Genetic relationships among Vietnamese local pigs investigated using genome‐wide SNP markers

Vietnam is one of the most important countries for pig domestication, and a total of 26 local breeds have been reported. In the present study, genetic relationships among the various pig breeds were investigated using 90 samples collected from local pigs (15 breeds) in 15 distantly separated, distinct areas of the country and six samples from Landrace pigs in Hanoi as an out‐group of a common Western breed. All samples were genotyped using the Illumina Porcine SNP60 v2 Genotyping BeadChip. We used 15 160–15 217 SNPs that showed a high degree of polymorphism in the Vietnamese breeds for identifying genetic relationships among the Vietnamese breeds. Principal components analysis showed that most pigs indigenous to Vietnam formed clusters correlated with their original geographic locations. Some Vietnamese breeds formed a cluster that was genetically related to the Western breed Landrace, suggesting the possibility of crossbreeding. These findings will be useful for the conservation and management of Vietnamese local pig breeds.     

The development of the gene pool in the microevolution of <Emphasis Type="Italic">Sus scrofa</Emphasis> and the role of heterozygosity in the breed-forming process

The gene pool formation of the modern domestic breeds of pig Sus scrofa domestica and their genesis based on hybridization of wild ancestral forms of the European and Asian origin were studied using molecular immunogenetic methods. Males of the European and Central Asian S. scrofa subspecies (S. s. scrofa and S. s. nigripes were hybridized with domestic pigs of the Swedish Landrace and Vietnamese Black Masked breeds. In addition, we examined the genotypic structure of 65 wild, aboriginal, and local populations as well as cultured breeds, including the stock breeds with different levels of selection. Frequencies of alleles and suballelles of the chromosome 4 locus controlling antigens of the L blood group system were analyzed. The origin of marker suballeles of the European and Asian origin was estimated in the most widespread world pig breeds. Unexpectedly, a strikingly high frequency of the Asian elements was found in the most productive European and American breeds, as well as in the best breeds of Russia and other CIS countries. Only one form of heterozygosity (bcgi/bdfi) was found in a population of wild European ancestors, whereas domestic pig breeds displayed heterozygosity for far more numerous suballeles of the locus studied. Animals with heterozygosity for alleles of the European and Asian origin showed higher adaptivity and fertility.__________Translated from Genetika, Vol. 41, No. 4, 2005, pp. 566–576.Original Russian Text Copyright © 2005 by Tikhonov.     

The origin and genetic differentiation of native breeds of pigs in southwest China: An approach from mitochondrial DNA polymorphism

Mitochondrial DNA (mtDNA) of six breeds of native domestic pigs from Yunnan province, southwest China, and two wild boars obtained from Sichuan, China, and Vietnam was analyzed using 20 restriction endonucleases that recognize six nucleotides. Restriction maps were made by double-digestion methods and polymorphic sites were located on the map. According to their mtDNA restriction types, all the breeds were classified into six groups. Genetic distances among groups were calculated to define their phylogenetic relationships. The relationship between the Sichuan wild boar and domestic pigs is close, while the Vietnamese wild boar is relatively far from them, so the domestic pigs in southwest China are likely to have originated from a wild pig which distributed in west China. We compare our results with previous reports in literature and discuss the relationship among Chinese pigs, Japanese pigs, and European pigs. The mtDNA cleavage pattern of the Mingguang pig digested byEcoRV was identical to that of Duroc; mutations at theEcoRI site, detected in the mtDNA of two Dahe pigs, are the same as in the Vietnamese wild boar, suggesting that mutational hot spots exist in the mtDNA of pigs.     

The development of the gene pool in the microevolution of Sus scrofa and the role of heterozygosity in the breed-forming process

The gene pool formation of the modem domestic breeds of pig Sus scrofa domestica and their genesis based on hybridization of wild ancestral forms of the European and Asian origin were studied using molecular immunogenetic methods. Males of the European and Central Asian S. scrofa subspecies (S. s. scrofa and S. s. nigripes were hybridized with domestic pigs of the Swedish Landrace and Vietnamese Black Masked breeds. In addition, we examined the genotypic structure of 65 wild, aboriginal, and local populations as well as cultured breeds, including the stock breeds with different levels of selection. Frequencies of alleles and suballelles of the chromosome 4 locus controlling antigens of the L blood group system were analyzed. The origin of marker suballeles of the European and Asian origin was estimated in the most widespread world pig breeds. Unexpectedly, a strikingly high frequency of the Asian elements was found in the most productive European and American breeds, as well as in the best breeds of Russia and other CIS countries. Only one form of heterozygosity (bcgi/bdfi) was found in a population of wild European ancestors, whereas domestic pig breeds displayed heterozygosity for far more numerous suballeles of the locus studied. Animals heterozygous for alleles of the European and Asian origin showed higher adaptivity and fertility.     

猪Mx1基因第14外显子多态性分析及新突变位点的 发现

采用PCR-RFLP方法对国内外7个猪种Mx1基因第14外显子的多态性进行分析, 共检测到3个等位基因, 6种基因型。其中杜洛克中仅存在AA基因型, 苏太猪中存在全部基因型, 只有在梅山猪和具有梅山猪血统的苏太猪中出现基因型BB。所有猪种中, 只有在地方猪种和培育猪种中出现等位基因B, 所有猪种除松辽黑猪外均以A为优势等位基因。卡方检验结果表明, 不同猪种间基因型分布差异较大, 梅山猪和松辽黑猪与其他所有猪种的基因型频率差异极显著(P＜0.01) , 苏太猪与除皮特兰猪外的所有猪种的基因型频率差异也极显著(P＜0.01) , 淮猪与杜洛克和约克夏这两个国外猪种基因型频率差异不显著(P＞0.05), 而与皮特兰和其他地方猪种的基因型频率均存在极显著差异(P＜0.01) 。通过测序在扩增片段中新发现了3种类型的碱基突变, 前2个分别导致了Thr和Glu向Ala和Arg的替换, 最后一个突变不引起氨基酸的变化, 且后两个突变位点为BB基因型所特有。     

21个野生,培育及地方猪种免疫及生化遗传标记基因位点的遗传分化研究

分析了亚,欧,美,非２１个野生,培育及地方猪种４个免疫遗传标记基因位点（Ｅ,Ｆ,Ｇ,Ｌ系统）和３人生化遗传标记基因位点（Ｃｐ,Ａｍ和Ｔｆ）的遗传多态性,认为Ｅ＾ａｅｇ,Ｆ＾ａ,Ｔｆ＾ｃ基因在亚洲猪种与欧美猪种间存在显著差异,是亚洲猪种３个重要的遗传标记基因,根据Ｆ＾ａ基因频率在亚,欧,美,非猪种的变化规律分析了其基因流向特点,证明欧美猪的育种过程中利用了中国地方猪种的血缘,计算了所测猪种间的Ｎｅｉ     

Population structure and genetic diversity of four Henan pig populations

To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping‐by‐sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor‐joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome‐wide association studies.     

Chromosome R-banding patterns and NOR homologies in the European wild pig and four breeds of domestic pig

Four European wild pigs and 27 domestic pigs were studied; three Landrace, 12 village pigs from Papua New Guinea, two Chinese pigs Meishan and 10 Creole pigs from the French Antilles. The R-banding patterns were identical for all domestic breeds despite their different history and geographical divergence. The European wild pigs showed a similar R-banding pattern and a centric fusion between pairs 15 and 17 (2n = 36). The nucleolar organizers (NORs) in the European wild pig and the four domestic breeds were localized on the secondary constriction of chromosomes 8 and 10. All animals exhibited in the majority of metaphases two NORs on both chromosomes 10. In some animals. the NORs were expressed only in one of the homologs of chromosome 8. The Chinese pigs had a high amount of silver precipitates on two homologs of chromosome 8. This study confirms several previous reports on the polymorphism of NOR patterns in different domestic pig breeds.     

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism

The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.     

Single nucleotide polymorphism analysis on melanocortin receptor 1 (MC1R) of Chinese native pig

Thecoatcolorisanimportantcharacteristicofapigbreed,andcanbeclassifiedintomanytypes.Thecolorvariationsareeitherduetothedistributionofmelanocytesintheskinortotheabilityofmelano-cytestoproducemelaningranules.Thesynthesisofmelaninoriginatedfromtheformationofneuralcrest-derivedcells,whichhavetwomigrationroutes[1,2].Themelanocytesaretheramificationswhiletheneuralcrest-derivedcellsmigrateviadorsalroute[3].Andtheyprovidethefactoryformelaninsynthesis.Al-thoughtherearemanykindsofpigmentsinvertebralanim…     

Single nucleotide polymorphism analysis on melanocortin receptor 1 (<Emphasis Type="Italic">MC1R</Emphasis>) of Chinese native pig

Melanocortin receptor 1 (MC1R) gene, one of the important candidate genes for coat color trait, was used to analyze the single nucleotide polymorphism (SNP) in Chinese native pig breeds by PCR-single strand conformation polymorphism (PCR-SSCP). The study had also taken 3 imported pig breeds as control. The results showed that the three mutations G284A, T309C and T364C found in Chinese native pigs were consistent to the mutation found in the European Large Black individuals. However, 68CC or C492T and G728A were only found in the imported individuals, which were obviously different from the Chinese native pigs. Accordingly, we presumed that the coat colors of Chinese native pigs belonged to dominant black color system, which was completely distinct to that of imported pig breeds. Thus it was implied thatMC1R gene was not the principal factor affecting the coat color differences of Chinese native pig breeds, but could be used to trace the molecular evolution of pig breeds.     

Genetic relationships among Chinese pigs and other pig populations from Hunan Province, China

In this study, protein-level polymorphisms of transferrin, pre-albumin, hemopexin, ceruloplasmin and amylase were investigated in Hunan native pigs and Large Yorkshire pigs collected from Hunan (a province of China), allowing calculations of allele frequencies, average heterozygosities, inbreeding coefficients and genetic distances. The genetic relationship between Southeast Asian native pigs and American pigs was more distant than those among Southeast Asian native pig breeds. The genetic relationship between Southeast Asian native pig breeds and Hampshire pigs was the most distant.     

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.     

Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus)

The Indian wild pig is a sub-species (Sus scrofa cristatus) which is different from the other pig breeds and is protected under Schedule-III of the Indian Wildlife (Protection) Act, 1972. In this study, complete mitogenome of two Indian wild pigs was sequenced and characterized by shotgun sequencing and de novo assembly, which revealed sequence size of 16,738 and 16,251?bp, respectively, (Accession no. MG725630 and MG725631). The mitogenome sequence in this study displayed 98% homology with previously reported mitogenome of pigs from different parts of the world. Mitogenome analysis by MITOS Web server revealed similarity of gene organization with the other vertebrates (13 protein-coding, 22 tRNAs, 2 rRNAs genes, and a control region). The mitogenomic sequences of Indian wild pig maintained a separate clade in the phylogenetic tree constructed by using 62 whole mitogenome sequences across the world. The phylogeny derived from mitogenomic sequences revealed distinct separate European–American and Asiatic pig clades. It was concluded that whole mitogenome sequencing using NGS without designing mitogenome-specific primer for amplification, is possible thereby reducing the cost and labor. This study is the first report of complete sequence of mitogenome of Indian wild pig.     

西部地区主要猪种H-FABP基因多态性,IMF含量及不同基因型脂肪细胞脂滴量的关系

H-FABP是FABP家族成员之一,在长链脂肪酸的吸收和代谢平衡中发挥关键作用,但它对猪IMF含量的影响还知之甚少,对中国西部地区的猪种更是如此.文章利用PCR-RFLP（HinfⅠ、HaeⅢ和Msp Ⅰ 3种限制性内切酶）分子标记技术,检测了杜洛克猪、长白猪、大白猪、内江猪、荣昌猪、汉江黑猪、汉中白猪、八眉猪和野猪共计265头猪H-FABP基因5＇-上游区和第二内含子区的遗传变异,利用最小二乘模型分析了H-FABP基因对猪肌内脂肪含量的遗传效应,并运用猪脂肪细胞培养,油红O染色和TG测定等技术检测了H-FABP基因不同基因型脂肪细胞内脂滴的形态和沉积的量.结果表明：（1）在HinfⅠ-RFLP位点上,上述品种和野猪均存在多态性,其中大白猪、八眉猪、汉江黑猪、汉中白猪和野猪表现为低度多态,杜洛克、长白猪、内江猪和荣昌猪为中度多态;除汉江黑猪（P＜0.05）和野猪（P＜0.01）外,其他猪种基因频率和基因型频率都处于Hardy-Weinderg平衡状态（P＞0.05）;而在HaeⅢ-RFLP和Msp Ⅰ-RFLP位点上,仅内江猪、荣昌猪、汉江黑猪和八眉猪为单态;（2）9种基因型对肌内脂肪（IMF）含量的影响,HH＞Hh＞hh,DD＜Dd＜dd,AA＜Aa＜aa,遗传效应值分别为：3.89,3.42,3.17,2.27,2.49,2.91,2.28,2.70,2.95,H-FABP基因可显著地提高IMF含量（P＜0.05）;（3）aaddHH型的脂肪细胞脂滴的形态,密度和含量与其他基因型细胞差异显著（P＜0.05）.结果提示：可通过提高＂aaddHH＂基因型的频率来增加IMF含量,达到改善猪肉质的目的.     

Genetic polymorphism of erythrocyte esterase-D in pigs

The erythrocyte esterase-D (Es-D) of four European-American pig breeds, two Taiwan native pigs (Taoyuan and Short ear breeds), Philippine native pig and wild boar populations (Sus scrofa riukiuanus) in Japan was investigated by using starch gel electrophoresis. Analysis of parentage records of the pigs revealed that the phenotypic variation of erythrocyte esterase-D was controlled by two codomi-nant alleles Es-D^A and Es-D^B. The allele Es-D^b was mostly found in three European -American pig breeds, Landrace (0.100), Hampshire (0.135) and Duroc (0.102). All of the wild boar populations were monomorphic for allele Es-D^A.     

The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.     

Genetic Diversity of Chinese Native Pigs Inferred from Protein Electrophoresis

We examined protein polymorphism of 20 nativepig breeds in China and 3 introduced pig breeds. Thirtyloci have been investigated, among which six loci werefound to be polymorphic. Especially, the polymorphismof malate dehydrogenase (MDH), adenylate kinase(AK), and two new alleles of adenosine deaminase (ADA)had not been reported in domestic pigs and wild pigs.The percentage of polymorphic loci (P), the meanheterozygosity (H), and the mean number ofalleles (A) are 0.200, 0.065, and 1.300, respectively.The degree of genetic variability of Chinese pigs as awhole was higher than that of goats, lower than thatof cattle and horses, and similar to that ofsheep. Using the gene frequencies of the 30 loci, Nei'sgenetic distance among the 20 native breeds in China and3 introduced pig breeds was calculated by theformula of Nei. The program NEIGHBOR in PHYLIP3.5c was chosen to construct an UPGMA tree and a NJtree. Our results show that, of the total geneticvariation found in the native pig breeds in China, 31%(0.31) is ascribable to genetic differencesamong breeds. About 69% of the total genetic variationis found within breeds. Most breeds are in linkagedisequilibrium. The patterns of genetic similaritiesbetween the Chinese native pig breeds were notin agreement with the proposed pig type classification.     

中国两头乌猪品种内源性逆转录病毒基因研究

目的对5个中国两头乌猪品种(通城猪、东山猪、沙子岭猪、赣西两头乌猪和金华猪)及3个国外品种(大白猪、长白猪和杜洛克猪)猪内源性逆转录病毒(PERV)的核心蛋白(gag)基因、多聚酶(pol)基因、囊膜(env)基因的3个亚型A、B、C,分别从DNA和RNA水平上进行研究,以发现中国两头乌猪品种在异种器官移植中的资源优势。方法利用PCR方法在DNA水平上对PERV基因的三个亚型进行鉴定,并通过半定量PCR方法在RNA水平上检测通城猪和大白猪PERV各亚型在心、肝、脾、肺、肾、肌肉、脂肪、淋巴和脑组织中的表达谱。结果4个华中两头乌猪种中env-AB型为主要PERV亚型,分别占被测总数的92%～100%。在这4个品种中均没有检测到C亚型,金华猪以及3个国外猪种中均检测到了C亚型,病毒亚型种类也更丰富。半定量PCR实验结果显示gag、pol基因在两个品种9个组织中广泛表达,env-A在通城猪的心、肝、肺、脂肪和淋巴组织中表达量较低,env-B在通城猪的心脏和淋巴组织中表达量较低,而env-B在大白猪的肾脏中表达很低,其他所测8个组织中表达量都较高。结论通城猪、东山猪、赣西两头乌猪和沙子岭猪可以做为较佳的异种移植候选供体,具有良好的应用前景。     

Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism

Phylogenetic relationships among Asian and European pig breeds were assessed using 1036 bp of mitochondrial DNA (mtDNA) D-loop sequences. An unweighted pair-group method with arithmetic mean (UPGMA) tree was constructed on the basis of maximum likelihood distances using sequences determined for three Cheju (Korea), 11 Chinese, one Westran (Australian feral origin) and two European pigs (Berkshire and Welsh), and also published sequences for four Japanese (including two Wild Boars), one Yucatan miniature, five European (including Large White, Landrace, Duroc, Swedish and Wild Boar) and two Meishan pigs. The Colombian collared peccary (Tayassu tajacu) sequence was also determined and used as an outgroup. The maximum parsimony with heuristic search method was used to determine bootstrap support values. Asian-type pigs clustered together (bootstrap support 33%), but were separate from European-type pigs that also clustered together (93%). The Westran pig, derived from the feral descendants of pigs inhabiting Kangaroo Island of South Australia, clustered with Asian pigs, demonstrating Asian origin of their mitochondria. Berkshire and Large White clustered with Asian pigs, indicating that Asian pigs were involved in the development of these breeds. Our findings clearly demonstrate that pigs indigenous to China, Korea and Japan are only recently diverged from each other and distinctly different from European-type pigs. European pig breeds consist of pigs with mitochondria of Asian and non-Asian type, some of which were formed from closely related maternal ancestors, if not from a single ancestor.