To investigate the genetic separation between the pure breeds and the hybrid, selective sweep analysis was performed to detect the selection signatures using
HP,
FST, XP-EHH, and
θπ ratio tests (
Figure 3). First, the
HP values of LBH, DP and STH were calculated, and 93, 140, and 219 genes (in total 385 genes) were detected with a cut-off of Z(
HP) <–4 from the 3 breeds, respectively (
Figure 4A;
Supplementary Figure S1;
Supplementary Table S3). Among them, 9 genes showed selection signatures in all 3 breeds and were significantly enriched in 11 gene ontology (GO) terms, including positive regulation of cell proliferation, histone deacetylase activity, rhythmic process, etc. (
Supplementary Figure S2). In addition, FST, XP-EHH, and θπ ratio tests were performed between LBH and STH as well as LBH and DP. In total, 182 (105 for
FST between LBH and STH, 89 for
FST between LBH and DP), 133 (50 for XP-EHH
STH to LBH, 86 for XP-EHH
DP to LBH) and 220 (164 for
θπ–LBH/
θπ–STH, 61 for
θπ-LBH/
θπ–DP) genes were detected with cut-offs of Z(
FST) >4, XP-EHH >0.7, and log
2(
θπ ratio) >2, respectively. Among them, 16 genes were detected by all four tests at the same time, and 223 genes were detected by at least two approaches and were considered candidate genes (
Figure 4B;
Supplementary Table S3). GO analysis revealed that these genes were significantly enriched in 29 GO terms (p<0.05), including anterior/posterior pattern specification, anatomical structure morphogenesis, embryonic skeletal system morphogenesis, etc. Subsequently, we investigated the general functions of candidate genes involved in developmental processes (Homeobox-A (HOXA) cluster genes; B-cell lymphoma 2-like 11 [
BCL2L11]; thyroid stimulating hormone receptor [
TSHR]), immunity (C-X-C motif chemokine ligand 6 [
CXCL6];
CXCL1; Src kinase associated phosphoprotein 2 [
SKAP2]; protein tyrosine kinase 6 [
PTK6]; macrophage stimulating 1 receptor [
MST1R]), growth (platelet derived growth factor D [
PDGFD]; fibroblast growth factor 18 [
FGF18]; serum response factor [
SRF]; suppressor of cytokine signalling 2 [
SOCS2]), and reproduction (breast cancer amplified sequence 3 [
BCAS3]; tripartite motif containing 24 [
TRIM24]; astacin like metalloendopeptidase [
ASTL]; fibronectin type III domain containing 3A [
FNDC3A]) (
Figure 4C). KEGG pathway analysis was also performed. Two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, had 6 enriched genes. HRas proto-oncogene (
HRAS), GTPase and phospholipase C beta 4 (
PLCB4) were enriched in both pathways. Due to the
HP and
FST tests could not discriminate positive selection or negative selection, the positive selection occurred in the LBH genome has been screened by comparing XP-EHH with them and 120 candidate genes have been detected (
Supplementary Table S4). GO analysis revealed that these genes were enriched in regulation of cell growth, in utero embryonic development, spermatogenesis, lactation, xenophagy, viral process, etc.
A strong selection signature was mapped to the HoxA gene cluster region, including 10 HoxA genes (
HOXA1–7,
HOXA9,
HOXA11, and
HOXA13). HOX transcription factors play an important regulatory role in embryonic development, cell differentiation, proliferation and apoptosis [
36]. In this study, the ten HoxA genes were enriched in several GO terms involved in development (such as anterior/posterior pattern specification, embryonic skeletal system morphogenesis, thyroid gland development) and reproduction (such as single fertilization, uterus development, spermatogenesis). Thus, we investigated the selection pattern of the HoxA gene cluster and adjacent genes in the genomic region of the three sheep breeds (
Figure 5). The results indicated that the HoxA gene cluster was under selection only in the genome of DP, whereas another candidate gene,
SKAP2, related to B cell activation was under selection only in the STH genome.