[Characterization of novel alleles and new mutation sites of porcine MHC class II DQA].

The primers, DQAp161 and DQAp443, were designed based on the homologous region of SLA-DQA cDNA sequences and HLA-DQA genomic sequences. The 731 bp fragment of SLA-DQA including completed intron 2, the near completed exon 2 and partial exon 3 was obtained by PCR. The nucleotide sequences of the fragment of SLA-DQA were obtained with cloning and direct sequencing. Both nucleotide sequences of exon 2 and amino acid sequences of alpha 1 domain were analyzed in a pedigree. The sequence data were compared with all sequences of SLA-DQA exon 2 in GenBank. Two novel alleles, DQA-SLT 26 and DQA-TC 21-1, were found according to the above analyses. Four amino acid changes were observed among SLA-DQA haplotype c, d and DQA-SLT 26. They were Val-->Ala(60), Lys-->Glu(65), Asp-->Gly(81) and Lys-->Ile(93). Comparing the amino acids sequence of the all SLA-DQA sequences with DQA-TC 21-1 revealed that the His (94) was changed into Tyr.

Genetic variation and relationships of eighteen Chinese indigenous pig breeds.

Chinese indigenous pig breeds are recognized as an invaluable component of the world's pig genetic resources and are divided traditionally into six types. Twenty-six microsatellite markers recommended by the FAO (Food and Agriculture Organization) and ISAG (International Society of Animal Genetics) were employed to analyze the genetic diversity of 18 Chinese indigenous pig breeds with 1001 individuals representing five types, and three commercial breeds with 184 individuals. The observed heterozygosity, unbiased expected heterozygosity and the observed and effective number of alleles were used to estimate the genetic variation of each indigenous breed. The unbiased expected heterozygosity ranged between 0.700 (Mashen) and 0.876 (Guanling), which implies that there is an abundant genetic variation stored in Chinese indigenous pig breeds. Breed differentiation was shown by fixation indices (FIT, FIS, and FST). The FST per locus varied from 0.019 (S0090) to 0.170 (SW951), and the average FST of all loci was 0.077, which means that most of the genetic variation was kept within breeds and only a little of the genetic variation exists between populations. The Neighbor-Joining tree was constructed based on the Nei DA (1978) distances and one large cluster with all local breeds but the Mashen breed, was obtained. Four smaller sub-clusters were also found, which included two to four breeds each. These results, however, did not completely agree with the traditional type of classification. A Neighbor-Joining dendrogram of individuals was established from the distance of -ln(proportions of shared alleles); 92.14% of the individuals were clustered with their own breeds, which implies that this method is useful for breed demarcation. This extensive research on pig genetic diversity in China indicates that these 18 Chinese indigenous breeds may have one common ancestor, helps us to better understand the relative distinctiveness of pig genetic resources, and will assist in developing a national plan for the conservation and utilization of Chinese indigenous pig breeds.

Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis.

Twelve Chinese indigenous goat populations were genotyped for twenty-six microsatellite markers recommended by the EU Sheep and Goat Biodiversity Project. A total of 452 goats were tested. Seventeen of the 26 microsatellite markers used in this analysis had four or more alleles. The mean expected heterozygosity and the mean observed heterozygosity for the population varied from 0.611 to 0.784 and 0.602 to 0.783 respectively. The mean FST (0.105) demonstrated that about 89.5% of the total genetic variation was due to the genetic differentiation within each population. A phylogenetic tree based on the Nei (1978) standard genetic distance displayed a remarkable degree of consistency with their different geographical origins and their presumed migration throughout China. The correspondence analysis did not only distinguish population groups, but also confirmed the above results, classifying the important populations contributing to diversity. Additionally, some specific alleles were shown to be important in the construction of the population structure. The study analyzed the recent origins of these populations and contributed to the knowledge and genetic characterization of Chinese indigenous goat populations. In addition, the seventeen microsatellites recommended by the EU Sheep and Goat Biodiversity Project proved to be useful for the biodiversity studies in goat breeds.

[Isolation, localization and expression of a novel expressed sequence tag from pig skeletal muscular tissue].

A novel expressed sequence tag (ESThp9-1, GenBank accession number: B1596262) was isolated from pig skeletal muscular tissue by using the mRNA differential display technique. BLAST analysis revealed that the 196 bp long EST (ESThp9-1) was not homologous to any of the known porcine genes in the database but similar to rat U3A small nuclear RNA (87% identity over 93 nucleotides) and mouse U3B.4 small nuclear RNA (85% identity over 96 nucleotides). Semi-quantitative reverse transcription polymerase chain reaction indicated that EST9hp-1 was expressed in most of tissue of the pig. ESThp9-1 was physically mapped on sus scrofa chromosome 12q1.1-q1.5 and linked with microsatellite S0090 by using somatic cell hybrid panel and radiation hybrid panel analysis. According to the homologous information and result of physical mapping, ESThp9-1 was presumed to be one member of the porcine U3 gene family.

Preparation and analysis of spermatocyte meiotic pachytene bivalents of pigs for gene mapping.

Well-spread meiotic pachytene bivalents were obtained by using the prolonged hypotonic treatment combined with high chloroform Carnory's fixative solution from cells of the testes of domestic pigs. Comparison in the division index and length of pachytene bivalents with metaphase chromosomes showed that those of the former are 5 times higher and 3.42(1.87-5.98) times longer than those of the latter. Comparative studies on chromomere maps of bivalents and mitotic chromosomal G-bands were conducted by using the chromosome 12 as a example. Sex vesicle and various shapes of synaptic sex chromosomes have been observed. Two-color PRimed IN Situ (PRINS) labeling has been conducted successfully on pachytene bivalents of pigs.