Fig 1: Analysis of the signatures of positive selection in the genome of chicken breeds and the adaptions to tropical Environments. (A) Schematic mechanisms of signaling pathways for genetic adaptions to tropical environments in chicken. The names of the KEGG pathways are shown in blue. The candidate genes positively selected in the two methods of FST and ?p ratio tests are shown in red. Dotted arrows indicate an indirect effect. (B) (D) log2 (?p ratios), FST value and Tajima’s D values around the SLC33A1 locus, TSHR locus, respectively. The black and red line represent FST and log2 (?p ratios) values, respectively. The blue and purple lines represent the WCC, LDC Tajima’s D values, respectively. (C) (E) Allele frequencies of two and three SNPs within the SLC33A1, TSHR gene across the four breeds, respectively. The red alleles are consistent with reference genome, and the blue alleles represent mutant alleles. (F)(G)(H) Genotype frequencies of three SNPs within the SLC33A1 gene were determined in our 119 individuals and chickens from Tanzania, Ghana, and Brazil using the Affymetrix 600 k SNP database, as well as in four Chinese breeds with PCR. For the abbreviations of the breeds, see supplementary table S16 and Supplementary Material online. (I)(J) Genotype frequencies of two SNPs within the TSHR gene were determined in our 119 individuals and chickens from Tanzania, Ghana, and Brazilian using the Affymetrix 600 k SNP database, as well as in four Chinese breeds with PCR. For the abbreviations of the breeds, see supplementary table S16 and Supplementary Material online. (E) Gene expression of SLC33A1, and the gene expression of the TSHR downstream genes, including ADCY1 and CREB3L3 in chicken liver of four breeds based on RNA-seq analysis. The FPKM (fragments per kilobase of transcript per million mapped reads) value is used to measure the expression level.