyptian buffaloes, we identified four haplotypes and nine polymorphic sites from the nine sequenced D-loop regions--while in the studied set of buffaloes we identified 28 polymorphic sites in the entire D-loop, and 49 polymorphic sites in the case of cows. Alignment between buffaloes and cows to evaluate the characteristics of the D-loop region showed that the second region of the conserved sequence block (CSB2) is apparently the most variable region in the D-loop between cows and buffaloes, with four insertions in all buffaloes and two substitutions, followed by the second region of the extended termination associated sequence (ETAS2) with a substitution rate of 1/10. The Egyptian buffaloes were shown to be closest to the Italian counterparts, exemplifying the closeness of ethnicity and the history of civilization of that region.

Autologous somatic cell nuclear transfer in pigs using recipient oocytes and donor cells from the same animal

The objective of the present study was to examine the feasibility of the production of autologous porcine somatic cell nuclear transfer (SCNT) blastocysts using oocytes and donor cells from slaughtered ovaries. Therefore, we attempted to optimize autologous SCNT by examining the effects of electrical fusion conditions and donor cell type on cell fusion and the development of SCNT embryos. Four types of donor cells were used: 1) denuded cumulus cells (DCCs) collected from in vitro-matured (IVM) oocytes; 2) cumulus cells collected from oocytes after 22 h of IVM and cultured for 18 h (CCCs); 3) follicular cells obtained from follicular contents and cultured for 40 h (CFCs); and 4) adult skin fibroblasts. The DCCs showed a significantly (p < 0.01) lower rate of fusion than the CCCs when two pulses of 170 V/mm DC were applied for 50 µsec (19 ± 2% vs. 77 ± 3%). The rate of DCC fusion with oocytes was increased by the application of two DC pulses of 190 V/mm for 30 µsec, although this was still lower than the rate of fusion in the CCCs (33 ± 1% vs. 80 ± 2%). The rates of cleavage (57 ± 5%) and blastocyst formation (1 ± 1%) in the DCC-derived embryos did not differ from those (55 ± 6% and 3 ± 1%, respectively) in the CCC-derived SCNT embryos. Autologous SCNT embryos derived from CFCs (5 ± 2%) showed higher levels of blastocyst formation (p < 0.01) than CCC-derived autologous SCNT embryos (1 ± 0%). In conclusion, the results of the present study show that culturing cumulus and follicular cells before SCNT enhances cell fusion with oocytes and that CFCs are superior to CCCs in the production of higher numbers of autologous SCNT blastocysts.

Complete mitochondrial genomes of Bos taurus and Bos indicus provide new insights into intra-species variation, taxonomy and domestication

The taurine and zebuine cattle breeds comprise the majority of the world cattle population but their taxonomic status is still controversial. The two forms of cattle are currently classified as Bos taurus and Bos indicus species and are differentiated primarily by the presence or absence of a hump. However, these two species hybridize readily, producing fully fertile offspring. We have determined and analyzed complete B. taurus and B. indicus mitochondrial genome sequences to investigate the extent of sequence divergences and to study their taxonomic status by molecular dating. The sequences encompassed 16,338 and 16,339 nucleotides, respectively, and differed at 237 positions. Estimated divergence times indicated that the two cattle lineages separated 1.7-2.0 million years ago. Combined phylogenetic analyses of 18 new and 130 previously reported extant B. taurus and B. indicus control region sequences with data from 32 archaeological specimens of the extinct wild aurochs (Bos primigenius) identified four major maternal lineages. B. primigenius haplotypes were present in all but the B. indicus lineage, and one B. taurus sequence clustered with B. primigenius P haplotypes that were not previously linked with domestic cattle. The B. indicus cluster and a recently reported new B. primigenius haplotype that represents a new lineage were approximately equidistant from the B. taurus cluster. These data suggest domestications from several differentiated populations of B. primigenius and a subspecies status for taurine (B. primigenius taurus) and zebuine (B. primigenius indicus) cattle.

Mitochondrial genome polymorphisms associated with longissimus muscle composition in Iberian pigs

We carried out a study to investigate the associations between mitochondrial DNA polymorphisms and meat quality traits (intramuscular fat and protein content of the longissimus) in an Iberian porcine line named Torbiscal. The studied pigs (n = 319) belong to 9 maternal lineages and were previously assigned to 6 mitochondrial haplotypes (H1 to H6), based on Cytochrome b and Dloop sequences. Statistical analyses, following a bivariate mixed model, show a greater fat content and lower protein content in H3 haplotype carriers than H1, H2, H4, H5, and H6 haplotype carriers. The magnitudes of these differences are close to 1 g of fat and -0.5 g of protein per 100 g of muscle. To identify the causative mutation of these effects on intramuscular fat and protein contents, the complete mitochondrial DNA sequence of 6 individuals was determined, each one carrying a different mitochondrial haplotype. The alignments of these 6 complete mitochondrial sequences allowed identification of 32 substitutions and 2 indels. Two polymorphic positions were exclusively detected in H3 carriers: a synonymous transition 9104C > T in the gene-coding region of Cytochrome c oxidase subunit III and a substitution 715A > G in 12S rRNA. Genotyping results of a larger number of Torbiscal samples showed the exclusive presence of 9104T and 715G alleles in H3 carriers. The detected candidate substitutions are located in essential mitochondrial genes, and although they do not change the amino acid composition, we cannot disregard a potential change in the secondary structure of their corresponding mRNA. The usefulness of these polymorphisms as markers in selection programs requires validation of the consistency of these results in other Iberian pig lines.

Mitochondrial DNA sequence and haplotype variation analysis in the chicken (Gallus gallus)

Although it is known to be useful for certain genotype:phenotype assignments, our knowledge of the nature and extent of variation in the entire chicken (Gallus gallus) mitochondrial genome (mtGenome) is limited. Here, we used experimental and in silico tools to identify nucleotide variants in the mtGenome, including the coding and non-coding (D-loop) regions. The distribution of the experimentally identified mitochondrial DNA variants in meat- (broilers) and egg-type (White Leghorn) chickens was also assessed. A total of 113 single-nucleotide polymorphisms (SNPs) were identified. The in silico analysis revealed a total of 91 SNPs, with 70 in the coding region and 21 in the non-coding region. Of the 41 experimentally identified SNPs, 27 were in the D-loop. Together, the experimentally identified SNPs in the non-coding region formed 11 haplotypes, whereas the 14 SNPs in the coding region formed 6. Though, 9 of the D-loop region haplotypes were observed only in broilers, 3 of the 6 haplotypes from the coding region occurred at a significantly higher frequency in broilers. To our knowledge, this investigation represents the first whole-mtGenome scan for variation and an evaluation, though limited in sample size, of the haplotype distribution in meat- and egg-type populations, using the SNPs and haplotypes identified.

Use of androgenesis for estimating maternal and mitochondrial genome effects on development and oxygen consumption in rainbow trout, Oncorhynchus mykiss

Chromosome set manipulation was used to produce rainbow trout, Oncorhynchus mykiss, with identical nuclear backgrounds, but different maternal backgrounds to determine mitochondrial effects on development rate and oxygen consumption. Significant differences in development rate and oxygen consumption were observed between groups from different females. Development rates ranged from a mean of 317.97 degree days ( degrees d) to 335.25 degrees d in progeny from different females. Mean oxygen consumption rates ranged from 3.31 micromol O2 g(-1) wet mass h(-1) to 9.66 micromol O2 g(-1) wet mass h(-1). Oxygen consumption and development rate analysis revealed the two slowest developing groups had the highest oxygen consumption rates. Development rate differences between second generation clonal females indicate that mitochondrial genomes play a significant role on early development and are comparable to development rate differences between clonal lines of rainbow trout. These results indicate that selection for mitochondrial genomes could increase growth rates and possibly food conversion ratios in aquaculture species.

Species-specific identification by inhibitor-controlled PCR of ruminant components contaminating industrial crude porcine heparin

With the emergence of bovine spongiform encephalopathy, the source of pharmaceutical heparin is currently restricted to porcine intestinal mucosa. To control the species origin of industrial crude heparin, molecular biology methods relying on species-specific protein or DNA analysis should be developed to identify the ruminant components that might be contaminants in industrial crude porcine heparin (ICPH). Because heparin contained in ICPH is a strong PCR inhibitory substance, it is necessary to explore DNA extraction methods specific for ICPH and develop analysis methods that could monitor the presence of PCR inhibitory substances. In the present studies, DNA was extracted from ICPH by seven methods, and their abilities to remove the PCR inhibitory substances were compared using inhibitory-controlled PCR (IC-PCR). The results showed that, based on the optimization of the final concentration of the internal processing control (IPC), IC-PCR was a rapid, sensitive and efficient way to monitor the presence of PCR inhibitory substances contained in DNA extracted from ICPH, and only the agarose gel purification method could be used to completely eliminate the PCR inhibitory substances contained in ICPH.

Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle

In order to clarify the origin and genetic diversity of cattle in North Eastern Asia, this study examined mitochondrial displacement loop sequence variation and frequencies of Bos taurus and Bos indicus Y chromosome haplotypes in Japanese, Mongolian, and Korean native cattle. In mitochondrial analyses, 20% of Mongolian cattle carried B. indicus mitochondrial haplotypes, but Japanese and Korean cattle carried only B. taurus haplotypes. In contrast, all samples revealed B. taurus Y chromosome haplotypes. This may be due to the import of zebu and other cattle during the Mongol Empire era with subsequent crossing with native taurine cattle. B. taurus mtDNA sequences fall into several geographically distributed haplogroups and one of these, termed here T4, is described in each of the test samples, but has not been observed in Near Eastern, European or African cattle. This may have been locally domesticated from an East Eurasian strain of Bos primigenius.

PCR identification of beef, sheep, goat, and pork in raw and heat-treated meat mixtures

A PCR assay has been developed for the specific and qualitative detection of pork (Sus scrofa domesticus), beef (Bos taurus), sheep (Ovis aries), and goat (Capra hircus) in raw and heat-treated meat mixtures. A forward common primer was designed on a conserved DNA sequence in the mitochondrial 12S ribosomal RNA gene (rRNA), and reverse primers were designed to hybridize on species-specific DNA sequences of each species considered. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear species identification. Analysis of experimental meat mixtures demonstrated that the detection limit of the assay was 1% (wt/wt) for each species analyzed. This assay can be useful for the accurate identification of these species, avoiding mislabeling or fraudulent species substitution in meat mixtures.