title: Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data.
abstract: BACKGROUND
  Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated.
  
  
  RESULTS
  Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed.
  
  
  CONCLUSIONS
  The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.
authors.affiliation: Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil.|Faculdade de Agronomia e Medicina Veterinária (FAMV), University of Passo Fundo, Passo Fundo, RS, Brazil.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Zanella
authors.affiliation: Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil.
authors.forename: Jane O
authors.initials: JO
authors.lastname: Peixoto
authors.affiliation: Embrapa Southern Region Animal Husbandry, Bagé, RS, Brazil.|Programa de pós-graduação em Zootecnia/UFPel, Pelotas, RS, Brazil.
authors.forename: Fernando F
authors.initials: FF
authors.lastname: Cardoso
authors.affiliation: Embrapa Southern Region Animal Husbandry, Bagé, RS, Brazil.
authors.forename: Leandro L
authors.initials: LL
authors.lastname: Cardoso
authors.affiliation: Programa de pós-graduação em Zootecnia/UFPel, Pelotas, RS, Brazil.
authors.forename: Patrícia
authors.initials: P
authors.lastname: Biegelmeyer
authors.affiliation: Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil.
authors.forename: Maurício E
authors.initials: ME
authors.lastname: Cantão
authors.affiliation: BRF/SA, Curitiba, PR, Brazil.
authors.forename: Antonio
authors.initials: A
authors.lastname: Otaviano
authors.affiliation: BRF/SA, Curitiba, PR, Brazil.
authors.forename: Marcelo S
authors.initials: MS
authors.lastname: Freitas
authors.affiliation: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.|Programa de pós-graduação em Ciências Animais/Universidade de Brasília, Brasília, DF, Brazil.
authors.forename: Alexandre R
authors.initials: AR
authors.lastname: Caetano
authors.affiliation: Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil. monica.ledur@embrapa.br.|Programa de pós-graduação em Zootecnia/Campus UDESC Oeste, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil. monica.ledur@embrapa.br.
authors.forename: Mônica C
authors.initials: MC
authors.lastname: Ledur
mesh_terms: D000818:Animals; D001938:Brazil; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006720:Homozygote; D007178:Inbreeding; D015810:Linkage Disequilibrium / Q000235:genetics; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D034421:Sus scrofa / Q000235:genetics*