Genomic structure of a crossbred Landrace pig population

Author(s):Show less -

Joaquim, Leticia Borges ^[1] ; Seleguim Chud, Tatiane Cristina ^[1] ; Petroli Marchesi, Jorge Augusto ^[1] ; Savegnago, Rodrigo Pelicioni ^[1] ; Buzanskas, Marcos Eli ^[2] ; Zanella, Ricardo ^[3] ; Cantao, Mauricio Egidio ^[4] ; Peixoto, Jane Oliveira ^[4] ; Ledur, Monica Correa ^[4] ; Irgang, Renato ^[5] ; Munari, Danisio Prado ^[1]

Affiliation

^[1] Univ Estadual Paulista Unesp, Fac Ciencias Agr & Vet, Sao Paulo - Brazil

^[2] Univ Fed Paraiba UFPB, Dept Zootecnia, Areia, Paraiba - Brazil

^[3] Univ Passo Fundo, Passo Fundo, RS - Brazil

^[4] Embrapa Suinos & Aves, Concordia, SC - Brazil

^[5] Univ Fed Santa Catarina, Dept Zootecnia & Desenvolvimento Rural, Ctr Ciencias Agr, Florianopolis, SC - Brazil

• Document type: Journal article
• Source: PLoS One; v. 14, n. 2 FEB 28 2019.
• Web of Science Citations: 0

Abstract

Single nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r(2)) was 0.291 +/- 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genome-wide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect. (AU)

• FAPESP's process: 15/08939-0 - Identification of copy number variations in Girolando cattle
• Grantee: Tatiane Cristina Seleguim Chud
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 13/20091-0 - Prediction of breeding values in a experimental mice population using selective genotyping
• Grantee: Rodrigo Pelicioni Savegnago
• Support Opportunities: Scholarships in Brazil - Post-Doctoral