f the several hundred breeds of pigs in the world, many are in danger of extinction and others are threatened by inefficient use or loss due to cross breeding. Special efforts are required to conserve these genetic resources for food security and rural development but it is not possible to conserve all breeds. Microsatellites, which are short tandem nucleotide repeats found scattered throughout the genome of eukaryotes, have been used to evaluate genetic diversity present within livestock populations to assist in rationalising breed conservation programmes and ensure the greatest possible conservation of diversity. This review provides insights into the use of microsatellite markers to reveal origin, genetic structure and diversity within and across various domestic pig breeds around the world. However, in future, microsatellites may be replaced by panels of single nucleotide polymorphism (SNP) markers for genome-wide population genetic analysis. Meanwhile, microsatellites are still widely employed and for some species may never be replaced by SNP.

Genetic diversity of domestic pigs as revealed by microsatellites: a mini review

Objective European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results The results showed that Thai pig populations had a high genetic diversity with mean total (TNA) and effective (Ne) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity (He) across loci (0.710). The polymorphic information content (PIC) per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher He compared to Ho in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean FST estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion Our study reveals a close genetic relationship between Thai native pigs and Chinese pigs. The genetic introgression from European breeds is found in some Thai native pig populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.

/pdf/genetic-diversity-analysis-of-thai-indigenous-pig-population-4z8kuw23ps.pdf

Genetic diversity analysis of Thai indigenous pig population using microsatellite markers

Aim: The present study was carried out to characterize Andaman Desi pig genetically using 23 FAO recommended microsatellite markers. Materials and Methods: 25 blood samples were collected from genetically unrelated Andaman Desi pigs and DNA was isolated by standard procedure of phenol/chloroform. The genomic DNA was amplified by polymerase chain reaction (PCR) at 23 microsatellite loci and the PCR products were resolved by denaturing urea polyacrylamide gel electrophoresis and alleles were visualized after silver nitrate staining. The data were analyzed for allele size range, number of alleles, allelic frequencies, heterozygosity and polymorphism information content (PIC) for each locus. Results: The allele size range varied from 86–116 bp at locus SW936 to 280–296 at locus IGFI. The total number of alleles ranged between 5 (S0228, SW122, SW951, SW24 and S0178) and 12 (S0355). The effective number of alleles ranged from 3.14 (SW24) to 8.1 (S0355). The mean observed and expected heterozygosities were 0.69±0.01 and 0.77±0.01 respectively. The mean PIC for all the 23 studied loci was 0.74±0.01. Conclusions: The Andaman Desi pig was characterized at genetic level and it was found that the genetic diversity of this indigenous breed was high.

/pdf/genetic-characterization-of-andaman-desi-pig-an-indigenous-4xvupxio45.pdf

Genetic characterization of Andaman Desi pig, an indigenous pig germplasm of Andaman and Nicobar group of islands, India by microsatellite markers.

Objective. The purpose of this study was to characterize a population of domestic pig (Sus scrofa domestica) in Cerete, Cordoba, using 20 microsatellite; calculate heterozygosity per locus and average heterozygosity. Materials and methods. Hair samples were collected from 62 specimens. DNA was extracted by proteinase K digestion and phenol-chloroform purification. Information from 20 microsatellites was selected out of those recommended for swine biodiversity studies. PCR products were separated by a vertical polyacrylamide gel electrophoresis. The bands were visualized by staining with silver nitrate. Results. All microsatellites used were polymorphic. Between 3 (SW1067) and 15 (IFNG) alleles were detected with an average number of 6.7 and a total de 134 alleles. The average expected and observed heterozygosities were 0.5278 and 0.5479, respectively. PIC values ranged between 0.1999 and 0.8300 for loci SW1067 and SW911, respectively. Conclusions. Levels of observed and expected heterozygosity found in the present study indicate that the domestic pig (Sus scrofa domestica) in Cordoba Cerete show high degree of genetic variability.

/pdf/genetic-characterization-of-the-domestic-pig-sus-scrofa-cam1jfkq49.pdf

Genetic characterization of the domestic pig (Sus scrofa domestica) in Cerete-Colombia, using microsatellite markers

To optimize the combination of microsatellite loci for genetic control of outbred swine stocks, 32 of 100 loci distributed among almost all chromosomes (except 12) were screened out by 1.5% agarose, 8% polyacrylamide gel and capillary electrophoresis scanning among 3 miniature swine outbred stocks, namely Bama (BM), Guizhou (GZ) and Tibeta (TB). The mean total and effective allele numbers among these stocks were 12.1 and 5.9, respectively. The mean heterozygosity for these breeds was 0.5428, 0.6978 and 0.7646, and polymorphism information content was 0.5469, 0.7296 and 0.7663, respectively. Accordingly, hereditary variation from low to high was BM < GZ < TB. This showed that the genetic relationship between BM and GZ pigs was closer, and both were distant from TB. Additionally, the effectiveness of the 32-locus combination for evaluation of genetic quality was demonstrated in Changchun-junmo-1 (CJ-1), a standard outbred Chinese pig stock, in which the mean total and effective allele numbers and mean heterozygosity were 6.1613, 3.8483 and 0.6903, respectively. Since our results were consistent with the breeding pedigrees, the 32 loci could be used for both genetic monitoring within the individual outbred miniature swine stocks and population structure analysis between them.

https://www.funpecrp.com.br/gmr/year2015/vol14-2/pdf/gmr4656.pdf

Selected representative microsatellite loci for genetic monitoring and population structure analysis of miniature swine.

In this study, 19 microsatellite loci were genotyped for 10 Chinese village pig populations including 817 individuals to investigate their genetic characteristics. The allele frequencies, effective num-bers of alleles ( n e ), average heterozygosity within popu-lations ( H ), genetic differentiation between populations ( F st ), and coefficient of gene differentiation ( G st ) were calculated. The results showed that village popula-tions had relatively large H and n e values, but with smaller average G st , compared with indigenous pure-bred pig populations. The smaller average G st (0.0386) suggested that the genetic difference between village populations was only 3.86%, and the other 96.14% was found within populations. Most of the pairwise F st -val-ues were significant ( P < 0.05), demonstrating differ-entiation among populations. A neighbor-joining tree constructed from modified Cavalli-Sforza genetic dis-tances divided Chinese village pig populations, Chinese indigenous pig breeds, and Euro-American pig breeds into 3 separate clusters. All of above genetic analyses showed that Chinese village pig populations are unique genetic resources, which could be used for future pig production.

Genetic uniqueness of Chinese village pig populations inferred from microsatellite markers.

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Genetic uniqueness of Chinese village pig populations inferred from microsatellite markers.