Abstract
Genomic information from crossbreds is routinely generated for genomic evaluations. The objective of this study is to investigate autozygosity and genetic differentiation in Landrace by Large-White breeds by using the genotypic information of SNP arrays in 1,173 crossbreds. A maximum likelihood approach was developed to estimate the probability of autozygosity (FL). Regions of differentiation between breeds were investigated using FST and the difference in allele frequencies between the two parental breeds (릌Δ) at each single-nucleotide polymorphism (SNP) position. A maximum likelihood approach was proposed to estimate allele frequencies in the parental populations. The average length of runs of homozygosity (ROH) across the genome was 3.91, 2.3, and 0.7 Mb for segments with at least 25, 15, and 5 SNPs, respectively. Average age to coalesce was 46, 414, and 388 years for segments with at least 25, 15, and 5 SNPs, respectively. The probability of autozygosity was not uniform along the crossbred genome, being higher at the center for most chromosomes. The correlation between autozygosity and distance to the closest telomere was positive and significant in most chromosomes, which could be attributed to the higher recombination rate near telomeres. We also report a relatively high negative correlation between probability of recombination (from a published map) and probability of autozygosity. It supports that structural characteristics of the chromosomes related to recombination rate determine autozygosity at each chromosomal position of the pig genome. The average is Δ across the genome was 0.17 (SD = 0.16). After testing for differences in allele frequencies between the parental breeds, there were 4,184 SNPs with a likelihood ratio test, LRT ≥ 32.02. The average FST across the genome was 0.038 (SD = 0.059). There were 2,949 SNPs with FST > 0.125. The correlation between estimates of FL and estimates of FST across the genome was -0.10 (SE = 0.006). Analysis of the gene content of the genomic regions with the 2000 SNPs with highest LRT for FL and high FST showed overrepresentation of genes with a regulatory function. Genes with biological functions associated with production, such as tissue development, anatomical structure, and animal organ development, were also overrepresented in regions with a high FST.
Highlights
Domestication of the pig took place some 9,000 years ago and occurred multiple times (Giuffra et al, 2000)
The probability of autozygosity had a clear trend to be larger in the central parts of the chromosome, whereas the opposite trend was observed for the distal parts of most chromosomes, which is consistent with a higher recombination rate near telomeres
Genetic analyses of crossbreds can reveal the location of common haplotypes and areas of genetic differentiation in the genomes of genetically distant breeds such as Landrace and Large White
Summary
Domestication of the pig took place some 9,000 years ago and occurred multiple times (Giuffra et al, 2000). A large variety of local types were created, both in Europe and in China. These local types were adapted to the environmental conditions where they were raised and were independently selected for behavior and conformation traits, until the creation of modern breeds in the 19th century (Amills et al, 2010). The creation of breeds required breeding in closed populations, in which both selection and genetic drift altered the genetic makeup of those populations by modifying allele frequencies at loci throughout the genome. Alleles are not necessarily segregating at a different frequency in the two breeds at all loci. Directional or stabilizing selection may be acting with the same intensity at the same allele (or chromosomal fragment) in the two breeds over time
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
