Genome resequencing and transcriptome data summary
We generated approximately 984.50 gigabases (Gb) of resequencing data for the whole genomes of 35 birds, achieving an average coverage of ~ 28-fold per individual on the T7 platform (Table S1). Additionally, we included previously published genome sequence data from 17 red jungle fowls (RJF) with an average coverage of ∼24-fold per individual, obtained from downloaded and analyzed datasets (GenBank accession numbers provided in Table S1) (Fig. 1B). Upon aligning this extensive dataset to the reference chicken genome, we identified around 2.54 million and 3.04 million single nucleotide polymorphisms (SNPs) for the Yanying and Luning chicken breeds, respectively. This dataset holds significant relevance for population genetics and future studies in chickens, providing a valuable resource for exploring diversifying selection and identifying candidate genes for selective breeding in chicken populations. As a result, 14.38 M and 12.66 M SNPs were identified in Yanying and Luning chicken breeds respectively (Table 1).
Table 1
SNP categories in two chicken breeds.
| Yanying Chicken | Luning chicken |
SNP Category | Number | Ratio | Number | Ratio |
Upstream | 215,063 | 1.49% | 187,587 | 1.30% |
Gene body | CDS | Synonymous | 137,633 | 0.96% | 120,216 | 0.84% |
Nonsyn/Syn ratio (ω) | 78,150 | 0.54% | 67,235 | 0.47% |
Stop gain | 963 | 0.01% | 829 | 0.01% |
Stop loss | 118 | 0.00% | 114 | 0.00% |
unknown | 48 | 0.00% | 44 | 0.00% |
Intronic | 6,131,097 | 42.61% | 5,417,951 | 37.66% |
Splicing | 488 | 0.00% | 425 | 0.00% |
Downstream | 188,618 | 1.31% | 164,832 | 1.15% |
Upstream/Downstream | 12,285 | 0.09% | 10,665 | 0.07% |
Intergenic | 7,407,013 | 51.48% | 6,506,611 | 45.22% |
Exonic | 216,897 | 1.51% | 188,426 | 1.31% |
Exonic/Splicing | 15 | 0.00% | 12 | 0.00% |
Total | 14,388,388 | 100.00% | 12,664,947 | 88.02% |
For a comprehensive exploration of mRNA expression profiles across various tissues and breeds in chickens, we constructed a total of 52 cDNA libraries. These libraries comprised samples from 18 ovaries, 18 pectoral muscles and 16 fat tissues, all obtained from 18 female chickens. The dataset, totaling 341.94 gigabases (Gb) of clean data, with an average of 6.58 per sample, was derived from Yanying, Luning and Roman chickens, providing a robust foundation for subsequent analysis (Table S2).
Genome-wide selective sweep signals in Yanying and Luning chickens
The selective sweep screen employed a method incorporating the sequence diversity statistic (θπ) [27], and the population differentiation statistic (FST) [28]. This methodology was specifically designed to identify genomic regions under selection in Yanying and Luning chicken breeds. Through this analysis, we identified 52.90 megabases (Mb) (5.00% of the genome) and 44.42 Mb (4.22% of the genome), in Yanying and Luning breeds, respectively. These regions encompassed 1,006 and 982 positively selected genes (PSGs) (Fig. 2A), indicating strong selective sweep signals in each breed. A total of 326 genes exhibiting robust selective sweep signals were identified and shared between the two chicken breeds. The selected regions, characterized by significantly high FST values (top 5%) were displayed for Yanying (Fig. 2B) and Luning chickens (Fig. 2C) when compared with RJFs (Fig. 3). Regions showing significant differences (p < 10− 16, Mann-Whitney U test) in the log 2 (θπ ratio) and FST values compared to the wild RJF genomic background, are highlighted for both Yanying (Fig. 2D) and Luning (Fig. 2E) chicken breeds, respectively.
Notably, in Yanying and Luning chicken breeds, 89 regions and 36 regions, respectively, exhibited FST values surpassing 0.5. Within these selected regions in Yanying, 21 known genes were identified, including HHLA2, COG6, PCLO, GNAT3, KCND2, KCNQ3, GRIK2, ASCC3, NKAIN2, LCORL, TSHR, NRXN3, ZSWIM8, FAM207A, STAT1, STAT4, NEGR1, RNF7, CBFB NCOR2, and CCDC189. Similarly, Luning chicken revealed11 known genes, including HAAO, MTA3, SNRPN, DDX27, ELMO2, ALPK1, MPHOSPH6, SEPTIN6, CDH13, IL1RAPL1, and PAPOLB within its selected regions.
Signature of selection in two chicken breeds
To probe the potential functions of the identified genes in the two chicken breeds, we utilized metascape and performed gene ontology enrichments [25, 26]. Among the 1,006 selected genes in Yanyng chicken, the gene ontology classification indicated predominant involvement in terms such as “nucleus”, “cytoplasm”, “cytosol”, “integral component of membrane” and “zinc ion binding” (Fig. 3A). The KEGG classification highlighted their main roles in pathways like “Downstream signal transduction”, “GPCR downstream signaling”, “Hemostasis”, “Rho GTPase cycle”, “Platelet activation, signaling and aggregation” (Fig. 3B). Furthermore, the Reactome classification unveiled their significant participation in terms such as “Focal adhesion”, “Adherens junction”, “MAPK signaling pathway”, “GnRH signaling pathway”, and “Metabolic pathways” (Fig. 3C).
Simultaneously, among the 986 genes selected in Luning Chicken, gene ontology annotations revealed their predominant involvement in terms such as “plasma membrane”, “integral component of membrane”, “integral component of plasma membrane”, “nucleus”, “glutamatergic synapse”, “cytoplasm” and “positive regulation of transcription by RNA polymerase II” (Fig. 3D). KEGG class analysis indicated that the selected genes primarily participated in pathways such as “Metabolic pathways”, “Adrenergic signaling in cardiomyocytes”, “Cardiac muscle contraction”, “Neuroactive ligand-receptor interaction”, and “Wnt signaling pathway”, pathway (Fig. 3E). The Reactome class analysis revealed that these selected genes were predominantly associated with terms like “Signal Transduction”, “WNT5A-dependent internalization of FZD2, FZD5 and ROR2”, “PCP/CE pathway”, “Lysosome Vesicle Biogenesis”, and “Muscle contraction” (Fig. 3F).
Analysis of differentially expressed genes
The analysis of differentially expressed genes (DEGs) aimed to explore variations between domesticated chickens (Yanying and Luning chickens) and Roman chickens across three distinct tissues, utilizing TPM for gene expression quantification. When comparing Yanying and Roman chickens, a total of 62 DEGs (17 upregulated and 45 downregulated genes) were identified in the ovary (Fig. 4A), 112 DEGs (64 down and 48 up genes) in the muscle (Fig. 4B) and 83 DEGs (59 down and 24 up genes) in the fat tissue (Fig. 4C. In the comparison between Luning and Roman chickens, 34 DEGs (23 upregulated and 11 downregulated genes) were identified in the ovary (Fig. 4D), 64 DEGs (17 down and 47 up genes) in the muscle (Fig. 4E) and 95 DEGs (46 down and 49 up genes) in the fat tissue (Fig. 4F). Notably, in the ovary, Yanying chickens exhibited upregulated expression of genes associated with immunity compared to Roman chickens, including AvBD7, CATH2 and AvBD6 (Table 2).
Table 2
Top five highly differentiated expressed genes in each tissue.
| Ovary | | | Muscle | | | Fat | | |
| gene | log2FC | sig | gene | log2FC | sig | gene | log2FC | sig |
Luning | CTXND1 | -17.04 | down | PLAU | -3.95 | down | CTXND1 | -19.14 | down |
| H2B-I | -4.61 | down | MHCY35 | -3.71 | down | KPNA7 | -19.08 | down |
| HIST1H2B5 | -4.38 | down | PRRT1B | -3.41 | down | GDF9 | -18.18 | down |
| ENSGALG00010003287 | -4.05 | down | BLEC3 | -3.08 | down | CPSF4L | -17.90 | down |
| ARSD | -3.75 | down | MMP11 | -2.91 | down | ENSGALG00010000201 | -17.68 | down |
| DCT | 5.07 | up | ENSGALG00010007443 | 18.54 | up | UTS2R | 6.31 | up |
| GBP4L | 5.01 | up | TCP10 | 18.15 | up | OVCH2 | 5.79 | up |
| ENSGALG00010003745 | 4.83 | up | ENSGALG00010012091 | 6.01 | up | CHAC1 | 5.64 | up |
| TGM4 | 4.22 | up | MMP7 | 5.73 | up | RRAD | 5.29 | up |
| TYR | 4.15 | up | TNFRSF6B | 5.03 | up | HSPB9 | 4.73 | up |
Yanying | AvBD7 | -20.85 | down | ENSGALG00010009067 | -7.64 | down | ENSGALG00010009067 | -7.74 | down |
| NAA38 | -20.82 | down | CA3A | -6.69 | down | RHEX | -7.27 | down |
| CATH2 | -18.88 | down | APOH | -6.59 | down | GBP1 | -5.15 | down |
| WFDC8 | -17.65 | down | ENSGALG00010028420 | -6.49 | down | ENSGALG00010004332 | -5.09 | down |
| AvBD6 | -17.50 | down | AvBD7 | -6.07 | down | H2B-I | -5.04 | down |
| MHCYL | 4.06 | up | ENSGALG00010007443 | 21.46 | up | CHAC1 | 5.00 | up |
| TNMD | 3.97 | up | TCP10L2 | 19.66 | up | ANKRD2 | 4.97 | up |
| AVD | 3.63 | up | MMP7 | 6.63 | up | TRIM62 | 3.56 | up |
| FST | 3.16 | up | TP53TG5 | 4.47 | up | ENSGALG00010016599 | 3.53 | up |
| ENSGALG00010003786 | 3.11 | up | WNT4 | 4.39 | up | SLC22A3 | 3.05 | up |
For Yanying chickens, the DEGs were predominantly associated with terms such as “Proteasome”, “Cytokine-cytokine receptor interaction”, “RNA-DNA hybrid ribonuclease activity”, “RNA endonuclease activity, producing 5'-phosphomonoesters”, “endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters”, “RNA endonuclease activity”, “endonuclease activity”, “RNA nuclease activity”, “RNA-directed DNA polymerase activity”, “DNA integration”, and “Phagosome” (adjusted P value < 0.05) (Fig. 5A). Meanwhile, for Luning chickens, the DEGs were mainly involved in terms such as “response to blue light”, “Melanogenesis”, “Tyrosine metabolism”, and “endothelin receptor activity” (adjusted P value < 0.05) (Fig. 5B).