Genomic structure of a crossbred Landrace pig population

PloS One
Letícia Borges JoaquimD P Munari

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 (r2) 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 in...Continue Reading

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Citations

Jan 14, 2020·Animal : an International Journal of Animal Bioscience·G SchiavoL Fontanesi
Oct 21, 2020·Animals : an Open Access Journal From MDPI·Natalia V DementievaMichael N Romanov
Jan 31, 2021·Genes·Ariene Fernanda Grando RodriguesMônica Corrêa Ledur

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Methods Mentioned

BETA
chip
genotyping

Software Mentioned

Scrofa
PLINK
REVIGO
STRUCTURE
ADMIXTURE
Ensembl
STRUCTURE HARVESTER
BEAGLE

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