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Abstract Tibetan pigs are a unique swine strain adapted to the hypoxic environment of the plateau regions in China. The unique mechanisms underlying the adaption by Tibetan pigs, however, are still elusive. Only few studies have investigated hypoxia-associated molecular regulation in the lung tissues of animals living in the plateau region of China. Our previous study reported that ssc-miR-101-3p expression significantly differed in the lung tissues of Tibetan pigs at different altitudes, suggesting that ssc-miR-101-3p plays an important role in the adaptation of Tibetan pigs to high altitude. To understand the underlying molecular mechanism, in this study, the target genes of ssc-miR-101-3p and their functions were analyzed via various methods including qRT-PCR and GO and KEGG pathway enrichment analyses. The action of ssc-miR-101-3p was investigated by culturing alveolar type-II epithelial cells (ATII) of Tibetan pigs under hypoxic conditions and transfecting ATII cells with vectors overexpressing or inhibiting ssc-miR-101-3p. Overexpression of ssc-miR-101-3p significantly increased the proliferation of ATII cells and decreased the expression of inflammatory and apoptotic factors. The target genes of ssc-miR-101-3p were significantly enriched in FOXO and PI3K-AKT signaling pathways required to mitigate lung injury. Further, FOXO3 was identified as a direct target of ssc-miR-101-3p. Interestingly, ssc-miR-101-3p overexpression reversed the damaging effect of FOXO3 in the ATII cells. In conclusion, ssc-miR-101-3p targeting FOXO3 could inhibit hypoxia-induced apoptosis and inflammatory response in ATII cells of Tibetan pigs. These results provided new insights into the molecular mechanisms elucidating the response of lung tissues of Tibetan pigs to hypoxic stress.

Copper (Cu) is recognized as an essential trace elements for the body; However, excessive levels of Cu can lead to toxic effects. We investigated the effects of Cu2+(75 μg/L, 150 μg/L, and 300 μg/L) on the rainbow trout liver. Combination of transcriptome and metabolome analyses, the regulatory mechanisms of the liver under Cu stress were elucidated. The results showed that Cu affected the antioxidant levels, leading to disruptions in the normal tissue structure of the liver. Combined transcriptome and metabolome analyses revealed significant enrichment of the insulin signaling pathway and the adipocytokine signaling pathway. Additionally, Cu2+ stress altered the amino acid metabolism in rainbow trout by reducing serine and arginine levels while increasing proline content. Apoptosis is inhibited and autophagy and lipid metabolism are suppressed; In summary, Cu2+ stress affects energy and lipid metabolism, and the reduction of serine and arginine represents a decrease in the antioxidant capacity, whereas the increase in proline and the promotion of apoptosis potentially serving as crucial strategies for Cu2+ resistance in rainbow trout. These findings provided insights into the regulatory mechanisms of rainbow trout under Cu2+ stress and informed the prevention of heavy metal pollution and the selection of biomarkers under Cu pollution.

Abstract Background Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. Results We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Conclusions In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

The rainbow trout (Oncorhynchus mykiss) is a typical cold-water species. However, due to global warming, it has experienced prolonged high-temperature stress. Research indicates that thermotolerance in rainbow trout varies by sex at multiple physiological levels. Specifically, females exhibit higher thermotolerance, which may be attributed to estrogen-mediated signal transduction pathways. This study involved culturing primary hepatocytes from rainbow trout and exposing them to estradiol and estrogen receptor antagonists to assess estradiol’s protective effects. The analysis focused on expression of ER, HSPs genes, hepatocyte viability, and antioxidant indices. Four experimental groups were treated with 17-βE2 at concentrations of 0, 0.1, 1, and 10 μM/mL for durations of 4, 8, 12, 24, and 48 h at 18 °C. 17-βE2 treatment led to increased hepatocyte viability and enhanced SOD, GSH-Px, and CAT levels but decreased MDA levels. hsp70a, hsp90β, era1, and erβ1 levels were notably higher, with the optimal 17-βE2 concentration being 1.0 μM/mL. Following heat stress (24 °C), the addition of 1.0 μM/mL 17-βE2 improved hepatocyte viability and increased SOD, GSH-Px, and CAT levels, while MDA content initially decreased before rising. The gene expression of hsp70a, hsp90β, era1, and erβ1 was significantly elevated compared to controls. Flow cytometry analysis showed increased apoptosis after heat exposure; however, 17-βE2 treatment significantly reduced the heat stress-induced effects (p < 0.05). In conclusion, 17-βE2 and mild heat stress collaboratively enhanced the expression of HSPs and estrogen receptors, thereby providing protection to hepatocytes from heat stress damage, indicating a beneficial protective role of estradiol in rainbow trout hepatocytes.

The Qinghai-Tibetan Plateau (QTP) has nurtured a rich diversity of species because of its unique geographical and environmental conditions. Gymnocypris species (subfamily Schizopygopsinae) are primitive fishes that live in the special environment of the plateau, and their evolution and distribution are inseparable from the historical changes of the QTP. Recently, the resources of Gymnocypris species have been decreasing due to habit deterioration and the intensification of human activities. Therefore, the scientific conservation of the genetic resources of Gymnocypris species is urgently required. In this study, we established two models for the priority conservation assessment of germplasm resources of Gymnocypris species on the basis of the genetic diversity and phylogenetic relationships of 674 individuals from eight Gymnocypris species populations. The results show that the Gymnocypris potanini (GPO), Gymnocypris eckloni (GE), and Gymnocypris przewalskii (GPR) populations are the most genetically diverse in terms of combined genetic diversity values and should be prioritized for conservation. In terms of genetic contribution, the GPO, GE, and GPR populations have a positive impact on maintaining the distinctiveness and diversity of the entire Gymnocypris species population and should be prioritized for conservation. However, in terms of different evolutionary clades, the Gymnocypris namensis, Gymnocypris waddellii, Gymnocypris dobula, and GE populations in clade A should be given priority for protection, the GE population in clade B should be given priority, and the GPR population in clade C should be given priority. In conclusion, the two models and assessment of conservation priorities will provide a scientific basis for the conservation of Gymnocypris species.

ABSTRACT: Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources.

Microcystin-LR (MC-LR) are biologically active cycloheptapeptide compounds that are released by cyanobacteria during water blooms and are extensively found in aquatic ecosystems. The Penaeus vannamei is a significant species in global aquaculture. However, the high level of eutrophication in aquaculture water frequently leads to outbreaks of cyanobacterial blooms, posing a significant threat to its sustainable cultivation. Astaxanthin (AX) is commonly utilized in aquaculture for its physiological benefits, including promoting growth and enhancing immune function in cultured organisms. This study aimed to examine the protective effect of astaxanthin on P. vannamei exposed to microcystin-induced stress. The experiment consisted of three groups: one group was fed formulated feed containing MC (100 μg/kg), another group was fed formulated feed containing MC (100 μg/kg) + AX (100 mg/kg), and the third group was fed basic feed (control group). After 15 days of feeding, the specific growth rate (SGR) was significantly higher in the MCAX group (2.21% day−1) compared to the MC group (0.77% day−1), and there was no significant difference between the MCAX group (2.21% day−1) and the control group (2.24% day−1). Similarly, the percent of weight gain (PWG) was also significantly higher in the MCAX group (14.61%) compared to the MC group (13.44%) and the control group (16.64%). Compared to the control group, the epithelial cells in the MC group suffered severe damage and detachment from the basement membrane. However, in the MCAX group, although there was still a gap between the intestinal epithelial cells and the basement membrane, the overall intestinal morphology was slightly less impaired than it was in the MC group. The analysis of the intestinal microbiota revealed a significant disparity in the community composition (chao 1 and ACE) between the MC and MCAX groups. When comparing the various bacterial genera, the MC group exhibited an increase in Vibrio abundance, whereas the MCAX group showed a decrease in both Shewanella and Vibrio abundance. The results indicate that AX has a positive impact on the growth performance and resistance of P. vannamei against MC by regulating the composition of the intestinal microbiota. AX can be utilized to mitigate the detrimental effects of MC in aquaculture practices. This function could be attributed to the role of AX in preserving the structural integrity of the intestinal mucosa and regulating the composition of the intestinal microbiota.

Because of the continuous intensification of global warming, extreme climate fluctuations, and high-density farming, cold-water rainbow trout (Oncorhynchus mykiss) are exposed to conditions of heat stress, which has severely impacted their survival and yield. Nano-selenium (nano-Se) shows higher biological activity and lower toxicity and has emerged as an ideal and ecological Se formulation. Herein rainbow trout were fed either a basal diet (control group) or basal diet plus 5 mg/kg nano-Se (treatment group). Samples were collected before (18 °C for 9 days; CG18, Se18) and after (24 °C for 8 h; CG24, Se24) heat stress. The DIA/SWATH approach was then applied to compare changes at the proteome level. We found 223 and 269 differentially abundant proteins in the CG18-CG24 and Se18-Se24 groups, respectively, which mainly included apoptosis-, heat stress-, and lipid-related proteins. In comparison with the CG18-CG24 group, the Se18-Se24 group showed higher abundance of molecular chaperone, such as Hsp70, Hsp90a.1, Hspa8, Hsp30, DNAJA4, Dnajb1, Bag2 and Ahsa1; on nano-Se supplementation, the heat stress-induced decline in the abundance of the selenoprotein MsrB2 was partially restored. Furthermore, nano-Se supplementation downregulated the abundance of lipid-related (CYP51, EBP, DHCR7, DHCR24, and APOB) and pro-apoptotic (caspase-8 and Bad) proteins. Protein–protein interaction analyses suggested that nano-Se inhibits apoptosis by upregulating the expression of Hsp70, Hsp90a.1, Hspa8, and Dnajb1; further, Hsp70/Hspa8 and MsrB2 appear to play a synergistic role in antioxidant defense under heat stress. Overall, our findings provide novel insights into nano-Se-mediated tolerance of heat stress, demonstrating that nano-Se exerts its anti-heat stress effects in rainbow trout by promoting protein repair, enhancing recovery of antioxidant enzyme activity, and alleviating lipid metabolism and apoptosis.

Abstract Background With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture. Understanding the molecular regulatory mechanisms of rainbow trout under heat stress is useful to develop approaches to relieve symptoms. Results Changes in nonspecific immune parameters revealed that a strong stress response was caused in rainbow trout at 24 °C, so we performed multiple transcriptomic analyses of rainbow trout liver under heat stress (HS, 24 °C) and control conditions (CG, 18 °C). A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified. A ceRNA regulatory network was constructed and a total of 301 circRNA-miRNA and 51 miRNA-mRNA negative correlation pairs were screened, and three regulatory correlation pairs were predicted: novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some target genes involved in metabolic processes, biological regulation or response to stimulus were highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as protein processing in the ER, the estrogen signaling pathway, and the HIF-1 signaling pathway. Conclusions These results extend our understanding of the molecular mechanisms of the heat stress response and provide novel insight for the development of strategies that relieve heat stress.

Objective Tibetan pigs, an excellent species unique to China, face serious threats, which in turn affects the development and utilization of the outstanding advantages of plateau hypoxia adaptability and reduces their genetic diversity. Therefore, a discussion of measures to conserve this genetic resource is necessary. The method, based on genetic diversity, genetic divergence and total genetic contribution rate of population, reflects the priority conservation order and varies depending on the three different purposes of conservation. Methods We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces and downloaded 564 mtDNA D-loop sequences from three indigenous pig breeds in Qinghai, Sichuan, and Yunnan Provinces distributed near the Tibetan pigs. Results We analyzed three different aspects: Changdu Tibetan pigs have the highest genetic diversity, and from the perspective of genetic diversity, the priority conservation is Changdu Tibetan pigs. Hezuo Tibetan pigs have the highest genetic contribution, so the priority conservation is Hezuo Tibetan pigs in the genetic contribution aspect. Rkaze Tibetan pigs were severely affected by indigenous pig breeds, so if considering from the perspective of introgression, the priority conservation is Rkaze Tibetan pigs. Conclusion This study evaluated genetic diversity and comprehensively assessed conservation priority from three different aspects in nine Tibetan pig populations.

Objective Evidence from previous reports indicates that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River. Further research identified two new origin centers for domestic pigs in the Tibetan Plateau and the islands of Southeast Asia. However, due to the small sample size of Tibetan pigs, details of the origin and spread of Tibetan pigs has not yet been established. Methods We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces. Comprehensive Tibetan pig samples were taken to perform the most detailed analysis of Tibetan pigs to date. Results The result indicate that Rkaze pigs had the lowest level of diversity, while Changdu pigs had the highest diversity. Interestingly, these two populations were both in the Tibetan Plateau area. If we calculate diversity in terms of each province, the Tibetan Plateau area had the lowest diversity, while the Chinese province of Gansu had the highest diversity. Diversity gradient analysis of major haplotypes suggested three domestication centers of Tibetan pigs in the Tibetan Plateau and the Chinese provinces of Gansu and Yunnan. Conclusion We found two new domestication centers for Tibetan pigs. One is in the Chinese province of Gansu, which lies in the upstream region of the Yellow River, and the other is in the Chinese province of Yunnan.

Heat stress leads to altered expression of associated heat shock proteins (HSPs), which are critical molecular chaperones related to cellular function in living organisms. Selenium nanoparticles (SeNPs), a nanocomposite form of Se, have a protective effect against heat stress-induced cellular damage. In this study, primary rainbow trout hepatocytes were isolated to identify the protective function of SeNPs in rainbow trout hepatocytes. Experiments were divided into five groups and SeNPs were added at concentrations of 0, 2.0, 3.0, 5.0 and 8.0 μg/mL and incubated at 18 ℃ for 4, 8, 12, 24 and 48 h respectively. Hepatocyte viability, GSH-Px and SOD activity were enhanced and MDA content was reduced following the addition of SeNPs. Expression of GSH-P1 and genes related to HSPs (including HSP70a, HSP60, HSP90β, HSP10 and HSP47) were significantly increased and the optimal concentration of SeNPs for adding to hepatocytes was identified as 5.0 µg/mL. Adding 5.0 µg/mL SeNPs following heat stress (24 ℃) increased hepatocyte viability, GSH-Px and SOD activity, while MDA levels first decreased and then increased. Expression of GSH-P1 and genes related to HSPs (including HSP70a, HSP60, HSP90β, HSP10 and HSP47) were significantly higher than controls. In summary, SeNPs and slight heat stress synergistically enhanced the expression of GSH-P1 and HSPs and protected hepatocytes from heat stress damage, suggesting that SeNPs is a potential hepatocyte protective therapeutic agent.

The population genetic structure of domestic animals and the protection of genetic resources are major issues of concern in the field of global biology. In this study, the mtDNA D-loop sequences of 1163 Chinese indigenous cattle (Bos taurus and Bos indicus) were used to analyze their maternal origin and population genetic structure and to prioritize conservation evaluations based on a population genetic evaluation model. The results revealed three maternal origins or domestication events among Chinese indigenous cattle and the occurrence of secondary expansions but also the phenomenon of gene penetration. The population genetic evaluation model results showed that the genetic diversity of Huangpi cattle (HHP), Mountainous cattle (CMO), Bashan cattle (SBS) and Guanling cattle (GGL)populations was highest and that the Zaosheng cattle (GZN), Qinchuan cattle (SQB) and Pingliang cattle (GPL) populations contributed most to the richness of Chinese indigenous cattle genetic resources, indicating that these populations should be protected first. Our research provides a scientific basis and effective evaluation methods for the protection of genetic resources of indigenous livestock varieties.

Chicken genetic resources are gradually decreasing in genetic diversity; thus, a theoretical basis for conservation is needed. The genetic diversity and phylogeography of domestic chickens from 10 countries in Asia and red jungle fowl were investigated by analyzing the mitochondrial DNA D-loop hypervariable segment (HVS). The order of domestic chickens distributed in 31 management units in Asia in terms of conservation priority was assessed based on genetic diversity and genetic contribution rate models. A total of 219 haplotypes were distributed in seven clades, with variants identified at 103 sites. Phylogenetic analysis revealed seven maternal origins of Asian domestic chickens. Multiple subspecies of red jungle fowl were involved in the domestication of chickens in the three centers of origin: the Indian subcontinent (clade D), China (clades B, C, E and F) and Southeast Asia (clade A). The domestication center of the G clade remains unknown. The order in terms of conservation priority based on genetic diversity was as follows: northwestern and northeastern Yunnan, China; Sri Lanka; Guangxi, China; Japan; etc. The order in terms of conservation priority based on the genetic contribution rate was as follows: northwestern Yunnan, China; Sri Lanka; Japan; Papua New Guinea; etc. This study provided new insights for the conservation and evaluation of native genetic resources.

A variety of native pig breeds have been developed over the long history of their domestication by human and in a complex geographical climate. Rational use and maximum protection of local genetics resources are the major concern to maintain global biodiversity. Scientific protection measures can effectively prevent the extinction of biological resources. Three genetic resource assessment models were established by analyzing the mtDNA hypervariable regions of 70 native pig breeds in China. The genetics resources of native pig breeds in China from different perspectives, such as genetic diversity, genetic contribution rate and erosion degree, were analyzed. The results show that most native pig breeds in China have low genetic diversity, especially for those distributed in Sichuan and Shandong Provinces. Tibetan pigs contribute more to the haplotype richness of native pigs and have a greater impact on the genetic resources of native pig breeds. The Meishan pig of Jiangsu Province (JSMS) are slight eroded by European pigs. The assessment models of genetic diversity, genetic contribution rate and erosion degree were established to evaluate the genetic resources of native pig breeds from different perspectives, which provide new insights for the scientific protection of native breeds. Keywords: Pigs, Genetic resources, Assessment model, Priority protection

Swine leukocyte antigen (SLA) class I molecules play a crucial role in generating specific cellular immune responses against viruses and other intracellular pathogens. They mainly bind and present antigens of intracellular origin to circulating MHC I-restricted cytotoxic T lymphocytes (CTLs). Binding of an appropriate epitope to an SLA class I molecule is the single most selective event in antigen presentation and the first step in the killing of infected cells by CD8+ CTLs. Moreover, the antigen epitopes are strictly restricted to specific SLA molecules. In this study, we constructed SLA class I complexes in vitro comprising viral epitope peptides, the extracellular region of the SLA-1 molecules, and β2-microglobulin (β2m) using splicing overlap extension polymerase chain reaction (SOE-PCR). The protein complexes were induced and expressed in an Escherichia coli prokaryotic expression system and subsequently purified and refolded. Specific binding of seven SLA-1 proteins to one classical swine fever virus (CSFV) and four porcine reproductive and respiratory syndrome virus (PRRSV) epitope peptides was detected by enzyme-linked immunosorbent assay (ELISA)-based method. The SLA-1∗13:01, SLA-1∗11:10, and SLA-1∗11:01:02 proteins were able to bind specifically to different CTL epitopes of CSFV and PRRSV and the MHC restrictions of the five epitopes were identified. The fixed combination of Asn151Val152 residues was identified as the potentially key amino acid residues influencing the binding of viral several CTL epitope peptides to SLA-1∗13:01 and SLA-1∗04:01:01 proteins. The more flexible pocket E in the SLA-1∗13:01 protein might have fewer steric limitations and therefore be able to accommodate more residues of viral CTL epitope peptides, and may thus play a critical biochemical role in determining the peptide-binding motif of SLA-1∗13:01. Characterization of the binding specificity of peptides to SLA class I molecules provides an important basis for epitope studies of infectious diseases in swine, and for the rational development of novel porcine vaccines, as well as for detailed studies of CTL responses in pigs used as animal models.

Previous studies have shown that Southeast Asian pigs were independently domesticated from local wild boars. However, the domestication of Chinese native pigs remains a subject of debate. In the present study, phylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. A total of 2466 domestic pigs formed 124 haplotypes and were assigned to four clades. Clade A comprised pigs distributed mainly in the Qinghai-Tibet Plateau and its surrounding areas; these pigs clustered into three groups. The pigs of clade B were mainly from the Mekong River Basin in Yunnan Province and had been exposed to genetic infiltration from European populations. Clade C comprised pigs mainly from the middle and lower reaches of the Yangtze River. The pigs of clade D were distributed mainly at the intersection of Yunnan, Sichuan, and Gansu provinces east of the Hengduan Mountains (YSGH). Compared with wild boar, at least three domestication centers and one expansion center of pigs in China were detected. Among the four centers detected, two were for Tibetan pigs and were in the Qinghai-Tibet Plateau and at the YSGH intersection, and the other two were in the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River.

The highly polymorphic swine major histocompatibility complex (MHC), termed swine leukocyte antigen (SLA), is associated with different levels of immunologic responses to infectious diseases, vaccines, and transplantation. Pig breeds with known SLA haplotypes are important genetic resources for biomedical research. Canadian Yorkshire and Landrace pigs represent the current specific pathogen-free (SPF) breeding stock maintained in the isolation environment at the Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences. In this study, we identified 61 alleles at five polymorphic SLA loci (SLA-1, SLA-2, SLA-3, DRB1, and DQB1) representing 17 class I haplotypes and 11 class II haplotypes using reverse transcription-polymerase chain reaction (RT-PCR) sequence-based typing and PCR-sequence specific primers methods in 367 Canadian SPF Yorkshire and Landrace pigs. The official designation of the alleles has been assigned by the SLA Nomenclature Committee of the International Society for Animal Genetics and released in updated Immuno Polymorphism Database-MHC SLA sequence database [Release 2.0.0.3 (2016-11-03)]. The submissions confirmed some unassigned alleles and standardized nomenclatures of many previously unconfirmed alleles in the GenBank database. Three class I haplotypes, Hp-37.0, 63.0, and 73.0, appeared to be novel and have not previously been reported in other pig populations. One crossover within the class I region and two between class I and class II regions were observed, resulting in three new recombinant haplotypes. The presence of the duplicated SLA-1 locus was confirmed in three class I haplotypes Hp-28.0, Hp-35.0, and Hp-63.0. Furthermore, we also analyzed the functional diversities of 19 identified frequent SLA class I molecules in this study and confirmed the existence of four supertypes using the MHCcluster method. These results will be useful for studying the adaptive immune response and immunological phenotypic differences in pigs, screening potential T-cell epitopes, and further developing the more effective vaccines. [ABSTRACT FROM AUTHOR]