Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.

The hypoxic environment imposes severe selective pressure on species living at high altitude. To understand the genetic bases of adaptation to high altitude in dogs, we performed whole-genome sequencing of 60 dogs including five breeds living at continuous altitudes along the Tibetan Plateau from 800 to 5100 m as well as one European breed. More than 150× sequencing coverage for each breed provides us with a comprehensive assessment of the genetic polymorphisms of the dogs, including Tibetan Mastiffs. Comparison of the breeds from different altitudes reveals strong signals of population differentiation at the locus of hypoxia-related genes including endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1) and beta hemoglobin cluster. Notably, four novel nonsynonymous mutations specific to high-altitude dogs are identified at EPAS1, one of which occurred at a quite conserved site in the PAS domain. The association testing between EPAS1 genotypes and blood-related phenotypes on additional high-altitude dogs reveals that the homozygous mutation is associated with decreased blood flow resistance, which may help to improve hemorheologic fitness. Interestingly, EPAS1 was also identified as a selective target in Tibetan highlanders, though no amino acid changes were found. Thus, our results not only indicate parallel evolution of humans and dogs in adaptation to high-altitude hypoxia, but also provide a new opportunity to study the role of EPAS1 in the adaptive processes.

The local origin of the Tibetan pig and additional insights into the origin of Asian pigs.

BACKGROUND: The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig. METHODS AND FINDINGS: We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively. CONCLUSIONS: We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region.

Genetic differentiations between randomly and selectively bred pig populations in Yunnan, China.

To assess the genetic diversity between randomly and selectively bred populations, we sequenced 438 bp of the mitochondrial DNA control region from 102 pigs. These samples represented four native pig breeds, one nucleus and one conservation herd from Yunnan, China. Twenty haplotypes with sixteen polymorphic sites were identified. The number of haplotypes in the nucleus herd of Saba pig and the conservation herd of Banna miniature pig were restricted to three and one, respectively, while the randomly bred pig populations exhibited over six haplotypes. Notably, haplotype diversity in randomly bred populations was significantly greater than the selectively bred populations (h=0.732 vs. 0.425 and 0, exact test, P<=0.0036). These findings demonstrate that selective breeding generated low genetic diversity compared to randomly bred pig breeds. A timely intervention and well programmed breeding approach would stop further genetic diversity reduction in the nucleus and conservation herds of native pig breeds. Otherwise, selective breeding would dramatically reduce genetic diversity in only several years, indicating that sharp contradictions exist between breeding, conservation and genetic diversity. Genetic relationships are discussed based on net genetic distances among pig populations.

Effects of chemical activation and season on birth efficiency of cloned pigs.

The effects of chemical activation on birth efficiency of cloned pigs were studied by investigating the developmental process from porcine oocyte activation to birth of cloned pigs. Three different activation methods were used: (i) Electroporation (Ele); (ii) Ele followed by incubation with 6-dimethylaminopurine (6-DMAP); and (iii) Ele followed by a treatment with cycloheximide (CHX). In experiment 1, the rates of cleavage, developmental rates and cell number of porcine parthenogenetic (PA) embryos were investigated in the three treatment groups. In experiment 2, NT embryos produced by the three different activation treatments were compared for the rates of cleavage, development and cell number. Finally, the effects of Ele and Ele+CHX activation methods on birth efficiency of cloned pigs were compared. The activated oocytes treated by combination activation generally showed a higher (P<0.05) blastocyst rate and produced more expanded blastocysts than oocytes activated with Ele. The rates of cleavage and total cell number of parthenotes were not significantly different. Parthenogenetic embryos activated with 6-DMAP developed into blastocyst and expanded blastocyst stages at a significantly (P<0.05) higher rate than those treated with Ele, but the developmental capability was dramatically decreased in NT embryos. With the CHX activation method, the NT embryo blastocyst rate was substantially (P<0.05) increased although the production of expanded blastocysts was not significantly different from that by the other two methods. The birth rate of cloned pigs increased in the CHX group, though the rate was not significantly different from Ele. The effects of season on developmental rate of the porcine PA embryos and birth rate of cloned pigs were also examined in our study. Porcine oocytes collected in the spring had higher developmental capabilities than those collected in the winter. However, no difference in birth rate of the cloned pigs was found between the oocytes collected in the two seasons. The results obtained from PA and NT embryos, following different activation methods, were inconsistent, suggesting that activation mechanisms are dissimilar in PA and NT embryos. Although the chemical activation in our study leads to an elevation of the blastocyst rate, it does not improve the oocyte's molecular programming and so does not significantly improve the efficiency of producing cloned pig births.

Hypoxic adaptations of hemoglobin in Tibetan chick embryo: high oxygen-affinity mutation and selective expression.

Tibetan chicks (Gallus gallus) survived with high hatchability (35.0%) and Recessive White Feather broilers (RWF) from low elevations survived rarely and with a low hatchability (3.0%) after simulated incubation under hypoxia of 13% O2. The functional mutation of Met-32D(B13)-Leu of alpha(D) globin chain was related with hypoxia based on allele distribution, homology model building and oxygen affinity assay. Whole embryos on days 3-8 and whole blood on days 9-18 were collected to investigate the stage expression profiles of all seven globins and HIF-1alpha by real-time PCR. Under hypoxia (12.0% O2) on days 3-8, HbE was overexpressed, HbA was expressed earlier and HbP expression was restricted, which completely overturned the expression profile under normoxia. The amount of hemoglobin expression in Tibetan chicks was remarkably higher than that of RWF. HIF-1alpha expression peaked early in both breeds, with. In conclusion, the special hypoxic expression profile on days 3-8 certainly is a common molecular mechanism of hypoxia tolerance in surviving Tibetan chick and RWF embryos; the mutation Met-32D(B13)-Leu and increasing hemoglobins are important mechanisms of hypoxia adaptation in Tibetan chick embryos, and we suggest that HIF-1alpha could be responsible for the hypoxic expression profile.

[Identification of a common deletion in different curly mutants in Drosophila melanogaster].

Curly is a easily distinguishable dominant mutant wing character. The Cy mutation is the most commonly used dominant marker for the second chromosome balancers in Drosophila melanogaster, but little is known about the Cy gene. Based on known genomic and cytogenetic information, a 102 bp deletion which is located between the Genes synaptotagmin (syt) and Activin Like Protein at 23B(Alp23B) on the Drosophila melanogaster genome (release 4) had been found to be commonly contained on Cy chromosome in three different curly strains. Meanwhile, when using the deletion as a DNA marker, the result suggested that Cy homozygote be lethal in embryo period. These results will provide some helpful information to investigate molecular mechanism of curly wings in the further study.

Hypoxia adaptation and hemoglobin mutation in Tibetan chick embryo.

Tibetan chick lives at high altitudes between 2600 and 4200 m with a high hatchability and low land breeds survive rarely with a hatchability of 3.0% under hypoxia of simulated 4200 m. Under hypoxia of whole 21 d, the hatchability of Tibetan chick and Recessive White Feather broiler differed with a greatest disparity from day 4 to 11 and also significantly in other stages except from day 1 to 3. Hypoxia in each stage did not reduce significantly survival rate of this stage except hatchability. These two results indicated that the hypoxia in the early stage had an adverse effect on the later stage. All exons encoding chick hemoglobins were sequenced to analyze gene polymorphism. The functional mutation Met-32(B13)-Leu, related with hypoxia, was found in alphaD globin chain and the mutation frequency increased with increased altitude. In addition, under hypoxic conditions, the population with higher mutation frequency had a higher hatchability. The automated homology model building was carried out using crystal structure coordinates of chick HbD. The results indicated that the substitution Met-32(B13)-Leu provides a more hydrophobic environment which leads to higher stability of heme and oxygen affinity of hemoglobin. The occurrence of the mutation Met-32(B13)-Leu is related to the origin of Tibetan chick.

Genetic diversity and relationship of Yunnan native cattle breeds and introduced beef cattle breeds.

In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and relationship in 134 samples belonging to two native cattle breeds from the Yunnan province of China (DeHong cattle and DiQing cattle) and four introduced beef cattle breeds (Brahman, Simmental, MurryGrey, and ShortHorn). Ten primers were used, and a total of 84 bands were scored, of which 63 bands (75.0%) were polymorphic. The genetic distance matrix was obtained by proportions of shared fragment. The results indicate that the Yunnnan DeHong cattle breed is closely related to the Brahman (Bos indicus), and the Yunnan DiQing cattle breed is closely related to the Simmental, ShortHorn, and MurryGrey (Bos taurus) breeds. Our results imply that Bos indicus and Bos taurus were the two main origins of Yunnan native cattle. The results also provide the basic genetic materials for conservation of cattle resources and crossbreeding of beef cattle breeds in South China.

Effects of marker-assisted selection under different initial frequency of QTL favorable allele.

A ten-generation continuous selection experiment on a single trait in a closed population was carried out by stochastic simulation. It assumed that the trait was controlled by polygenes and a single autosomal bi-allelic marked quantitative trait locus (QTL). Individual breeding values were estimated through animal model marker-assisted best linear unbiased prediction (MB-LUP), and breeding animals were selected according to their breeding values. The effects of three levels initial frequencies of QTL favorable allele on marker-assisted selection (MAS) were studied. The results showed that it would gain higher genetic response when implementing MAS on those traits with lower initial frequency of QTL favorable allele. When the initial frequency of QTL favorable allele was low, although the generation number required for fixing QTL favorable allele in the population would be lengthened, its frequency would be increased faster. However, the initial frequency of QTL favorable allele had little effects on the inbreeding rates.

Primary factors affecting the evaluation accuracy of animal model MBLUP.

Marker-assisted best linear unbiased prediction (MBLUP) is one important method of implementing marker-assisted selection (MAS). The computer stochastic simulation method was used to study the effects of heritability of trait, QTL variance and map distance between two adjacent markers on the evaluation accuracy of animal model MBLUP. With the higher heritability, the smaller QTL variance and the shorter map distance between two adjacent markers, the evaluation accuracy of animal model MBLUP would be increased. On the contrary, the evaluation accuracy of animal model MBLUP would be decreased when the heritability was lower, QTL variance was larger and map distance between two adjacent markers was longer.

[Primary analysis of mitochondrial DNA D-loop region sequence in Baoshan pig].

To investigate the genetic diversity and genetic data of Baoshan pig in Yunnan province,the mitochondrial DNA D-loop hypervariable segment I sequences 15 363 approximately 15 801 (438 bp) in 19 individuals of Baoshan pig were sequenced. Ten mitochondrial haplotypes were identified in the samples, with 8 sites showing polymorphism, which were 5 T/C and 1 G/A transitions, 1 G/C and 1 A/T transversions. The contents of A,T,G and C were 35.4%,26 9%,13.2% and 24.5%,respectively. The content of A+T (62.3%) was significantly higher than that of G+C (37.3%). It will be of importance to conservation and sustainable utilization in Baoshan pig.