[Runs of homozygosity and its application on livestock genome study].

With the rapid development of high-throughput SNP array and significant reduction of sequencing cost, the techniques of genome-resequencing and SNP chip arrays are widely applied in livestock genomic studies. Long runs of homozygosity (ROH) arose when identical haplotypes were inherited from each parent and thus a long tract of genotypes is homozygous. Nowadays, cumulative studies reported that ROH has progressively served as one of the important indexes to estimate the degree of inbreeding and genetic structure of livestock populations. However, the evaluating criteria of ROH in livestock is still inadequate. In this review, we introduce the history, theory and identification methods of ROH analysis. Meanwhile, we also systematically overview the applications and perspectives of ROH in population genetic structure analysis, genome functional assay, quality investigation and dynamic monitoring of livestock genetic resources.

[Genetic diversity of seven miniature pig breeds (strains) analyzed by using microsatellite markers].

Twenty-seven microsatellite markers recommended by the Food and Agriculture Organization (FAO) and the International Society for Animal Genetics (ISAG) were used to analyze the genetic diversities of 7 Chinese native miniature pig breeds/strains (Jiuyang Xiang Pig, Jianbai Xiang Pig, Congjiang Xiang Pig, Huanjiang Xiang Pig, Black Xiang Pig, Wuzhishan Pig, and Diannan Small Ear Pig) and 3 western pig breeds (Duroc, Large White, and Landrace). The results indicate that there exists, in general, a high degree of genetic variability within the 7 miniature pig breeds. However, the genetic variability in Jiuyang Xiang Pig, Jianbai Xiang Pig, Huanjiang Xiang Pig, and Congjiang Xiang Pig (average PICs being 0.61-0.64) was significantly lower than that in the other three miniature pig breeds (average PICs being 0.60-0.84). The genetic divergence among Jiuyang, Jianbai, Huanjiang, and Congjiang was very small (Nei's standard genetic distances being 0.12-0.22), but it was large between them and the other three miniature pig breeds (Nei's standard genetic distances being 1.61-1.96), and even larger between them and the three foreign breeds (Nei's standard genetic distances being 1.99-3.30). Cluster analysis reveals three obvious clusters for the 10 breeds: Jiuyang, Jianbai, Huanjiang, and Congjiang are in one cluster, the other three miniature pig breeds in the other, and the three foreign breeds in the third. These results are consistent with the geography distribution and origin of these breeds.

Genetic diversity of microsatellite loci in fifty-six Chinese native pig breeds.

The genetic diversity of fifty-six indigenous pig breeds in China, and three introduced pig breeds (Duroc, Landrace and Large White) was surveyed using twenty-seven microsatellites recommended by the International Society for Animal Genetics (IS-AG) and Food and Agriculture Organization (FAO). By means of the allele frequencies, mean heterozygosity, effective number of alleles, estimator of gene differentiation, polymorphism information content, genetic distance and dendrogram analysis, the genetic variability and population structure of native pig breeds were estimated. Genetic variabilities within native pig breeds are as follows: Effective number of alleles vary from 2.12 to 9.03, from 0.44 to 0.87 for mean heterozygosity, from 0.39 to 0.86 for polymorphism information content. Nei's genetic distance and Nei's standard genetic distance were estimated and used to construct UPGMA and NJ dendrograms, which were evaluated by the bootstrap test. Fifty-six Chinese indigenous pig breeds were clustered into twelve groups based on the dendrogram. Compared with the classification in Pig Breeds in China, I, II and III groups in the study are equivalent to North-China type, IV group basically accords with Lower-Changjiang River Basin type, V, VI, VII, VIII and IX groups quite correspond with Central-China type, X and XI group largely correspond to South-China type, the last group, XII is equal to South-west type at large. Suggestions that the conservation farms together with conservation areas are appropriate methods for the preservation of native pig breeds in our country were proposed. The results could provide basic molecular data for the research on the germplasm characteristics of local breeds in our country and scientific basis for the conservation and utilization of those breeds.