白色基因座(I)在中国地方猪种毛色遗传中的作用研究

通过利用PCR—RFLP和PCR—SSCP技术对中国地方猪种KIT基因内含子17、18的序列进行多态性分析。结果表明：内含子17上的替换突变(G→A)发生于毛色为白色的个体——白色五指山猪、大白猪、长白猪上,其基因型(AB型)频率分别为1、1和0．8;其他中国地方猪种的此基因型频率均为0。内含子18上的缺失突变(AGTT)也同样发生在上述3个猪种的白色个体中,其基因型(AA型)频率分别为1、1和0．93;而且同样在其他的地方品种中其基因型频率均为0。这充分证明KIT基因对于猪的白毛色有重要的调控作用,而且I基因座对于其他的经典遗传基因座有上位作用。另一方面,中国地方猪种荣昌猪虽然在表型上与引入猪种大白猪、长白猪相似(白毛色),但是在KIT基因上发生的突变完全不同,推测它们分别属于不同的毛色遗传体系。     

A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive

The number of piglets born alive (NBA) per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS) were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3), Austria (1) and Switzerland (1). The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.     

猪CAST基因的单核苷酸多态性及其对肉质性状的效应

CAST基因作为肉质性状的主要候选基因.以80头外来猪和190头地方猪为材料,在CAST基因内含子24上检测到两个多态性位点(A916G 和C1633G ).在916位点上,长白猪和大白猪以A基因为优势基因,其频率分别为0.88和1.00;莱芜猪,大薄莲猪,沂蒙黑猪和里岔黑猪以B基因为优势基因,其频率分别为0.93, 0.97, 0.78和0.68.在1633位点上,长白猪和大白猪以C基因为优势基因,其频率分别为0.82和0.79:莱芜猪,大薄莲猪,沂蒙黑猪和里岔黑猪以D基因为优势基因,其频率分别为1.00, 1.00, 0.88, 0.78.在试验猪种中,共检测到6种单倍型(AACC,AACD,AADD,ABCC,BBCC,BBDD).单倍型分布的多重比较结果表明,外来猪种(长白猪和大白猪)与地方猪种(莱芜猪,大薄莲猪,沂蒙黑猪和里岔黑猪)比较差异极显著(P < 0.01).固定效应模型分析结果表明,嫩度,屠宰45 min后pH值和滴水损失单倍型间差异显著(P < 0.05).最小二乘分析结果表明,外来猪种与地方猪种在嫩度,屠宰45 min后pH值和滴水损失间差异显著(P < 0.05).BBDD单倍型个体与其它单倍型个体比较,嫩度及滴水损失差异显著(P < 0.05);AADD,BBCC,BBDD单倍型个体与其它单倍型个体比较,屠宰45 min后pH值差异显著(P < 0.05).因此,在育种过程中将CAST基因应用于标记辅助选择,将有利于改善猪肉品质,加快育种进程.     

Investigation of candidate genes for meat quality in dry-cured ham production: the porcine cathepsin B (CTSB) and cystatin B (CSTB) genes

Excessive softness is a serious defect of dry cured hams which seems related to high activity of lysosomal cysteine proteinases, such as cathepsin B, in fresh pork muscles a few days after slaughtering. As it has been shown that cathepsin B activity has a moderate heritability in Italian Large White pigs we started a candidate gene approach to identify the gene(s) that affect(s) this parameter. Here, we studied two candidate genes: cathepsin B (CTSB) and cystatin B (CSTB). We amplified and sequenced porcine DNA fragments for these two genes that were used to identify polymorphisms by SSCP and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Four and two alleles were detected at the CTSB and CSTB loci, respectively. Sequencing of the CSTB alleles showed a missense mutation that changes a codon for aspartic acid into a codon for asparagine in exon 3 of the gene. Allele frequencies for the two loci differed among the pig breeds studied (Large White, Landrace, Duroc, Belgian Landrace, Hampshire, Piétrain, Meishan, Cinta Senese, Casertana, Calabrese and Nero di Sicilia). Linkage, somatic cell hybrid panel and radiation hybrid panel analyses assigned CTSB to porcine chromosome (Sscr) 14 and CSTB to Sscr 13. The markers identified at the CTSB and CSTB loci were used in association studies with several traits of economic importance including parameters that may indicate the suitability of pig meat to produce dry-cured hams. Significant associations were observed between CTSB and back-fat thickness and between CSTB and average daily gain. In this study, cathepsin B activity was not associated with the polymorphisms identified at the CTSB and CSTB loci.     

Bi-PASA genotyping of a new polymorphism in the APOB gene shows no evidence for an association with fatness in pigs

Sequence analysis of PCR products of a 343-bp fragment from exon 29 of the porcine APOB gene of four Erhualian and four Landrace pigs revealed a missense G/C substitution at position of 6117 in this gene. Two allele-specific primers were designed to genotype this polymorphism using the Bi-PASA technique. Genotyping of 146 animals from Erhualian, Hampshire, Large White, Landrace and Duroc breeds revealed large breed differences in allele frequency. No association with fatness was observed within each of the four European breeds, where animals had been selected to be those with the highest and those with the lowest backfat depth at 100 kg liveweight from a large carcass dissection project.     

Estimation of the extent of linkage disequilibrium in seven regions of the porcine genome

Linkage disequilibrium (LD) refers to the correlation among neighboring alleles, reflecting non-random patterns of association between alleles at (nearby) loci. A better understanding of LD in the porcine genome is of direct relevance for identification of genes and mutations with a certain effect on the traits of interest. Here, 215 SNPs in seven genomic regions were genotyped in individuals of three breeds. Pairwise linkage disequilibrium was calculated for all marker pairs. To estimate the extent of LD, all pairwise LD values were plotted against the distance between the markers. Based on SNP markers in four genomic regions analyzed in three panels from populations of Large White, Dutch Landrace, and Meishan origin, useful LD is estimated to extend for approximately 40 to 60 kb in the porcine genome.     

SNPs in the porcine <Emphasis Type="Italic">PPARGC1a</Emphasis> gene: Interbreed differences and their phenotypic effects

Due to its function, the peroxisome proliferative activated receptor-γ, coactivator-1α (PPARGC1A) gene is a candidate in the search for genes that may affect production traits in the pig. The purpose of this study was to screen for new SNPs in exon 8 of the porcine PPARGC1A gene and to test their possible association with production traits. Altogether 736 pigs representing five breeds Polish Landrace, n=242; Polish Large White, n=192; Hampshire, n=27; Duroc, 21; Pietrain, n=12) and synthetic line 990 (n=242) were scanned via SSCP assay. Four SNPs were found; two new ones: C/G (His338Gln) and G/A Thr359Thr), and two previously reported ones: C/A (Arg369Arg) and T/A Cys430Ser). The missense T/A and C/G SNPs demonstrated pronounced interbreed variability in terms of allele frequencies, including the exclusive presence of the C/G substitution in the Hampshire breed. The tested SNPs occurred in five putative haplotypes, and their frequency also differed substantially between breeds. The association of the SNPs with production traits was tested for G/A (Thr359Thr), C/A (Arg369Arg) and T/A (Cys430Ser) substitutions in Polish Large White, Polish Landrace and line 990. The analysis revealed only breed-specific associations. The T/A (Cys430Ser) SNP was related to the feed conversion ratio in the Polish Large White (P=0.02), and the silent G/A and C/A substitutions were respectively associated with abdominal fat in line 990 and backfat thickness in Polish Landrace (P=0.04). The combined effects of the substitutions were estimated as haplotype effects. Three significant contrasts between haplotypes were calculated, but the observed associations were again only breed-specific.     

Linkage disequilibrium decay and haplotype block structure in the pig

Linkage disequilibrium (LD) may reveal much about domestication and breed history. An investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total, 371 single-nucleotide-polymorphisms located in three genomic regions were genotyped. The extent of LD differed significantly between European and Chinese breeds, extending up to 2 cM in Europe and up to 0.05 cM in China. In European breeds, LD extended over large haploblocks up to 400 kb, whereas in Chinese breeds the extent of LD was smaller and generally did not exceed 10 kb. The European wild boar showed an intermediate level of LD between Chinese and European breeds. In Europe, the extent of LD also differed according to genomic region. Chinese breeds showed a higher level of haplotype diversity and shared high levels of frequent haplotypes with Large White, Landrace, and Duroc. The extent of LD differs between both centers of pig domestication, being higher in Europe. Two hypotheses can explain these findings. First, the European ancestral stock had a higher level of LD. Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds.     

The swine histo compatibility system SLA: serological studies in the common Swiss and Danish swine breeds

Alloantisera were produced in common Swiss and Danish swine breeds by immunization with leucocytes or skin-grafts. Out of the 126 antisera, 66 were chosen for further study based on titrations employing lymphocytes from unrelated pigs typed with French SLA antisera (Vaiman, Chardon & Renard, 1979). The 66 selected antisera and the French reagents defining 26 SLA specificities were used to type lymphocytes from 595 unrelated pigs of the common Swiss and Danish breeds. The reaction-patterns of the French, Swiss and Danish antisera were adequately correlated for the French SLA specificities Nos FJ 2, 3, 6, 7, 8, 9, 11, 14, 19, 20 and 24 and for the haplotypes FJ 15.1.18 and FJ 5.4. In addition, a cluster of correlated Danish and Swiss antisera characterized a new specificity, provisionally designated CPH 31. This specificity was frequent in the Danish Landrace pigs.
Using the reagents identified in this report, the segregation of SLA markers was studied. Back-cross families demonstrated segregation of 15 distinct SLA haplotypes of which 14 are common in French Landrace or Large White. Differences were found in haplotype frequencies in both the Swiss and the Danish Landrace and Large White breeds.     

The swine histocompatibility system SLA: serological studies in the common Swiss and Danish swine breeds

Alloantisera were produced in common Swiss and Danish swine breeds by immunization with leucocytes or skin-grafts. Out of the 126 antisera, 66 were chosen for further study based on titrations employing lymphocytes from unrelated pigs typed with French SLA antisera (Vaiman, Chardon & Renard, 1979). The 66 selected antisera and the French reagents defining 26 SLA specificities were used to type lymphocytes from 595 unrelated pigs of the common Swiss and Danish breeds. The reaction-patterns of the French, Swiss and Danish antisera were adequately correlated for the French SLA specificities Nos FJ 2, 3, 6, 7, 8, 9, 11, 14, 19, 20 and 24 and for the haplotypes FJ 15.1.18 and FJ 5.4. In addition, a cluster of correlated Danish and Swiss antisera characterized a new specificity, provisionally designated CPH 31. This specificity was frequent in the Danish Landrace pigs. Using the reagents identified in this report, the segregation of SLA markers was studied. Back-cross families demonstrated segregation of 15 distinct SLA haplotypes of which 14 are common in French Landrace or Large White. Differences were found in haplotype frequencies in both the Swiss and the Danish Landrace and Large White breeds.     

Relations between genetic distance of parental pig breeds and heterozygosity of their F1 crosses measured by genetic markers

The aim of this paper is to examine the extent to which increment of heterozygosity in F₁ crosses can be predicted from genetic distance of parental breeds. For this purpose, 38 polymorphic marker loci (blood groups, allotypes, polymorphic proteins and enzymes) were tested in 1115 purebred animals (Duroc, Hampshire and Czech Meat Pig as sire breeds; Landrace, Large White and Black Pied Přeštice as dam breeds) and in 1428 crossbred animals of the resulting nine crossbred groups. The number of animals in each genetic group ranged from 75 to 230. On the basis of the allele frequencies of the scored loci, three measures of genetic diversity (heterozygosity, standardized heterozygosity, effective number of alleles) were calculated in all 15 genetic groups. Furthermore, two measures of genetic distance (Nei's standard genetic distance and Gregorius' absolute genetic distance) were calculated between the parental populations. High correlations (Pearson product-moment correlation 0.62 to 0.73; Spearman rank correlation 0.58 to 0.85) were found between the increment of heterozygosity in the crosses (in relation to the mean of the heterozygosities of parental populations) and the genetic distance between the parental populations.     

猪MyoG基因内含子1的一个遗传多态性及其遗传效应分析

以长白猪(73),大白猪(68),沂蒙黑猪(57)和莱芜猪(83)为研究对象,采用PCR-SSCP方法 对猪MyoG基因遗传多态性进行分析,并研究基因型与初生重、日增重、肌肉嫩度和背膘厚的相关性.根据猪MyoG 基因的DNA序列（M14331）设计引物,结果在内含子1扩增的片段上发现了一个多态性,检测到2个等位基因(A、B),3种基因型（AA、AB、BB）,并对纯合子进行测序,发现2　943位G→C突变.基因型在不同猪种分布的多重比较,结果表明,大白猪与长白猪、沂蒙黑猪和莱芜猪比较差异显著（P<0.05）,莱芜猪与长白猪和沂蒙黑猪比较差异显著（P<0.05）,长白猪与沂蒙黑猪比较差异不显著（P>0.05）.固定效应模型分析结果表明,初生重及嫩度基因型间差异显著（P<0.01）,而日增重及背膘厚基因型间差异不显著（P>0.05）.最小二乘分析结果表明,BB基因型个体与AA基因型个体比较肌肉嫩度的差异显著（P<0.05）,AA基因型个体与AB和BB基因型个体比较背膘厚的差异显著（P<0.05）.因此,推测MyoG基因对猪肉品质、生长速度及背膘厚存在一定的影响,将 MyoG基因应用于猪育种过程中的标记辅助选择将可以改善猪肉品质,提高生长速度,加快猪的育种进程.     

Two new common alleles of erythrocyte adenosine deaminase (ADA) in pigs

New adenosine deaminase variants ADA C and ADA D were found by means of agarose gel electrophoresis in pig erythrocytes. Family data supported the hypothesis that these are controlled by codominant alleles ADAC and ADAD. The ADAC allele was present in Large White (q = 0.076), Landrace (q = 0.037) and their crosses with other breeds. The ADAD allele was present in Duroc (q = 0.067) and its crosses. Allele frequencies for six pig breeds are given.     

Variability of canine microsatellites within and between different dog breeds

Polymorphic animal microsatellites have proved valuable genetic markers. For this project, the variability of 19 canine microsatellite loci was examined within and between three pure breeds of dog: Greyhounds, Labradors, and German Shepherds. The number of alleles, absolute and relative frequencies, and the statistics that express polymorphism within a breed were determined. The evolutionary relationships among these closely related dog breeds were estimated by genetic distance measures developed for use with microsatellite loci. According to the pairwise genetic distances, Greyhounds and German Shepherds had longer diverse evolutionary histories than Greyhounds and Labradors or Labradors and German Shepherds. Although a few breed-specific alleles were observed, the significant differences between breeds are in their relative frequencies and distribution of the alleles across a locus. None of the three pure dog breeds corresponds to Hardy-Weinberg equilibrium. A considerable reduction in intrapopulation variation was observed within three pure breeds, compared with the population of individuals belonging to 15 dog breeds. This reduction was especially pronounced in the Greyhound breed, which expressed the lowest degree of variation. Intrapopulation variations of Labradors and German Shepherds did not differ significantly, that of Labradors being only slightly higher. The intra-species variation of dogs is lower than in humans, mouse, or rat, but similar to that in domestic animals, probably reflecting similarly high inbreeding coefficients. However, some highly informative loci were common to all dog breeds tested so far. Such population data are necessary for mapping studies and linkage analysis in dogs. Received: 31 July 1996 / Accepted: 21 October 1996     

猪整合素β1基因CRS-PCR多态性与产仔数的关联性分析

文章采用CRS-RFLP技术对长白猪、大白猪和杜洛克猪3个品种的整合素β1基因第5外显子T32207C位点及第7外显子A35230G位点进行单核苷酸多态性分析,并将基因多态性与猪的产仔数进行关联分析。结果表明:32207多态位点的基因型效应对3个品种的总产仔数(TNB)和产活仔数(NBA)影响均不显著;35230多态位点的基因型效应对大白猪和长白猪头胎、二胎及所有胎次的TNB和NBA的影响达到显著(P<0.05)或者极显著水平(P<0.01),基因型GG、AG与AA对产仔数的影响存在差异,其效应为GG,AG>AA。可见整合素β1基因35230位点的G等位基因对大白猪和长白猪的产仔数性状有显著影响。     

Novel Polymorphisms in Porcine 3′UTR of the Leptin Gene,Including a Rare Variant within Target Sequence for MIR-9 Gene in Duroc Breed,not Associated with Production Traits

The leptin gene (LEP) is considered as a functional candidate for production traits in livestock due to its crucial role in energy homeostasis. Because polymorphisms in regulatory sequences may affect gene expression, we searched for them in the 3′UTR of LEP and analyzed their association with production traits. Four breeds and a composite line were studied. In the Polish Landrace and Polish Large White breeds, 8 SNPs and 1 indel were observed; whereas, in the Duroc breed, 9 specific SNPs were found. Pietrain and Line 990 were monomorphic. One SNP (g.+168C>T), observed in the Duroc breed only, was located within a target site for microRNA (miR-9). Association studies showed a weak association between one SNP (c.+846C>T) and abdominal fat weight in the Polish Landrace only. Thus, we concluded that contribution of polymorphisms in the 3′UTR to phenotypic variability of pig production traits is marginal. Moreover, we presented an overview of known polymorphisms (128) in the pig leptin gene.     

Plasma alpha-protease inhibitors in Norwegian Landrace and Czech Landrace pigs

The studies on alpha-protease inhibitors systems, controlled by four tightly linked loci, were performed within 159 families of Norwegian Landrace (NL) and 40 families of Czech Landrace (CL) pigs. Significant differences in allele and haplotype frequencies between the two breeds were shown. The SE-F and SSsS haplotypes (Pi1, Po1A, Po1B, Pi2 loci) appeared to be the most frequent haplotypes in NL and CL breeds respectively. This system of blood plasma proteins can be very useful for studying the relationship between breeds.     

Influence of major histocompatibility complex on reproduction and production traits in swine

The effects of the swine lymphocyte antigen (SLA) system on different performance traits were investigated in Swiss pig breeds. Litter size and piglet weight at birth and at weaning were considered and in gilts the average daily weight gain, backfat and muscle thickness as well as percentage valuable cuts were measured. These data were analysed with least squares procedures. Although the effect of SLA on these traits was very small, a few haplotypes seemed to have some influence. Sows of the Large White breed carrying H12 had a significant smaller and those with H24 had a bigger litter size at weaning. Some mating studies were performed to investigate the effects of SLA homozygosity. The obtained results suggest that this has a negative effect on the litter size, especially when H19 in the Large White breed and H7 in Landrace are involved.     

猪MyoG基因3'端PCR-SSCP遗传多态性及其遗传效应

采用PCR—SSCP方法对长白猪、大白猪、杜洛克猪、山西黑猪和马身猪共636头猪的肌细胞生成素（Myogenin,简称MyoG）基因3’端的遗传多态性进行检测,分析MyoG基因对猪的初生体质量、断奶体质量、6月龄体质量和背膘厚的影响。根据已发表的猪MyoG基因3’端侧翼序列设计3对引物,发现F1／R1引物对扩增的片段有多态性。统计结果发现：长白、大白、杜洛克猪种B基因为优势基因,其基因频率分别为0．8807、0．7256和0．8581：山西黑猪种4基因为优势基因,其基因频率为0．9359;马身猪种只检测到4基因。χ^2独立性检验表明,基因型分布在外来猪种（长白猪、大白猪、杜洛克猪）与地方猪种（山西黑猪、马身猪）间存在极显著差异（P〈0．01）。固定效应模型分析结果表明,初生体质量基因型闻差异显著（P〈0．05）,而断奶体质量、6月龄体质量和背膘厚基因型闻差异不显著（P〉0．05）。最小二乘分析结果表明,BB基因型与其它2种基因型比较有较大的初生质量,同似和AB型比较差异极显著（P〈0．01）。因此,推测MyoG基因对个体的初生体质量存在一足的影响,选择带有B等位基因的个体有望提高个体的初生体质量。