Biomaterial Database

Diversity across major and candidate genes in European local pig breeds. 2018

María Muñoz, and Riccardo Bozzi, and Fabián García, and Yolanda Núñez, and Claudia Geraci, and Alessandro Crovetti, and Juan García-Casco, and Estefania Alves, and Martin Škrlep, and Rui Charneca, and Jose M Martins, and Raquel Quintanilla, and Joan Tibau, and Goran Kušec, and Ivona Djurkin-Kušec, and Marie J Mercat, and Juliette Riquet, and Jordi Estellé, and Christoph Zimmer, and Violeta Razmaite, and Jose P Araujo, and Čedomir Radović, and Radomir Savić, and Danijel Karolyi, and Maurizio Gallo, and Marjeta Čandek-Potokar, and Luca Fontanesi, and Ana I Fernández, and Cristina Óvilo

Departamento Mejora Genética Animal, INIA, Madrid, Spain.

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.

UI	MeSH Term	Description	Entries
D008460	Meat	The edible portions of any animal used for food including cattle, swine, goats/sheep, poultry, fish, shellfish, and game.	Meats
D010641	Phenotype	The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.	Phenotypes
D001947	Breeding	The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.	Breedings
D005828	Genetics, Population	The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.	Population Genetics
D005838	Genotype	The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.	Genogroup,Genogroups,Genotypes
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D013030	Spain	Country located between France on the northeast and Portugal on the west and bordered by the Atlantic Ocean and the Mediterranean Sea. The capital is Madrid.	Balearic Islands,Canary Islands
D013552	Swine	Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).	Phacochoerus,Pigs,Suidae,Warthogs,Wart Hogs,Hog, Wart,Hogs, Wart,Wart Hog
D020641	Polymorphism, Single Nucleotide	A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.	SNPs,Single Nucleotide Polymorphism,Nucleotide Polymorphism, Single,Nucleotide Polymorphisms, Single,Polymorphisms, Single Nucleotide,Single Nucleotide Polymorphisms
D040641	Quantitative Trait Loci	Genetic loci associated with a quantitative trait.	Quantitative Trait Loci Genes,Loci, Quantitative Trait,Locus, Quantitative Trait,Quantitative Trait Locus,Trait Loci, Quantitative,Trait Locus, Quantitative