Genetic variation and phylogenetic analyses of conserved Lanyu pigs and exotic pig breeds in Taiwan by microsatellite markers
Date Issued
2006
Date
2006
Author(s)
Chang, Wei-Hua
DOI
zh-TW
Abstract
The Lanyu pig is an indigenous pig breed from Lanyu Islet and is classified as a miniature pig breed. For the purpose of developing laboratory swine, Lanyu pigs were introduced into Taiwan by the Department of Animal Husbandry, National Taiwan University and Taitung Animal Propagation Station in 1975 and 1980, respectively. These pigs were reared in isolation as two herds and performed random mating until 2004. The genetic diversity within all the conserved Lanyu pigs remained unknown. Many exotic pigs breeds including Taoyuan, Meishan, Landrace, Duroc and Yorkshire breeds were introduced into Taiwan during 1877~1994. It is possible the genes of these exotic pigs introgress into Lanyu pigs after 1877.
The aims of the present study were to investigate the genetic variation within conserved Lanyu pigs and the genetic lineage among Lanyu and exotic pig breeds in Taiwan by polymorphisms of microsatellite markers. Genomic DNAs of 242 individuals from Lanyu, Taoyuan, Meishan, Landrace, Duroc, Yorkshire and Berkshire were extracted. Nineteen microsatellite markers were applied in this study that separately located on 15 porcine chromosomes, and were amplified using fluorescence dye labelled primers by PCR. The fragment length polymorphisms of each microsatellites were analyzed by capillary electrophoresis, based on polymorphisms of these microsatellites. The genetic distance were applied for studying the phylogenetic relationships among these pig breeds. The result showed that Lanyu pig had the shortest genetic distance with Meishan (0.2254), Berkshire (0.2351) and Yorkshire (0.2368) compared to the other exotic breeds. The neighbor-joining (NJ) tree was constructed by genetic distance from seven pig breeds with 1000 bootstarp resampling. It showed that the 7 breeds formed 2 major clades (bootstrap value = 99.6), one composed of all the exotic European breeds, and the Asian breeds were classified into another clade, including Lanyu Taoyuan and Meishan pig breeds, and in Asian clade, Lanyu formed a unique subclade (bootstrap value = 73.4). The Neighbor-Joining tree based on genetic distance among 242 individuals of 7 breeds in this study was constructed. All individuals of Lanyu pigs were clustered into a unique clade in NJ tree, suggesting that the conserved Lanyu pigs didn’t suffer gene introgression from exotic pig breeds.
Our data showed 15 of 19 microsatellite loci in Lanyu pigs genome deviating from Hardy-Weinberg equilibrium and FIS value of 19 microsatellite loci were all positive, indicated that inbreeding or Wahlund effect during rearing the conserved Lanyu pigs. For the purpose to prevent the inbreeding depression and maintain the genetic diversity of Lanyu pig, the population structure of Lanyu pig was constructed according to microsatellite polymorphisms. The Lanyu pigs was divided as 4 subpopulations, all individuals of NTU herd were formed an independent subpopulation with the probability higher than 80%. The Lanyu pigs in TAPS could be separated into another 3 subpopulations. This result indicated Lanyu pigs in NTU formed the different allele frequency of microsatellite loci from TAPS, the genetic distance between this two populations also supported this result.
In conclusion, the Lanyu pig is a unique breed without gene introgression from exotic pig breeds, but it had sustained loss of heterozygosity. In future, these results can be applied in population management of Lanyu pig to maintain the genetic diversity and as a guideline for producing inbreed laboratory Lanyu breed.
Subjects
蘭嶼豬
微衛星標記多型性
哈溫平衡
近親配種
遺傳距離
Lanyu pig
microsatellite marker
polymorphisms
Hardy-Weinberg equilibrium
inbreeding
genetic distance
Type
thesis
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