Diversity of pig breeds reared in the Czech Republic
The aim of the study was to compare the diversity parameters of the dam pig breeds: Czech Large White (CLW) and Czech Landrace (CL) based on pedigree and SNP data. Total number of animals in pedigree were 16 438 and 7266 for CLW and CL, respectively. A slight increase in the inbreeding and the proportion of inbred animals used in the breeding was observed. The average inbreeding rates in 2010, 2015, 2020 and 2022 for the CLW were 0.7%, 1.5%, 1.7% and 2.0%, respectively. The proportion of inbred animals included in the breeding program in these years was 39.5%, 83.1%, 97.8% and 97.4%, respectively. The CL breed had slightly higher values in those years. The effective population size ranged from 99 (CLW) to 181 (CL) animals. Selected DNA isolates (603 and 201 animals of CLW and CL, respectively) were applied to a GGP Porcine 50k chip using the Illumina HD Infinium technology protocol. A total of 50,697 SNPs were identified in the selected DNA isolates. The average „call rate“ was 0.99, 0.97 and 0.96 for bristle, insemination batch and ear graft samples used as source, respectively. Thus, data from 590 CLW and 196 CL animals containing 45 065 and 46 257 SNPs, respectively, were used for further evaluation. The genomic inbreeding coefficient was calculated for each ROH class (FROH). The effective population size based on genomic data was calculated using GONE software. The inbreeding coefficient obtained from SNP data was lower than that obtained from pedigree data. It was 0.40% for the CLW breed and 2.23% for the CL breed. The differences were probably due to smaller number of genotyped animals. The effective population size over the last 9 generations exceeded 300 individuals for both breeds, although a decrease in effective population size was observed, especially in the last three years.
|Projekt||Vytvoření referenční populace a vývoj postupů pro odhad genomických plemenných hodnot znaků prasat zařazených do Českého národního šlechtitelského programu, Dlouhodobý koncepční rozvoj výzkumné organizace|
|Oddělení||Genetika a šlechtění hospodářských zvířat|
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