Additional file 2 of Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes
Creators: name: Yang, Ruifei
name: Jin, Siqi
name: Fang, Suyun
name: Yan, Dawei
name: Zhang, Hao
name: Nie, Jingru
name: Liu, Jinqiao
name: Lv, Minjuan
name: Zhang, Bo
name: Dong, Xinxing
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Principal component analysis (PCA) of pig breeds using whole-genome SNPs. PC1, PC2, and PC3 explained 6.24%, 2.58%, and 1.60% of the genetic variance, respectively. Figure S2. Heatmap based on the IBS distance matrix of all pigs. The figure presents the IBS distance matrix of all pigs without an outgroup (n = 228). Figure S3. Neighbour-joining (NJ) tree and heatmap based on the p-distance matrix of all pigs. NJ tree and pairwise relationship-based the p-distance matrix (n = 228). Figure S4. Cross-validation (CV) error of the Admixture results for K = 2 to 10. The red dot represents the lowest CV error (K = 6, CV error = 0.512). Figure S5. Gene flow analysis between EP and indigenous Chinese pigs. (a) D-statistics with D (sister group, target group, EP, Outgroup) (y-axis) to detect introgression into the target group from EP, where the Outgroup was Sumatran pig, the x-axis represents the sister group with no significant EP introgression (GZTIB, LTTIB, and SLTIB), and the lines in the legend with different colours depict the respective target groups. (b) Outgroup-f3 statistics for all indigenous Chinese populations and EP, i.e. f3 (Chinese indigenous population, EP; Outgroup). Figure S6. Mean weightings for the three possible taxon topologies across the whole genome, the topologies for the four taxa as rooted, with Sumatran wild boars as the outgroup. (a) Topology analysis for LJP, SCDP, and EP. (b) Topology analysis for NCDP, SCDP, and EP. (c) Topology analysis for TIBP-E, SCDP, and EP. (d) Topology analysis for SWCDP, SCDP, and EP. Figure S7. Total size of introgression blocks from European pigs (EP) into Northern Chinese domestic pigs (NCDP), Lijiang pigs (LJP), and Tibetan (specifically Diqing and Daocheng) pigs (TIBP-E) after down-sampling for LJP (n = 18). To exclude the effect of sample size, LJP was down-sampled to 18. Figure S8. Site-pi of SNPs in the region of 51 window bins for direct introgression (DI), indirect introgression (IDI) and for genomic segments from TIBP in TIBP-E. a, b, c represent the significance for Duncan’s test of DI, IDI, and TIBP (p &lt; 2.2e-6), respectively. Figure S9. Maximum-likelihood tree of single nucleotide polymorphisms (SNPs) in the bins of indirect (a) and direct (b) introgressed regions from EP. The maximum-likelihood trees based on SNPs located within the bins identified as introgression from EP or LJP. Figure S10. Summary of thoracic vertebra numbers. LJP were grouped according to the number of thoracic vertebrae, including a group of individuals with fewer thoracic vertebrae (LJL, less than 14, n = 17) and a group of individuals with more thoracic vertebrae (LJM, more than 14, n = 27). Figure S11. Boxplot of thoracic vertebrae number based on haplotypes on chromosomes 7 (region: Chr7-96323262_97614707) and 10 (region: Chr10-14341483_14343476). The region represents the haplotype block with a high LD level, including blocks on chromosomes 7 and 10. Figure S12. Interaction network centred by the STUM protein. The interaction network of STUM analysis was based on the STRING human database, where CPNE7 and LRRC5 were identified as co-expressed proteins.