Additional file 1: Table S1. of Expression of genes involved in progesterone receptor paracrine signaling and their effect on litter size in pigs

Primers used for Real-time PCR (RT-PCR). (DOCX 19 kb

Additional file 2: Table S2. of Expression of genes involved in progesterone receptor paracrine signaling and their effect on litter size in pigs

Primer pairs and PCR conditions used for SNPs detection. (DOCX 20 kb

Additional file 5: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Table S4. Summary of overlapping candidate regions under positive selection detected by at least two of the three methods FST, iHS and CLR. (XLSX 16 kb

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, most selection signatures were population specific. Few studies have focused on selection footprints of indigenous breeds. Laiwu pigs are an invaluable Chinese typical indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. In this study, based on GeneSeek Genomic profiler for Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (Composite Likelihood Ratio) were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 193 candidate selected regions were obtained by at least two of the three methods, which covered 48.25 Mb genomic regions and corresponded to 1.72% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, <i>NPY1R</i>, <i>NPY5R</i>, <i>PIK3R1, Rab11-FIP2</i> and <i>JAKMIP1</i>, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies.<br

Additional file 10: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

The ped PLINK file of SNP genotyping data for the 50 Laiwu pigs and 52 Yorkshire pigs. (TXT 21549 kb

Additional file 6: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Table S5. Gene contents in candidate regions under positive selection. (XLSX 38 kb

Additional file 2: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Table S1. Summary of selected regions under positive selection detected by FST. (XLSX 51 kb

Additional file 9: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Table S8. Summary of QTL overlapped with candidate selected regions. (XLSX 150 kb

Additional file 7: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Table S6. Significantly enriched Gene Ontology terms of candidate genes. (XLSX 12 kb

Additional file 4: of Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

Supplemental Figure. Including Figures S1–S3. (PDF 2259 kb