Impact of genetic drift on access and benefit sharing under the Nagoya Protocol: the case of the Meishan pig.

Genetic drift (GD) randomly impacts small breeds and imported populations. Therefore, it can impact policies that affect conservation of animal genetic resources. This paper evaluates GD for a population of Meishan pigs imported into the United States and explores the ramifications of GD on access and benefit sharing of genetic resources under the Nagoya Protocol (NP) of the United Nations' Convention on Biological Diversity. The NP was motivated by concerns about fair and equitable benefit sharing of genetic resources across life forms. In this experiment, 35 microsatellite markers were used to quantify the level of GD that occurred between Meishan pigs (Meishan-China; n = 22) imported into the United States in the late 1980s and contemporary Meishan (Meishan-US; n = 42), which have been randomly bred since importation. The Meishan-US consisted of 2 subpopulations (Meishan-MARC and Meishan-ISU). Five other breeds were also included in the analysis to serve as reference populations: Fengjing and Minzhu, which were imported with Meishan-China, and Duroc, Berkshire, and Yorkshire from the United States. Mean shift in allele frequency was 0.11 (SE = 0.019) due to GD for Meishan-US vs. Meishan-China with some loci having changed allele frequencies by greater than 0.20. Principle coordinate analysis confirmed divergence among the Meishan populations. Model-based clustering tended to place the U.S. and Chinese breeds into 2 distinct clusters, likely due to differences in allele frequencies between U.S. and Chinese breeds. Contemporary Meishan-US has become differentiated from the original imported animals due to GD. Attributing future performance of Meishan-US to Meishan-China, as set forth by NP, is problematic due to GD. As an imported breed becomes established there will be an increasing number of breeders who may have different selection goals and private treaty contracts will govern the exchange of stock between them. Therefore, considering biological phenomena and social dynamics simultaneously draws into question whether a rigorous access and benefit sharing protocol as envisioned in the NP will be operational.

Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations.

As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K = 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.

A QTL study of cattle behavioral traits in embryo transfer families.

Two behavioral traits, temperament and habituation, were measured in 130 calves from 17 full-sib families which comprise the Canadian Beef Cattle Reference Herd. Using variance components, heritability was calculated as 0.36 for temperament and 0.46 for habituation. Genotyping of 162 microsatellites at approximately 20 cM intervals allowed the detection of six quantitative trait loci (QTL) for behavior traits on cattle chromosomes 1, 5, 9, 11, 14, 15.

Detection of quantitative trait loci affecting milk production traits on 10 chromosomes in Holstein cattle.

Sons (n = 71 to 75) of each of six Holstein sires were genotyped at 69 microsatellite loci covering a total of 676 cM on chromosomes 3, 5, 9, 10, 13, 15, 17, 20, 23, and 26. Estimates of quantitative trait loci (QTL) effect and location were made using a least squares interval mapping approach based on daughter yield deviations of sons for 305 d milk, fat, and protein yield and fat and protein percentage. Thresholds for statistical significance of QTL effects were determined from interval mapping of 10,000 random permutations of the data across the bull sire families and within each sire family separately. Analyses combining data across sires indicated the presence of QTL affecting milk, fat, and protein yield on chromosomes 20 and 26 and a QTL affecting fat and protein percentage on chromosome 3. Analyses within each sire family separately indicated the presence of segregating QTL in at least one family on 7 of the 10 chromosomes. Statistically significant estimates of QTL effects on breeding value ranged from 438 to 658 kg of milk, from 17.4 to 24.9 kg of fat, 13.0 to 17.0 kg of protein, 0.04 to 0.17% fat, and 0.07 to 0.10% protein.

Development of the Canadian beef reference herd for gene mapping studies.

A project to map quantitative trait loci (QTL), in beef cattle using a full-sib design was initiated using six Bos taurus breeds. Embryo transfer was used in a large scale, short timeframe experiment to develop this herd for gene mapping. Full-sib families allowed for genetic information to be followed through both the sire and the dam and for both parents to be slaughtered so that carcass quality data could also be obtained from both of them at close to typical slaughter ages. Repeatability of response to superovulation was significant among the 3 flushes per female. Response to superovulation was negatively correlated with backfat of the donor. Crossbred embryos were found to have higher survival than purebred embryos.

Detection of QTL for milk production on Chromosomes 1 and 6 of Holstein cattle.

Seventy to 75 sons of each of six Holstein sires were assayed for genotypes at a number of microsatellite loci spanning Chromosomes (Chrs) 1 and 6. The number of informative loci varied from three to eight on each chromosome in different sire families. Linkage order and map distance for microsatellite loci were estimated using CRI-MAP. Estimates of QTL effect and location were made by using a least squares interval mapping approach based on daughter yield deviations of sons for 305-d milk, fat, protein yield, and fat and protein percentage. Thresholds for statistical significance of QTL effects were determined from interval mapping of 10,000 random permutations of the data across the bull sire families and within each sire family separately. Across-sire analyses indicated a significant QTL for fat and protein yield, and fat percentage on Chr 1, and QTL effects on milk yield and protein percentage that might represent one or two QTL on Chr 6. Analyses within each sire family indicated significant QTL effects in five sire families, with one sire possibly being heterozygous for two QTLs. Statistically significant estimates of QTL effects on breeding value ranged from 340 to 640 kg of milk, from 15.6 to 28.4 kg of fat, and 14.4 to 17.6 kg of protein.

Transmitochondrial differences and varying levels of heteroplasmy in nuclear transfer cloned cattle.

To assess the extent of cytoplasmic genetic variability in cloned cattle produced by nuclear transplantation procedures, we investigated 29 individuals of seven male cattle clones (sizes 2-6) from two different commercial sources. Restriction enzyme and direct sequence analysis of mitochondrial DNA (mtDNA) detected a total of 12 different haplotypes. Transmitochondrial individuals (i.e., animals which share identical nuclei but have different mitochondrial DNA) were detected in all but one of the clones, demonstrating that mtDNA variation among cloned cattle is a very common phenomenon which prevents true genetic identity. The analyses also showed that the cytoplasmic genetic status of some investigated individuals and clones is further complicated by heteroplasmy (more than one mtDNA type in an individual). The relative proportions of different mtDNA-types in two animals with mild heteroplasmy were estimated at 2:98% and 4:96% in DNA samples derived from blood. This is in agreement with values expected from karyoplast-cytoplast volume ratios. In contrast, the mtDNA haplotype proportions observed in six other heteroplasmic animals of two different clones ranged from 21:79% to 57:43%, reflecting a marked increase in donor blastomere mtDNA contributions. These results suggest that mtDNA type of donor embryos and recipient oocytes used in nuclear transfer cattle cloning should be controlled to obtain true clones with identical nuclear and cytoplasmic genomes.

Evolutionary applications of MIRs and SINEs.

It is believed that short interspersed elements (SINEs) are irreversibly inserted into genomes. We use this concept to try to deduce the evolution of whales using sequence and hybridization studies. The observation that microsatellites are associated with SINEs lead us to screen sequences surrounding cetacean microsatellites for artiodactyl-derived SINEs. Two sequences that were thought to be cetacean SINEs and the bovine SINE were aligned for comparison to sequences flanking microsatellites from ungulates. The bovine SINE was observed only in ruminants while CetSINE1 and 2 were found in mammals. Hybridization studies using these three SINEs revealed that CetSINE1 was found in all ungulates and cetaceans with the strongest hybridization signal observed in the hippopotamus and beluga; CetSINE2 hybridized to all ungulate suborders, while the bovine SINE was only observed in Ruminantia. It is proposed that these putative SINEs are not 'generic' SINEs but mammalian-wide interspersed repeats (MIRs). Caution is urged: what initially appears to be a SINE may instead be a MIR and have reduced evolutionary resolving power.

Analysis of mitochondrial DNA indicates that domestic sheep are derived from two different ancestral maternal sources: no evidence for contributions from urial and argali sheep.

To investigate the origins and phylogenetic relationships of domestic sheep, mitochondrial DNA (mtDNA) from 243 sheep of five European, one African, and four Asian breeds and several mouflon (Ovis musimon), urial (O. vignei bochariensis), and argali (O. ammon nigrimontana, O. a. collium) were assayed for restriction fragment length polymorphisms (RFLP). Twenty haplotypes were identified which occurred in three major phlogenetic groups: urial/argali, mouflon/domestic, and domestic sheep. From the branches that contain mouflon and domestic sheep, two major domestic sheep lineages are apparent. One lineage, termed European lineage, contains the majority of haplotypes detected among European domestic sheep. These mtDNAs resemble mouflon haplotypes. The other lineage, termed Asian lineage, consists of haplotypes found in central Asian and some European domestic sheep. The mean sequence difference between these two lineages (0.72%) is of similar magnitude as that between two argali subspecies. To accurately estimate sequence differences between the European and Asian mtDNA types, the mitochondrial control region of one animal from each lineage and of one mouflon and urial were completely sequenced. Sequence comparisons show that Asian and European domestic sheep lineages differ by 4.43%. The mouflon sequences diverges from the Asian type by 4.52%, but by only 1.36% from the European type. Our data supports the hypothesis that some modern domestic sheep and European mouflon derive from a common ancestor and provide evidence of an additional wild ancestor, other than the urial and argali groups, which has yet to be identified.

Development of bovine nuclear transfer embryos made with oogonia.

The pluripotency of embryonic germ cells in the mouse suggests that mitotic bovine fetal germ cells might also be a source of pluripotent cells. To investigate the pluripotency of bovine oogonia, the development in vitro of bovine embryos reconstructed by fusing oogonia with enucleated oocytes was compared with that of embryos made similarly with either blastomeres or granulosa cells. The donor cells (fresh oogonia, cryopreserved oogonia, 16- to 32-cell-stage blastomeres, or granulosa cells) were fused to the enucleated oocytes electrically. The proportions of reconstructed embryos that had cleaved at 40 h after fusion using these types of donor cells were not significantly different (37%, 33%, 56%, and 31%, respectively; p > 0.05). However, the proportions of cleaved reconstructed embryos that developed to the blastocyst stage were 9%, 13%, 36%, and 3%, respectively, significantly higher (p < or = 0.05) with blastomeres than with the other three types of donor cells. After transfer of 3 morulae and 4 blastocysts made with oogonia into three recipient heifers, embryonic and extra-embryonic tissues developed in one animal. On recovery after 43 days gestation, this conceptus was shown to be genetically identical, at 11 microsatellite loci, to the fetus that had provided the oogonia. Cytological analysis of the embryos made with oogonia at 40-44 h after fusion and at the morula and blastocyst stages revealed that aberrant cytokinesis and nucleokinesis had given rise to multinucleated, anucleate, and polyploid cells in the reconstructed embryos. It is concluded that limited pluripotency of bovine oogonia has been demonstrated, warranting further study in this area.

Detection of Mycobacterium paratuberculosis in formalin-fixed paraffin-embedded tissues by the polymerase chain reaction.

The polymerase chain reaction (PCR) utilizing primers specific for the IS900 sequence of Mycobacterium paratuberculosis was applied to tissue sections of formalin-fixed, paraffin-embedded ileum from cattle with Johne's disease and the results compared to those obtained with acid-fast (Ziehl-Neelsen) and immunohistochemical staining. The PCR was positive in 19/21 tissues (90%) while Ziehl-Neelsen staining was positive in 18/21 (86%) and immunohistochemical staining in 21/21 (100%). The Ziehl-Neelsen and immunohistochemical stains are not, however, specific for M. paratuberculosis. The PCR for detection of M. paratuberculosis using the IS900 sequence is a specific and relatively sensitive method for confirmation of Johne's disease and its application to formalin-fixed, paraffin-embedded tissues may be useful for confirmation of dubious cases, for retrospective studies and for epidemiological analyses.

A parentage evaluation test in North American elk (Wapiti) using microsatellites of ovine and bovine origin.

DNA microsatellites originally detected in sheep and cattle are also detectable in North American elk (Wapiti) using polymerase chain reactions. We have developed a parentage test in elk using eleven microsatellite markers that are highly polymorphic and informative.

Survival rates and sex ratio of bovine IVE embryos frozen at different developmental stages on day 7.

Two experiments were designed to determine the effects of stage of development on Day 7 of in vitro-produced bovine embryos on survival after deep freezing and on sex ratio. Bovine IVF embryos and bovine oviductal epithelial cells (BOEC) were co-cultured in TCM-199 and, on Day 7 after insemination (Day 0), were morphologically evaluated and divided into groups by developmental stage. In Experiment 1, embryos classified as early blastocysts, blastocysts and full-expanding blastocysts were randomly subdivided into 2 groups by replicate: 50% of the embryos were placed immediately in a new BOEC co-culture (fresh group), while the other 50% were frozen, thawed and placed in a new BOEC co-culture (frozen/thawed group). Embryos were frozen in 1.5 M glycerol using a standard slow cooling technique. Fresh and frozen/thawed embryos were compared for survival rate (embryos hatching/hatched) in BOEC co-culture over the following 3 d (i.e., Days 7 to 10). The overall survival of the 425 embryos (early to full-expanding blastocysts) was 33% and was not different between fresh (35%) and frozen/thawed (30%) embryos. Survival of embryos cultured fresh or after freezing/thawing was higher for full-expanding blastocysts than for early blastocysts or for blastocysts, both of which were not different. In Experiment 2, all frozen/thawed embryos used in Experiment 1 plus all morulae and hatched blastocysts collected and frozen on Day 7 without regard to survival were sexed utilizing the polymerase chain reaction (PCR) technique. Sex of the embryos, by stage of development on Day 7, was determined in order to compare the rate of development in BOEC co-culture with the sex ratio (percentage of males). A total of 235 embryos was sex-determined with an overall percentage of males of 51%, which was not different from the expected 1:1 sex ratio. Both full-expanding blastocysts and hatched blastocysts had a significantly higher (P < 0.05) proportion of males (68 and 100%, respectively), while morulae had a significantly lower proportion of males (24%). Early blastocysts and blastocysts did not differ from a 1:1 sex ratio. The results indicate that male embryos develop faster in vitro than female embryos. The higher survival rate of full-expanding blastocysts after freezing/thawing, and the production of a higher number of males than females among embryos of this developmental stage suggest that a greater number of male fetuses may result from the successful freezing and transfer of in vitro-produced bovine embryos.

Production of four identical calves by the separation of blastomeres from an in vitro derived four-cell embryo.

The blastomeres of two in vitro derived four-cell embryos were separated and transferred individually into surrogate zonae pellucidae, then co-cultured with bovine oviductal epithelial cells for five days until blastulation. Pairs of the quarter blastocysts were co-transferred with trophoblastic vesicles into each of four synchronised Holstein heifers, three of which were diagnosed pregnant at 28 days gestation, carrying twin fetuses. Four genetically identical bull calves were delivered by elective caesarean section at term pregnancy. One pregnancy was terminated at 56 days.

Restriction fragment length polymorphism in the mitochondrial DNA of cloned cattle.

The clonal origin of 4 Holstein bulls was determined by hybridization experiments with 2 different minisatellite probes, and all 4 animals showed identical genomic DNA fingerprints, hence confirming monozygosity. Extra-chromosomal differences were observed among these 4 Holstein bulls. Mitochondrial DNA restriction fragment length polymorphisms with restriction endonucleases Avall and Hhal sites were found, and these polymorphisms can be explained by the loss of a single site for each of these 2 enzymes. Since mitochondrial DNA are maternally transmitted, all 4 bulls would produce genetically equivalent spermatozoa and offspring. The combination of embryo cloning and specific cytoplasmic markers would provide an ideal system for the study of maternal cytoplasmic effects on quantitative traits.