Abstract
BackgroundThe frequency of recombination events varies across the genome and between individuals, which may be related to some genomic features. The objective of this study was to assess the frequency of recombination events and to identify QTL (quantitative trait loci) for recombination rate in two purebred layer chicken lines.MethodsA total of 1200 white-egg layers (WL) were genotyped with 580 K SNPs and 5108 brown-egg layers (BL) were genotyped with 42 K SNPs (single nucleotide polymorphisms). Recombination events were identified within half-sib families and both the number of recombination events and the recombination rate was calculated within each 0.5 Mb window of the genome. The 10% of windows with the highest recombination rate on each chromosome were considered to be recombination hotspots. A BayesB model was used separately for each line to identify genomic regions associated with the genome-wide number of recombination event per meiosis. Regions that explained more than 0.8% of genetic variance of recombination rate were considered to harbor QTL.ResultsHeritability of recombination rate was estimated at 0.17 in WL and 0.16 in BL. On average, 11.3 and 23.2 recombination events were detected per individual across the genome in 1301 and 9292 meioses in the WL and BL, respectively. The estimated recombination rates differed significantly between the lines, which could be due to differences in inbreeding levels, and haplotype structures. Dams had about 5% to 20% higher recombination rates per meiosis than sires in both lines. Recombination rate per 0.5 Mb window had a strong negative correlation with chromosome size and a strong positive correlation with GC content and with CpG island density across the genome in both lines. Different QTL for recombination rate were identified in the two lines. There were 190 and 199 non-overlapping recombination hotspots detected in WL and BL respectively, 28 of which were common to both lines.ConclusionsDifferences in the recombination rates, hotspot locations, and QTL regions associated with genome-wide recombination were observed between lines, indicating the breed-specific feature of detected recombination events and the control of recombination events is a complex polygenic trait.
Highlights
The frequency of recombination events varies across the genome and between individuals, which may be related to some genomic features
Characterizing recombination frequency may have an impact on the interpretation of trait association studies and on the consistency of marker effects estimates for genomic prediction
An understanding of the creation and loss of haplotypes caused by recombination during meiosis will enhance our ability to define optimal lengths of haplotypes and to reconstruct haplotype blocks, in order to improve imputation accuracy and genomic prediction accuracy
Summary
The frequency of recombination events varies across the genome and between individuals, which may be related to some genomic features. The objective of this study was to assess the frequency of recombination events and to identify QTL (quantitative trait loci) for recombination rate in two purebred layer chicken lines. Meiotic recombination occurs between homologous chromosomes and produces crossovers and gene conversions [1]. Characterizing patterns and rates of recombination is important for understanding genome-wide genetic diversity. Characterizing recombination frequency may have an impact on the interpretation of trait association studies (narrowing down the quantitative trait loci, known as QTL regions) and on the consistency of marker effects estimates for genomic prediction. An understanding of the creation and loss of haplotypes caused by recombination during meiosis will enhance our ability to define optimal lengths of haplotypes and to reconstruct haplotype blocks, in order to improve imputation accuracy and genomic prediction accuracy. Recombination events occur more frequently in hotspots, which are defined as short intervals with significantly greater recombination rates compared to surrounding regions [3]
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