A total of 269 selective sweep regions were obtained from a previous study on the Landrace breed to identify nsSNPs related to selective sweeps [
7], and a total of 345 nsSNPs were identified from 55 Landrace selective sweep regions (
Figure 3) by re-analyzing the data of previous study resequencing data of Landrace and Yorkshire [
7]. Information of 345 nsSNPs in the selective sweep regions of the Landrace genome belonged to 90 genes were shown in
Table 1. The average number of nsSNPs per gene was 3.83, and the gene length was not correlated to the number of nsSNPs (
Figure 4). The deleted in malignant brain tumors 1 (
DMBT1) gene consisted of 18 exons harboring 26 nsSNPs that were evenly distributed; this gene had the highest number of nsSNPs among the 90 genes. Moreover, there were considerable frequency differences between Landrace and other breeds (Yorkshire and wild boar) in nsSNPs of the
DMBT1 gene (
Figure 5). This suggests that DMBT1 is significantly affected by many nsSNPs in Landrace breed establishment. Previous studies strongly suggested an important role of DMBT1 in the process of fertilization in pigs; it was shown to be secreted in the oviduct and involved in the mechanism of fertilization in porcine species [
25,
26]. In particular, Ambruosi et al [
25] reported that oviduct fluid containing DMBT1 protein was strongly related to the preparation of gametes for fertilization, fertilization itself, and subsequent embryonic development. Therefore, we assumed that nsSNPs of
DMBT1 of Landrace might correlate with the fertilization capacity that was acquired during artificial selection, making the reproductive capacity of Landrace pigs superior to that of other breeds [
27].
Among 90 genes, the functions of 64 genes were predicted, and we performed GO network analysis of these 64 genes using ClueGO [
21] to draw inferences on the biological effects of nsSNPs in Landrace selective sweep regions. The information on these networks is shown in
Figure 6 and
Table 2. The GO network analysis revealed that 19 of the total of 64 genes were associated with five major GO terms, and these major terms were closely related to the reproductive capacity or growth and development of the Landrace breed during the perinatal period. In the GO network, seven genes (C-C motif chemokine ligand 1 [
CCL1],
CCL23, hemopexin, mucolipin 1, leucine zipper and EF-hand containing transmembrane protein 2, phospholipase A2 group VI [
PLA2G6], and protein tyrosine phosphatase, receptor type, C [
PTPRC]) were related to cellular metal ion homeostasis in seven major GO terms, and this cluster was the largest in this network. Moreover, these terms were similar to the GO results of a positively selected region identified in Wang’s study of Landrace selective sweeps [
7]. Metal ions are one major group of mineral; since components of follicular fluid such as Ca, Cu, and Fe significantly increase as the follicles increase in size, some minerals appear to play an important role in pig reproduction [
28]. Five genes (ATPase phospholipid transporting 8A1 [
ATP8A1],
CCL1, kinesin family member 20B, plasminogen, and
PTPRC) were shown to be involved in the positive regulation of locomotion, and its network consisted of four GO terms (positive regulation of locomotion, positive regulation of cellular component movement, positive regulation of cell motility, and positive regulation of cell migration). This cellular movement is a central process in the development and maintenance of multicellular organisms. In addition, tissue formation during embryonic development requires the orchestrated movement of cells in a particular direction. It is reasonable to assume that several genes of these four significant GO terms in the selective sweep regions of the Landrace genome might be related to the superior growth and development of Landrace during the perinatal period. Ten genes (
ATP8A1, bridging integrator 2, CD93 molecule [
CD93], exophilin 5, GRB2 associated binding protein 2, n-ethylmaleimide-sensitive factor attachment protein, beta,
PLA2G6,
PTPRC, and vesicle associated membrane protein 1 [
VAMP1]) were associated with exocytosis, and five genes (
ATP8A1,
CD93,
DMBT1,
PTPRC, and
VAMP1) were classified under the secretory granule membrane term in the GO network. The acrosome contains a single secretory granule and is located in the head of mammalian sperm; secretion from this granule is an absolute requirement for fertilization [
29]. Acrosome exocytosis is a synchronized and tightly regulated all-or-nothing process, which provides a unique model for studying the multiple steps of the membrane fusion cascade [
29]. Therefore, we assumed that these genes containing nsSNPs in the selective sweep region, which are related to exocytosis and the secretory granule membrane, might have been influenced by artificial selection, considering the distinctive reproductive capacity of the Landrace breed [
27].