Chinese Meishan Research Articles

Genetic diversity in the stress regulatory gene LUMAN/CREB3 of Yorkshire and Meishan pigs

A candidate-gene high-density single-nucleotide polymorphism (SNP) scanning approach was used to investigate the swine LUMAN/CREB3 locus for polymorphisms in 232 Ontario Yorkshire and 29 Chinese Meishan pigs. Inter- and intra-breed differences in genetic diversity were characterized. In the Yorkshire breed, eight variations (three coding and five non-coding) were identified. Two linkage disequilibrium (LD) blocks (550 bp and ∼4 kb in length) featuring two and three haplotypes, respectively, were reconstructed. In the Meishan breed, six variations (two coding and four non-coding) and one LD block (∼3 kb in length) with three haplotypes were detected. This investigation may provide insight into variable stress responsiveness among pigs.

Breed differences in placental development during late gestation between Chinese Meishan and White crossbred gilts in response to intrauterine crowding

The objective of this study was to evaluate placental development during late gestation (day 100) between Chinese Meishan (CM; n = 7) and White crossbred (WC; n = 5) gilts following intrauterine crowding induced by unilaterally hysterectomy-ovariectomy. Gross placental morphology and areolae density as well as histological morphology (i.e., folded bilayer and placental stroma) were analyzed using computer-assisted morphometry for placentas of the smallest and largest fetuses within each litter. There was a breed by fetal size interaction (P < 0.01) for areolae density in which placentas for large CM fetuses had greater areolae density compared to small CM fetuses, but the density of areolae was greater for CM fetuses compared to WC fetuses, irrespective of fetal size. The width of the folded bilayer was greater (P < 0.01) in placentas for WC gilts compared to CM gilts, irrespective of fetal size. Placentas for small fetuses had greater (P < 0.01) folded bilayer width compared to large fetuses, irrespective of breed. The placental stromal width was greater (P < 0.01) in placentas for large fetuses compared to small, irrespective of breed. The difference between stromal width in placentas between divergent-sized littermates, however, was greater (P = 0.05) in WC gilts compared to CM gilts, indicating there was a limited response to intrauterine crowding in CM gilts. These results indicate there is an altered placental development during late gestation in CM compared to WC gilts, thus, there are likely different mechanisms for responding to intrauterine crowding between breeds.

Embryonic and fetal development in different genotypes in pigs

It is widely accepted that uterine capacity, not ovulation rate, is the greatest restraint on litter size in pigs. Recently, the reproductive strategy(s) of the Chinese Meishan pig, a breed which farrows three to five more piglets per litter than US or European pig breeds, has come under intense scrutiny. It was initially determined that the Meishan female could farrow more viable piglets per litter than US or European pig breeds, with a uterine size and ovulation rate equivalent to those of less prolific breeds. It has become apparent that the Meishan conceptus exhibits a reduced trophectoderm mitotic rate during the preimplantation period, elongates from fewer cells and remains smaller throughout gestation compared with conceptuses from less prolific US or European pig breeds. This strategy by the Meishan conceptus for a lower growth rate results in a marked reduction in conceptus loss through day 18 of gestation compared with less prolific breeds. An additional strategy is required in the Meishan to allow the larger number of viable fetuses to survive after day 30 of gestation when uterine capacity becomes limiting. Our research has demonstrated that the rapid growth of the fetus in US pig breeds appears to require continued placental growth to increase the surface area for nutrient exchange. In contrast, the increased number of smaller Meishan fetuses achieve the same increase in placental efficiency by markedly increasing the density of placental blood vessels at the fetal-maternal interface. This proliferation of placental blood vessels obviates the need for marked increase in placental size.

Endocrineand follicular studies in Meishan pig

The enhanced early embryonic survival in Chinese Meishan compared with Large- White gilts may be due, in part, to differences in ovarian and endocrine function, particularly during the periovulatory period. The overall patterns of oestradiol, LH and FSH secretion were not different between Meishan and Large-White hybrid controls during this period, although circulating inhibin concentrations were higher in Meishan gilts. Thus, there appeared to be a decreased sensitivity to inhibin feedback on FSH secretion in Meishan gilts. Behavioural oestrus was exhibited earlier relative to the LH surge in Meishan gilts than in Large-White hybrid gilts, but the time interval from the oestradiol peak until the LH surge was similar in both breeds. This finding suggests that Meishan gilts are more sensitive in terms of initiating a behavioural response, but not in terms of positive feedback. Although preovulatory follicular characteristics were as variable in Meishan as in Large-White hybrid gilts, follicles from Meishan gilts were smaller, but contained a higher concentration of oestradiol in the follicular fluid. This was probably due to increased aromatase activity in both granulosa and theca cells of Meishan follicles. The enhanced maturation of the intrafollicular environment in Meishan gilts was reflected in the oocyte population which was at a more advanced stage of development in the period preceding ovulation. In addition to decreasing the time between onset of oestrus and ovulation, advancing the LH surge to coincide with onset of oestrus (via hCG administration) decreased embryo survival at day 30 of gestation. It is concluded that both endocrine and follicular mechanisms have a role in ensuring the prolificacy in the Meishan breed.

Earlyembryonic development in prolific Meishan pigs

Prenatal mortality in European pigs is estimated at 30-40%, the majority of which occurs between days 12 and 18 after mating. Chinese Meishan pigs are prolific, averaging three to five more pigs per litter than do European breeds. Early reports into the fecundity of Meishan females suggested that their prolificacy resulted from lower embryonic mortality when compared with European females exhibiting the same ovulation rate. The preponderance of evidence suggests that there are no differences between Meishan and European breeds in either morphological embryo diversity within a litter or embryo mortality before day 12 after mating. Recent studies from our laboratory suggest that preimplantation embryos from Meishan females exhibit markedly reduced growth rates and oestrogen secretory activities through day 12 when compared with embryos from Yorkshire females. The significantly reduced conceptus sizes of Meishan versus European breeds on day 30 of gestation provide additional evidence of the reduced growth rate of Meishan embryos. Furthermore, because embryonic oestrogen production is known to alter uterine secretion of histotroph, the lower oestrogen production by Meishan embryos in the Meishan uterus may result in more gradual alterations in the uterine environment that are beneficial for conceptus survival and subsequent litter size. Recent studies using cross-transfer of Meishan and Yorkshire embryos on day 2 after mating have led to the suggestion that there is a major effect of recipient genotype on embryonic growth rate and oestrogen secretion. In these studies, both Meishan and Yorkshire embryos transferred to Meishan uteri exhibited marked decreases in morphological development and oestrogen content on day 12 when compared with embryos transferred to Yorkshire recipients. These data suggest the presence of factor(s) in endometrial secretions from Meishan females that reduce the growth rate and oestrogen secretory potential of preimplantation conceptuses.

CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

BackgroundReproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood.ResultsIn this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by next-generation sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight.ConclusionsThe present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.

Identification of functional mutations at FOXP3 binding site within BIC gene that alter the expression of miR-155 in pigs.

MiR-155 is an immune microRNA encoded within the BIC gene. Dozens of researches have uncovered the importance of high expression of miR-155 in promoting the development of immune organs and strengthening immune response and inflammatory response. Some natural mutations located in the miR-155/BIC region were revealed to disturb the expression level of miR-155 in several mammalian species, and our previous study also identified several mutations occurring near the miR-155/BIC region in pigs. However, the consequences of BIC locus-harbored mutations in pig genome remain unclear. In this study, we used Chinese Meishan and British Large White pigs to identify mutations within the miR-155/BIC region, and explore whether there are effects on expressions of miR-155 and its target genes. Target sequencing identified six potential FOXP3 protein binding sites (AAACA) in the BIC gene, among which there were two A/C mutations (AAACC) at the -108bp and -305bp upstream of the miR-155 precursors in Meishan pigs, but not in Large White pigs. A series of experiments confirmed that the FOXP3 protein mainly binds to the -305bp position, and the binding efficiency of the CC haplotype to FOXP3 protein was higher than that of the wild type, resulting in increased expression of miR-155, and consequentially decreased the expressions of its target genes. Our newly identified mutations are functional, which explain partial reasons for the difference in immunity between Meishan and Large White pigs, and provide potential molecular markers to genetically improve the disease resistance in the pig breeding practice.

Microbial Mechanistic Insights into the Role of Sweet Potato Vine on Improving Health in Chinese Meishan Gilt Model.

Simple SummarySweet potato vine as a source of fiber had been used in China for many years. We investigated the effects of fresh sweet potato vine on intestinal and plasma metabolites as well as colon microbial composition in Chinese Meishan gilts. Results suggest that sweet potato vine promoted intestinal muscle development, decreased gut permeability, endotoxin and pro-inflammatory cytokines concentrations, and increased butyrate production as well as beneficial flora, thus improving gut health.This study explored the impact of fresh sweet potato vine on the growth as well as the metabolites and colon microbial composition in Chinese Meishan gilt. Twenty Meishan gilts (body weight 30 ± 0.18 kg, n = 10 per treatment) were randomly assigned to a control (CON) or sweet potato vine (SPV) supplementation diet treatment. Gilts were housed in individual stalls. In the SPV treatment, 2 kg fresh sweet potato vine was used instead of 0.18 kg basal diet which provided the same amount of digestive energy and crude protein with the exception of crude fiber (CON, 51.00 g/d vs. SPV, 73.94 g/d) in terms of dry matter intake. Gilts were slaughtered and samples were collected on day 19 after the third estrus cycle. The SPV treatment tended to increase slaughter weight of gilts (p = 0.07); it also increased (p < 0.05) gastrointestinal tract weight and intestinal muscle layer thickness. SPV treatment also decreased (p < 0.05) carcass yield and subcutaneous adipose tissue. The concentration of zonulin and endotoxin in plasma was decreased (p < 0.05) as the gilt consumed the SPV diet. Colonic fecal concentrations of endotoxin, lipocalin-2, and tumor necrosis factor-α (TNF-α) were decreased (p < 0.05), and interleukin-10 (IL-10) was increased (p < 0.05) in the SPV treatment. Butyric acid and acetate concentration in colonic content as well as acetate concentration in caecal content were increased (p < 0.05) in the SPV treatment. Furthermore, the expression of carnitine palmityl transferase (CPT-1) and peroxisome proliferator-activated receptor-α (PPAR-α) in gilt liver in SPV treatment was increased (p < 0.05) in comparison with CON treatment. Meanwhile, the composition of the colon microbes was also altered by SPV; representative changes included an increase in Lactobacillus, Bacteroides, Roseburia, and Lachnospira. These results indicate that gilt fed with sweet potato vine had decreased gut permeability, endotoxin and pro-inflammatory cytokines concentrations; colonic fecal microbiota was also changed, which may be further beneficial to the intestinal health of Chinese Meishan gilt.

Effect of Sweet Potato Vine on the Onset of Puberty and Follicle Development in Chinese Meishan Gilts.

Simple SummarySweet potato vine, as a by-product of sweet potato, has been previously used for various purposes in southern China. The aim of this study was to investigate the effects of sweet potato vine on the onset of puberty and follicular development in the ovaries of Chinese Meishan gilts. Our results suggested that sweet potato vine supplementation delayed puberty onset and improved the follicular development, which was associated with enhanced reproductive performance in Chinese Meishan gilts.This study was conducted to evaluate the effects of sweet potato vine on the onset of puberty and the follicular development in the ovaries of Chinese Meishan gilts. A total of 20 Meishan gilts (initial body weight at 30 ± 0.18 kg) were randomly fed a control (CON) or sweet potato vine (SPV) supplemented diet until 19 days following the third estrous. Sweet potato vine was instead of part of basal diet with the same amount of energy and protein in the sweet potato vine group. The results indicate that gilts fed with sweet potato vine reached puberty 9.4 days later. The development of ovaries was enhanced by sweet potato vine supplementation, characterized by an increase (p < 0.05) in the relative weight of the ovaries and the number of large follicles (>5 mm). Sweet potato vine supplementation increased (p < 0.05) the total superoxide dismutase (T-SOD) and reduced (p < 0.05) the concentration of malondialdehyde (MDA) in the serum of the gilts. Also, the expression of superoxide dismutase-1 (SOD1) and luteinizing hormone receptor (LHR) mRNA in the granulosa cells from the large follicle (>5 mm) of gilts in the SPV group were increased (p < 0.05) as compared with the CON group. These results indicate that gilts fed with sweet potato vine exhibited delayed puberty as well as improved follicular development, which may contribute to the reproductive performance of Chinese Meishan gilts.

The morphological changes of oviductal mucose in oestral cycle of sows

The morphological changes of oviductal mucose in oestral cycle of sows

Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs.

The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole‐genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50‐kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions supports that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as NR6A1. Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the NR6A1 gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as AHR and PGRMC2, associated with fertility, and SAL1, associated with meat quality, were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genomewide association study and genomic prediction by providing ancestry information of variants.

Genomic signatures reveal selection of characteristics within and between Meishan pig populations.

The Chinese Meishan pig breed is well known for its high prolificacy. Moreover, this breed can be divided into three types based on their body size: big Meishan, middle Meishan (MMS) and small Meishan (SMS) pigs. Few studies have reported on the genetic signatures of Meishan pigs, particularly on a genome-wide scale. Exploring for genetic signatures could be quite valuable for revealing the genetic architecture of phenotypic variation. Thus, we performed research in two parts based on the genome reducing and sequencing data of 143 Meishan pigs (74 MMS pigs, 69 SMS pigs). First, we detected the selection signatures among all Meishan pigs studied using the relative extended haplotype homozygosity test. Second, we detected the selection signatures between MMS and SMS pigs using the cross-population extended haplotype homozygosity and FST methods. A total of 111398 SNPs were identified from the sequenced genomes. In the population analysis, the most significant genes were associated with the mental development (RGMA), reproduction (HDAC4, FOXL2) and lipid metabolism (ACACB). From the cross-population analysis, we detected genes related to body weight (SPDEF, PACSIN1) in both methods. We suggest that rs341373351, located within the PACSIN1 gene, might be the causal variant. This study may have achieved consistency between selection signatures and characteristics within and between Meishan pig populations. These findings can provide insight into investigating the molecular background of high prolificacy and body size in pig.

Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase

ObjectiveO-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) catalyzes the addition of O-GlcNAc and GlcNAcylation has extensive crosstalk with phosphorylation to regulate signaling and transcription. Pig OGT is located near the region of chromosome X that affects follicle stimulating hormone level and testes size. The objective of this study was to find the variations of OGT between European and Chinese pigs.MethodsPigs were tested initially for polymorphism in OGT among European and Chinese pigs by polymerase chain reaction and sequencing at the U.S. Meat Animal Research Center (USMARC). The polymorphism was also determined in an independent population of pigs including European and Chinese Meishan (ME) breeds at the National Institute of Animal Science (NIAS, RDA, Korea).ResultsThe intron 20 of OGT from European and Chinese pigs was 514 and 233 bp, respectively, in the pigs tested initially. They included 1 White composite (WC) boar and 7 sows (2 Minzu×WC, 2 Duroc [DU]×WC, 2 ME×WC, 1 Fengzing×WC) at USMARC. The 281-bp difference was due to an inserted 276-bp element and GACTT in European pigs. When additional WC and ME boars, the grandparents that were used to generate the 1/2ME×1/2WC parents, and the 84 boars of 16 litters from mating of 1/2ME×1/2WC parents were analyzed, the breeds of origin of X chromosome quantitative trait locus (QTL) were confirmed. The polymorphism was determined in an independent population of pigs including DU, Landrace, Yorkshire, and ME breeds at NIAS. OGT was placed at position 67 cM on the chromosome X of the USMARC swine linkage map.ConclusionThere was complete concordance with the insertion in European pigs at USMARC and NIAS. This polymorphism could be a useful marker to identify the breed of origin of X chromosome QTL in pigs produced by crossbreeding Chinese and European pigs.

A genomic landscape of mitochondrial DNA insertions in the pig nuclear genome provides evolutionary signatures of interspecies admixture.

Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0.0078% of the nuclear genome. Numt integration events were correlated (0.99) to the chromosome length. The longest numt sequence (about 11 kbp) was located on SSC2. Six numts were sequenced and PCR amplified in pigs of European commercial and local pig breeds, of the Chinese Meishan breed and in European wild boars. Three of them were polymorphic for the presence or absence of the insertion. Surprisingly, the estimated age of insertion of two of the three polymorphic numts was more ancient than that of the speciation time of the Sus scrofa, supporting that these polymorphic sites were originated from interspecies admixture that contributed to shape the pig genome.

Differential expression of genes BPI, TAP1, SLA-1 and SLA-3 in Escherichia coli F18-resistant and sensitive Meishan post-weaning piglets

The genetic basis and mechanism of sensitivity or resistance to the significant pathogen Escherichia coli F18 is not clear in native Chinese pig breeds and may differ from that in non-native breeds. Our previous research showed that the genes BPI, TAP1, SLA-1 and SLA-3 may play important roles in resistance to E. coli F18 in post-weaning piglets. This study was based on success in selecting and identifying full sib Chinese native Meishan breed post-weaning E. coli F18-resistant and sensitive piglets. Real-time PCR was used to detect expression levels of the genes BPI, TAP1, SLA-1 and SLA-3 in liver, spleen, thymus, lymph node, duodenum, and jejunum tissues between E. coli F18-resistant and -sensitive Meishan piglets. Only the BPI gene was obviously tissue specific; it was highly expressed in the duodenum and jejunum, but expressed at a low level in other tissues. The other three genes were expressed in all the studied tissues, and particularly highly in immune organs and intestinal tissues. The expression level of BPI in the duodenum of the resistant group was significantly higher than that in the sensitive group (P < 0.01). The SLA-3 expression level in the thymus of the resistant group was significantly higher than that in the sensitive group (P < 0.05). TAP1 and SLA-1 gene expression levels were generally higher in the resistant group than the sensitive group, but there were no significant differences. Genes BPI and SLA-3 play an important role in the processes of resistance to E. coli F18 in Meishan weaned piglets. We speculate that BPI protein may have a direct killing effect on Gram-negative bacteria such as E. coli strain F18 in the intestine; the resistance of Meishan weaned piglets to E. coli F18 is likely to be related to the upregulation of intestinal BPI. The upregulation of SLA-3 may increase the resistance of weaned piglets to E. coli F18 by regulation of the immune response.

Divergent activity of the gonadotropin-releasing hormone receptor gene promoter among genetic lines of pigs is partially conferred by nuclear factor (NF)-kB, specificity protein (SP)1-like and GATA-4 binding sites

BackgroundBinding of gonadotropin-releasing hormone (GnRH) to its receptor (GnRHR) on gonadotropes within the anterior pituitary gland is essential to reproduction. In pigs, the GnRHR gene is also located near a genetic marker for ovulation rate, a primary determinant of prolificacy. We hypothesized that pituitary expression of the GnRHR gene is alternatively regulated in genetic strains with elevated ovulation rates (Chinese Meishan and Nebraska Index) vs. standard white crossbred swine (Control).MethodsLuciferase reporter vectors containing 5118 bp of GnRHR gene promoter from either the Control, Index or Meishan swine lines were generated. Transient transfection of line-specific, full length, deletion and mutation constructs into gonadotrope-derived αT3-1 cells were performed to compare promoter activity and identify regions necessary for divergent regulation of the porcine GnRHR gene. Additionally, transcription factors that bind the GnRHR promoter from each line were identified with electrophoretic mobility shift assays (EMSA).ResultsDramatic differences in luciferase activity among Control, Index and Meishan promoters (19-, 27- and 49-fold over promoterless control, respectively; P < 0.05) were established. A single bp substitution (−1690) within a previously identified upstream enhancer (−1779/−1667) bound GATA-4 in the Meishan promoter and the p52/p65 subunits of nuclear factor (NF)-κB in the homologous Control/Index promoters. Transient transfection of vectors containing block replacement mutations of either the GATA-4 or NF-κB binding sites within the context of their native promoters resulted in a 50 and 60 % reduction of luciferase activity, respectively (P < 0.05). Furthermore, two single-bp substitutions in the Meishan compared to Control/Index promoters resulted in binding of the p52 and p65 subunits of NF-κB and a specificity protein 1 (SP1)-like factor (−1235) as well as GATA-4 (−845). Vectors containing the full-length Meishan promoter harboring individual mutations spanning these regions reduced luciferase activity by 25 and 20 %, respectively, compared to native sequence (P < 0.05).ConclusionsElevated activity of the Meishan GnRHR gene promoter over Control/Index promoters in αT3-1 cells is partially due to three single nucleotide polymorphisms resulting in the unique binding of GATA-4 (−1690), the p52/p65 subunits of NF-kB in combination with a SP1-like factor (−1235), and GATA-4 (−845).Electronic supplementary materialThe online version of this article (doi:10.1186/s12958-016-0170-0) contains supplementary material, which is available to authorized users.

Difference in expression patterns of placental cholesterol transporters, ABCA1 and SR-BI, in Meishan and Yorkshire pigs with different placental efficiency.

Cholesterol is a key cell membrane component and precursor of steroid hormones. The maternal cholesterol is an important exogenous cholesterol source for the developing embryos and its transportation is mediated by ABCA1 and SR-BI. Here we reported that during the peri-implantation period in pigs, ABCA1 was expressed by uterine luminal epithelium (LE) and interestingly, its expression was more abundantly in LE on mesometrial side of uterus. However, SR-BI was expressed primarily by LE, glandular epithelial cells (GE) and trophoblast cells (Tr). During the placentation period, the expression levels of ABCA1 and SR-BI proteins at epithelial bilayer and placental areolae were significantly higher in Chinese Meishan pigs compared to Yorkshire pigs. Consisitently, mRNA levels of HMGCR, the rate-limiting enzyme for cholesterol synthesis, were significantly higher in Meishan placentas than in Yorkshire placentas. Our findings revealed the routes of transplacental cholesterol transport mediated by ABCA1 and SR-BI in pigs and indicated that ABCA1 related pathway may participate in anchoring the conceptus to the mesometrial side of uterus. Additionally, an ABCA1 dependent compensatory mechanism related to the placental efficiency in response to the smaller placenta size in Meishan pigs was suggested.

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Both growth and immune capacity are important traits in animal breeding. The animal quantitative trait loci (QTL) database is a valuable resource and can be used for interpreting the genetic mechanisms that underlie growth and immune traits. However, QTL intervals often involve too many candidate genes to find the true causal genes. Therefore, the aim of this study was to provide an effective annotation pipeline that can make full use of the information of Gene Ontology terms annotation, linkage gene blocks and pathways to further identify pleiotropic genes and gene sets in the overlapping intervals of growth-related and immunity-related QTLs. In total, 55 non-redundant QTL overlapping intervals were identified, 1893 growth-related genes and 713 immunity-related genes were further classified into overlapping intervals and 405 pleiotropic genes shared by the two gene sets were determined. In addition, 19 pleiotropic gene linkage blocks and 67 pathways related to immunity and growth traits were discovered. A total of 343 growth-related genes and 144 immunity-related genes involved in pleiotropic pathways were also identified, respectively. We also sequenced and genotyped 284 individuals from Chinese Meishan pigs and European pigs and mapped the single nucleotide polymorphisms (SNPs) to the pleiotropic genes and gene sets that we identified. A total of 971 high-confidence SNPs were mapped to the pleiotropic genes and gene sets that we identified, and among them 743 SNPs were statistically significant in allele frequency between Meishan and European pigs. This study explores the relationship between growth and immunity traits from the view of QTL overlapping intervals and can be generalized to explore the relationships between other traits.

Length polymorphism in OGT between Korean native pig, Chinese Meishan, and the Western pig breeds.

BackgroundThe Korean native pig (KNP) is generally thought to have come from northern China to the Korean peninsula approximately 2000 years ago. KNP pigs were at the brink of extinction in the 1980s, since then efforts have been made to restore the breed by bringing together the remaining stocks in South Korea. As a result, KNP was registered as a breed in 2006. To find additional breed-specific markers that are distinct among pig breeds, variations in O-linked N-acetylglucosamine transferase (OGT) were investigated. OGT is located on chromosome X and catalyzes the post-translational addition of a single O-linked-β-N-acetylglucosamine to target proteins.FindingsLength polymorphism in the intron 20 of OGT was identified. The intron 20 of OGT from Duroc, Landrace, and Yorkshire breeds was 281-bp longer than that from either KNP or Chinese Meishan pigs. The difference between the Western pig breeds (BB genotype) and KNP or Meishan pigs (AA genotype) was due to an inserted 276-bp element and the 5-bp ACTTG.ConclusionsThe polymorphism in OGT identified in this study may be used as an additional marker for determining the breed of origin among Meishan and the Western pig breeds. The length polymorphism suggests that the locus near OGT is not fixed in KNP. This marker would be relevant in determining the breed of origin in crossbred pigs between KNP pigs with known genotypes and the Western pig breeds with BB genotypes, thus confirming the contribution of the X chromosome from each breed.

MC1R, KIT, IGF2, and NR6A1 as markers for genetic differentiation in Thai native, wild boars, and Duroc and Chinese Meishan pigs.

Mutations in melanocortin 1 receptor (MC1R) gene and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) gene have been shown to affect coat color patterns in pigs. Additional functional marker genes, such as insulin like growth factor-2 (IGF2) and orphan nuclear receptor, germ cell nuclear factor (NR6A1), have been described for variations in factors such as fat deposition, litter size, and vertebra number in pigs. In this study, we investigated 129 pigs representing 4 breeds: Thai indigenous, classified into black (similar to Raad or Ka done pig) and black and white (similar to the Hailum and Kwai pig) coat color types; wild boar; Duroc; and Chinese Meishan. Mutations of MC1R, KIT, IGF2, and NR6A1 were detected using polymerase chain reaction-restriction fragment length polymorphism. The genotypes variation in MC1R and KIT genes could be used to differentiate four groups of coat color: solid black, black and white, red, and wild type. For IGF2, the GG genotype was present in wild boar only; for NR6A1 the TT genotype was found only in Duroc pigs. We identified novel 14-bp deletions in KIT that were associated with black and white coat color in Thai indigenous pigs. Insights into variations in genes presented in this study will be useful in future developmental breeding programs for the Thai native pig.