Landscape of recombination rates in GGS and domestic chickens.

(A) The distribution of the recombination rate (c/bp). Estimates are normalized using 1-Mb sliding windows. (B) Pearson’s rank correlation coefficient for the recombination rate for macrochromosomes (left) and microchromosomes (right) from each pair of populations. Macrochromosomes include chr1-5 and the rest are microchromosomes. Dot chromosomes were excluded from this analysis due to their limited length and high missing rate in variant calling. GGS, Gallus gallus spadiceus; CH, Chahua chicken; JNBR, Jining Bairi Chickens; LX, Luxi Fighting; NX, Nixi; WL, White Leghorn.

Recombination hotspots variation across genomes.

(A) Identification of shared and breed-specific recombination hotspots in GGS and chickens. (B) The localization of recombination hotspots on each chromosome is depicted in concentric circles, with GGS, NX, LX, JNBR, CH, and WL represented from innermost to outermost circles. (C) Comparison of recombination rates between regions associated with four histone modifications (H3K27ac, H3K27me3, H3K4me1, and H3K4me3) and randomly selected regions (Random_1000, n=1000) of equal length from the rest of the genome. *** indicates P < 0.001 by one-sample t-test.

The distribution of the predicted motif for the recombination hotspot across different populations.

(A) Results of the composite motif detected by RHSNet. The top shows the motif embeddings in each chicken population, and the bottom heatmap indicates the frequency of 2-mer occurrence in the detected motifs. (B) Pearson’s correlation coefficients between the frequency of 2-mer motif between each pair of populations. (C) Average GC content in the whole genome and motif sequences. *** indicates P < 0.001 by one-sample t-test.

Correlation between introgression frequency and recombination rate.

(A) The population topology for the detection of GGM introgressed regions in WL. (B) Correlation between the recombination rate and the frequency of introgression. (C) The topology for the four populations used in the simulations. In each of the five models, the population size for O, P3, and P2 is set to N0, and the population size for P1 is set to 0.1*N0, 0.2*N0, N0, 2*N0, and 10*N0, respectively. (D) Pearson’s correlation coefficients between the frequency of gene flow and the recombination rate under five models.