Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data.

Emil Krupa,Nina Moravčíková,Zuzana Krupová,Eliška Žáková

doi:10.3390/genes12121972

Emil Krupa, Nina Moravčíková + Show 2 more

Open Access

https://doi.org/10.3390/genes12121972

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Abstract

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

Highlights

Academic Editor: Hirohide UenishiReceived: 8 November 2021Accepted: 8 December 2021Published: 10 December 2021Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.Licensee MDPI, Basel, Switzerland.The Přeštice Black-Pied (PBP) is a Czech local pig breed (Figure 1)
The present study reports a detailed analysis of the local PBP pig breed based on all available data
It is evident that the PBP pig population showed a high degree of inbreeding

Summary

Introduction

The Přeštice Black-Pied (PBP) is a Czech local pig breed (Figure 1). 19th century, the local pig breeds (mostly, Yorkshire, Sussex, Berkshire, and Essex British breeds) were crossed with boars imported into the Bohemia territory [1,2]. Pig breeds including Wessex Saddleback (in 1952), Pietrain (in 1966), Welsh (in 1985), and Landrace (in 1986) were used in crossing of the PBP breed [3]. During the WWII, the first bottleneck effect on genetic variation of pigs was observed after the ban on breeding black-spotted breeds of pigs was tightened even when their breeding was secretly maintained. The use of unlicensed boars and inbreeding contributed to the stability of the breed, there was an apparent impact on the genetic diversity of PBP pigs [1]

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