Abstract:The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphis… Show more
“…The isolation of Turopolje breed is not surprising, as this breed is among the oldest ones in Europe, apparently being locally domesticated in the Middle Ages 31 , while Black Slavonian breed was formed at the end of the 19th century by crossing Mangalitsa with several imported breeds of pig. However, as both breeds were raised in the past in the same geographical area, the observed few exceptions in clustering may result from uncontrolled mating between them 32 . Moreover, previous works using microsatellite markers already showed higher genetic heterogeneity in the Black Slavonian population with one herd being clustered together with Turopolje pigs, suggesting moderate gene flow between the Black Slavonian breed and the Turopolje population, matching our results 20 .Figure 3Genetic structure of the investigated 20 porcine breeds and Wild Boar population.…”
Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.
“…The isolation of Turopolje breed is not surprising, as this breed is among the oldest ones in Europe, apparently being locally domesticated in the Middle Ages 31 , while Black Slavonian breed was formed at the end of the 19th century by crossing Mangalitsa with several imported breeds of pig. However, as both breeds were raised in the past in the same geographical area, the observed few exceptions in clustering may result from uncontrolled mating between them 32 . Moreover, previous works using microsatellite markers already showed higher genetic heterogeneity in the Black Slavonian population with one herd being clustered together with Turopolje pigs, suggesting moderate gene flow between the Black Slavonian breed and the Turopolje population, matching our results 20 .Figure 3Genetic structure of the investigated 20 porcine breeds and Wild Boar population.…”
Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.
“…The implementation of the systems based on DNA analysis is becoming more and more popular in the analysis of the genetic structure of local pig breeds. Different DNA markers have been used to assess genetic diversity in local pig breeds, including mitochondrial DNA analysis (Zhang et al, 2016, Gvozdanović et al, 2019, microsatellites (Cortés et al, 2016, Kramarenko et al, 2018, and single nucleotide polymorphism (SNP; Yang et al, 2017, Muñoz et al, 2019.…”
“…The most frequent alleles in a population are the most primitive and conservative, and the lower frequency alleles are caused by mutations during the evolution of the population, so the polymorphic performance of microsatellites more objectively reflects the evolution of the population and conservation effect. The statistical analyses of Ne, He, and PIC show that the microsatellites used in this study were suitable for genetic diversity analysis [31].…”
At present, there is an abundance of quality domestic rabbit breeds in China. However, due to the lack of technical standards for the genetic evaluation of rabbit germplasm resources, there have been a number of problems, such as poor breed conservation. By studying the genetic diversity of 130 New Zealand white rabbits (regardless of generation), we obtained the best simple sequence repeat (SSR) marker combination. We found that, when using microsatellite markers for the effective genetic evaluation of domestic rabbits, the number of records should be greater than 60 and the marker number more than 22. Through the comparative analysis of 30 combinations of 22 markers, the optimal combination of 22 markers was determined, and the 22 SSR polymorphic loci were distributed on different chromosomes. We performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations, using the best SSR polymorphic loci combination. There were no significant differences in the genetic diversity parameters between the two generations of rabbits (p > 0.05), indicating that the characteristics of this excellent rabbit germplasm have been effectively preserved. At the same time, we verified that the established method can be used to evaluate the breed conservation of rabbit germplasm resources.
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