Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under highaltitude hypoxia

Background: Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude.However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear.Methods: Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland(TH, n = 4) and lowland(TL, n = 4), as well as Yorkshire pigs grown in the highland(YH, n = 4) and lowland(YL, n = 4), using methylated DNA immunoprecipitation sequencing.Results: We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed6829, 11997, 2828, and 1286 differentially methylated regions(DMRs), respectively. These DMRs contained 384, 619,192, and 92 differentially methylated genes(DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs.Conclusions: This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.     

藏猪促红细胞生成素的表达与低氧适应分析

为了解藏猪肾脏中促红细胞生成素（erythropoietin,EPO）的表达与其低氧适应之间的关系,采用Western blotting技术检测西藏林芝地区（海拔约3000 m）的高海拔藏猪（ZZ）和高海拔大约克夏猪（YZ）、北京中顺景盛养殖场（海拔约100 m）的低海拔藏猪（ZB）和安徽合肥市（海拔约为36 m）的低海拔大约克夏猪（YH）肾脏组织EPO蛋白的表达量。结果发现,ZZ、ZB、YZ、YH的EPO表达量,在A组试验中,高海拔藏猪与高海拔大约克夏猪差异显著（P<0.05）,高海拔大约克夏猪与低海拔藏猪、低海拔大约克夏猪差异极显著（P<0.01）;B组试验中,高海拔藏猪与低海拔藏猪差异不显著（P>0.05）,高海拔藏猪与高、低海拔大约克夏猪差异显著（P<0.05）;C组试验中,高、低海拔藏猪间差异显著（P<0.05）,低海拔藏猪与高、低海拔大约克夏猪差异极显著（P<0.01）。当大约克夏猪处在高海拔应急状态下时,EPO的表达量高于藏猪。而长期生活在高原的大约克夏猪EPO的表达量较藏猪低,但高于低海拔大约克夏猪。EPO的稳定表达是藏猪适应高原低氧环境的一个重要因素,而高原大约克夏猪肾脏组织内EPO的高表达,则是大约克夏猪适应高原低氧环境的生理调节过程。     

藏猪和大约克猪CKMT2基因多态性分析及其组织表达模式

为探究藏猪和大约克猪肌节线粒体肌酸激酶2（creatine kinase,mitochondrial 2,CKMT2）基因多态性位点及其在各组织中的表达差异,试验采用Sanger测序法对藏猪（50头）和大约克猪（60头）CKMT2基因起始密码子上游1 000 bp区域进行单核苷酸多态性（single nucleotide polymorphism,SNP）筛选与基因分型;180日龄藏猪和大约克猪（各10头）屠宰后分别采集心脏、背脂和背最长肌组织,采用实时荧光定量PCR技术检测CKMT2基因在各组织中的表达水平。结果显示,在CKMT2基因起始密码子上游1 000 bp区域,筛选到5个SNPs位点：G-357A、T-469C、G-649T、A-784G和A-953G,且藏猪与大约克猪等位基因频率差异明显。转录因子预测发现,这些SNPs位点与骨骼肌生长发育、肌肉能量代谢、抗缺氧有关。藏猪CKMT2基因在背最长肌和心脏组织中的mRNA表达量极显著高于大约克猪（P<0.01）,在背脂中的mRNA表达量极显著低于大约克猪（P<0.01）,推测CKMT2基因具有正向调控抗低氧和肌肉组织生成、负向调控脂肪生成的作用,该分析结果与藏猪和大约克猪的品种特性相吻合。本试验结果为进一步探索猪生长发育、脂肪沉积和低氧适应性提供了一定的新思路。     

Polymorphism and Tissue Expression Patterns of CKMT2 Gene in Tibetan and Yorkshire Pigs

In order to explore the polymorphism site and difference of expression level of creatine kinase,mitochondrial 2 (CKMT2) gene in muscle segments of Tibetan and Yorkshire pigs,in this experiment,Sanger sequencing method was used to screen and genotype the single nucleotide polymorphism (SNPs) in the 1 000 bp region upstream of the initiation codon of CKMT2 gene in 50 Tibetan and 60 Yorkshire pigs.The expression of CKMT2 gene was detected by Real-time quantitative PCR in heart,back fat and longissimus dorsi muscle of 180-day-old of 10 Tibetan and 10 Yorkshire pigs.The results showed that 5 SNPs (G-357A,T-469C,G-649T,A-784G and A-953G) were found in the upstream 1 000 bp region of the initiation codon of CKMT2 gene,the allele frequency of Tibetan pigs at all sites were significantly different from those of Yorkshire pigs.These SNPs were related to skeletal muscle growth and development,muscle energy metabolism and anti-hypoxia.The mRNA expression of CKMT2 gene in longissimus dorsi muscle and heart of Tibetan pigs were extremely significantly higher than Yorkshire pigs (P<0.01),and the mRNA expression in back fat of Tibetan pigs was extremely significantly lower than Yorkshire pig (P<0.01),which indicated that CKMT2 gene could positively regulate anti-hypoxia and muscle tissue production,and negatively regulate fat production,the analysis results were consistent with the breed characteristics of Tibetan and Yorkshire pigs.This experiment results provided some new ideas for further exploration of pig growth and development,fat deposition and hypoxia adaptability.     

基于iTRAQ技术挖掘猪肾组织高原低氧适应性关键蛋白

旨在探究高原低氧环境下藏猪与大约克猪肾组织中低氧适应的差异表达蛋白（differentially expressed protein,DEPs）。本试验选择藏猪与大约克猪两个品种无亲缘关系的去势公猪,饲养于海拔3 000 m的高原,按自由采食方式饲养至180日龄,每个品种随机选择生长情况相近的 9头猪采集肾组织。利用同位素标记相对和绝对定量（isobaric tags for relative and absolute quantification,iTRAQ）技术对藏猪和大约克猪肾组织中蛋白差异表达情况进行分析,并对差异表达蛋白进行GO（Gene Ontology）功能注释及KEGG通路分析。结果发现,在两猪种肾脏组织中共获得4 370个蛋白质,以FC>1.2或<0.833,P<0.05为筛选条件共筛选出181个DEPs,其中在藏猪中上调的蛋白质有138个,下调的有43个。这些DEPs主要功能富集在HIF-1信号通路、PPAR信号通路、补体和凝血级联信号通路、氧化还原酶活性、碳代谢、血压调节、线粒体等与低氧适应相关的条目和通路上,进一步综合分析后共筛选出5个与低氧适应相关的重要DEPs（CD59、A2M、eNOS、CDKN1B和PGK1）。这些DEPs分别在维持血液动力学、调节能量代谢与生理环境稳态等方面的调节中起到重要作用,为进一步研究猪的高原低氧适应性提供一定理论依据。     

藏猪和大约克猪ACADM基因表达量与脂肪沉积性状的相关性分析

为探究中链酰基辅酶A脱氢酶(ACADM)基因在不同品种猪组织中的表达水平,并分析其与猪脂肪沉积性状的相关性,采用Sanger测序法对藏猪(58头)和大约克猪(60头)ACADM基因起始密码子上游1 kb区域进行了单核苷酸多态性(SNPs)筛选与基因分型,选取180日龄藏猪和大约克猪各10头屠宰后分别采集肝脏、背脂、心脏和背最长肌组织,利用RT-qPCR技术检测了ACADM基因的表达水平,同时测定其背膘厚和背最长肌组织中肌内脂肪含量。结果显示:在ACADM基因起始密码子上游1 kb区域,存在C-101G和C-569G这2个突变位点,藏猪与大约克猪等位基因频率呈极显著差异(P<0.01);在藏猪与大约克猪的肝脏、背脂、背最长肌和心脏组织中ACADM基因表达趋势完全一致,藏猪极显著高于大约克猪(P<0.01);经ACADM基因表达量与背膘厚、肌内脂肪含量相关性分析发现,ACADM基因mRNA相对表达量与背膘厚和肌内脂肪含量呈显著正相关(P<0.05)。通过以上结果推测这2个突变位点可能是调控ACADM基因表达的重要功能位点,从而导致猪脂肪沉积性状的差异。本研究为进一步开展ACADM基因对猪脂肪沉积的调控机制研究提供了重要支撑。     

利用DNA池和测序技术快速筛查SNPs及估算基因频率

选取具有明显品种差异的3个猪品种(可乐猪、白香猪和大约克)构建品种DNA池,采用PCR产物直接测序法研究公猪外周致密纤维(ODFP)基因3'UTR、CDS、5'UTR序列(994 bp)的多态性,快速筛查到2个可能与精液品质相关的SNPs(C675T、C786T);其中,C675T导致天冬氨酸变成异亮氨酸。进一步利用测序图中SNPs等位基因峰高的比值估算各猪品种等位基因的频率。     

SPF大白猪和长白猪CIITA基因剪接突变体的鉴定分析及在不同组织中的表达模式

为了鉴定分析SPF大白猪和长白猪CIITA剪接突变体，研究其在猪不同组织中的表达模式。本研究以5周龄的8头SPF大白猪和7头SPF长白猪为研究对象，设计特异性引物对CIITA基因进行扩增、克隆和测序，对获得的序列分析其剪接突变体特征，利用在线软件对不同剪接突变体进行生物信息学分析，同时利用荧光定量PCR方法检测CIITA基因剪接突变体在2头SPF长白猪8种组织中的表达模式。结果显示，在SPF大白猪和长白猪CIITA基因CDS区存在3种不同的剪接突变体（CIITA-A、CIITA-B和CIITA-C），其CDS长分别为939、984和1 698 bp。CIITA-A和CIITA-B突变体由于Exon 11部分核苷酸缺失（40和199 bp）使终止密码子提前，从而致使编码CIITA蛋白的结构域受到了剪接的影响，缺失了末端富含亮氨酸的4个重复结构域，蛋白结构发生了明显的改变。进化树结果表明，针对CIITA，猪与绵羊和牛具有较近的亲缘关系，在不同猪品种中具有较高的保守性。同时，CIITA不同剪接突变体在猪8种组织中均有表达，且表达量趋于一致，均在脾或肺中表达量较高，其次是肾、脊髓、甲状腺、肝、胸腺，在心脏中表达最低。本研究从SPF大白猪和长白猪上共获得了3个CIITA剪接突变体，其中两个蛋白结构缺失了4个富含亮氨酸的重复结构域，且不同剪接突变体在猪不同组织中均有表达，表达量稍有差异，为后续CIITA基因在机体内的免疫调控功能研究奠定了理论基础。     

Study on Differential Expression of PRRSV Receptor Genes in Lung Tissues of Different Breeds of Pig Infected with HP-PRRSV

In order to understand the molecular mechanism of host susceptibility differential to highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRSV) infection among three breeds of pig, Tibetan pig,ZangMei Black and Yorkshire,the mRNA level of five reported PRRSV receptor genes (HSPG2,SIGLEC1,CD163,VIM and NMMHC-ⅡA) expressed in lung were investigated on 0,4, 7 and 14 days post infection (dpi) with HP-PRRSV JXA1 isolate.The Real-time RT-PCR results showed that the expression of HSPG2 in Tibetan pig increased significantly on 4 and 14 dpi and decreased significantly on 7 dpi compared with the expression on 0 dpi (P < 0.05), and its expression in ZangMei Black on 14 dpi was significantly higher than that of on 7 dpi (P < 0.05);An increased expression of SIGLEC1 in Tibetan pig was observed on 4 and 14 dpi (P < 0.05), and a decreased expression of the same gene was detected in Yorkshire on 4,7 and 14 dpi (P < 0.05);The expression of CD163 elevated significantly on 14 dpi in both Tibetan pig and ZangMei Black (P < 0.05), however its expression reduced significantly on 7 and 14 dpi in Yorkshire (P < 0.05); The expression of VIM gene was significantly higher on 7 dpi in Tibetan pig and significantly lower on 7 dpi in Yorkshire (P < 0.05); And the expression of NMMHC-ⅡA was significantly higher on 4 dpi in ZangMei Black, which was also significantly higher in Yorkshire on 4 and 14 dpi (P < 0.05).In conclusion, SIGLEC1 and VIM might be important genes to influence the host resistance of Tibetan pig,ZangMei Black and Yorkshire to HP-PRRSV infection.     

不同品种猪感染HP-PRRSV后肺组织间PRRSV受体基因差异表达的研究

为进一步了解藏猪、藏梅猪和大约克夏猪对高致病性猪繁殖与呼吸综合征病毒（HP-PRRSV） JXA1分离株具有不同易感性的分子机理,本研究建立实时荧光定量RT-PCR方法比较分析藏猪、藏梅猪和大约克夏猪感染JXA1分离株前、感染后4、7和14 d肺脏中HSPG2、SIGLEC1、CD163、VIM和NMMHC-ⅡA 5个PRRSV受体基因的差异表达情况。结果显示,藏猪感染JXA1分离株后4和14 d肺脏中HSPG2的表达量显著高于感染前（P < 0.05）,而感染后7 d HSPG2的表达量显著低于感染前（P < 0.05）,藏梅猪在感染后14 d HSPG2的表达量显著高于感染后7 d（P < 0.05）;藏猪感染后4和14 d肺脏中SIGLEC1的表达量显著高于感染前（P < 0.05）,大约克夏猪感染后4、7和14 d SIGLEC1的表达量均显著低于感染前（P < 0.05）;藏猪和藏梅猪感染后14 d肺脏中CD163的表达量均显著高于感染前（P < 0.05）,大约克夏猪则感染后7和14 d均显著低于感染前（P < 0.05）;藏猪感染后7 d肺脏中VIM的表达量显著高于感染前（P < 0.05）,大约克夏猪在感染后7 d显著低于感染前（P < 0.05）;藏梅猪感染后4 d肺脏中NMMHC-ⅡA的表达量显著高于感染前（P < 0.05）,大约克夏猪在感染后4和14 d NMMHC-ⅡA的表达量显著高于感染前（P < 0.05）。结果表明,5个PRRSV受体基因中,SIGLEC1和VIM基因可能是影响藏猪、藏梅猪和大约克夏猪对JXA1分离株易感性存在差异的潜在关键基因。     

藏猪EGLN1基因exon 4及部分内含子变异研究

青藏高原的高寒低氧极端环境影响动物的正常生存和物种繁衍,藏猪在长期的适应性驯化中对低氧环境有着更强的适应能力。本研究对高海拔猪种藏猪(甘孜藏猪、迪庆藏猪、西藏藏猪和合作藏猪)和八眉猪以及低海拔猪种烟台黑猪、长白猪和大白猪EGLN1基因exon 4及部分内含子的核苷酸序列进行测定和分析。结果表明:在EGLN1基因exon 4序列的266bp处发生了C→T的颠换,藏猪和八眉猪在该位点均为C,而烟台黑猪和引入的选育猪种长白猪、大白猪在该位点出现了C/T杂合现象;基于变异位点的等位基因C和T共界定了3种基因型(CC、CT、TT),C和CC分别是高海拔地方猪种藏猪和八眉猪的唯一等位基因和基因型;而在低海拔选育猪种中,CC基因型频率仅为0.20,其他2种基因型均为0.40,T为优势等位基因,频率达到0.60,而等位基因C的频率仅为0.40。本研究认为,高海拔猪种(2 300 m以上)藏猪和八眉猪与低海拔猪种烟台黑猪、长白猪和大白猪在EGLN1基因上存在特征性遗传变异,根据等位基因(C和T)及基因型(CC、CT、TT)在海拔上的特征差异,推测可能与不同地理区域条件下的长期适应性驯化有关。     

品种及杂交组合效应对育肥猪猪肉羟脯氨酸和pH值的影响

通过对不同品种及杂交组合氟烷基因显性纯合子育肥猪肌肉中羟脯氨酸和pH值2个指标的测定,来分析品种及杂交组合效应对猪肉质的影响。试验结果表明,品种及杂交组合效应对猪肉的嫩度有影响。在屠宰后的前4 d大长猪(大白猪×长白猪)猪肉中羟脯氨酸含量低于长大猪(长白猪×大白猪),说明其嫩度要好于长大猪;猪肉离体后pH值先下降后上升。随着冷藏时间的延长,长白猪和大白猪猪肉pH值的升高速度要比杜洛克猪、长杜猪(长白猪×杜洛克猪)、长大猪、大长猪的速度要慢,说明长白猪和大白猪肉的货架期较长。长白猪与大白猪正反交,对肌肉pH值影响差异不显著(P>0.05)。     

UCP3基因在巴马猪和藏猪脂肪组织中的表达和甲基化分析

为探究解偶联蛋白3（uncoupling protein 3,UCP3）基因在巴马猪和藏猪皮下脂肪组织中的表达和甲基化水平,试验采用实时荧光定量PCR技术检测UCP3基因在巴马猪和藏猪皮下脂肪组织中的mRNA表达水平;针对猪UCP3基因启动子区域（-3 580~+920 bp）,利用在线软件MethPrimer对该区域进行CpG岛预测,并采用亚硫酸氢盐测序法（bisulfite sequencing PCR,BSP）检测其甲基化水平,探究UCP3基因甲基化水平在巴马猪和藏猪中的差异。结果显示,巴马猪皮下脂肪组织UCP3基因表达量显著高于藏猪（P<0.05）;在UCP3基因启动子区预测到3个CpG甲基化岛,分别是CpG island1（-3 171~-2 928 bp）、CpG island2（-154~-2 bp）和CpG island3（+648~+806 bp）,其中CpG island1和CpG island3的甲基化水平在巴马猪和藏猪中差异较小,而藏猪CpG island2的甲基化水平（42.61%）高于巴马猪（24.49%）。本研究绘制了2个猪种CpG island2甲基化水平的黑白点图,其中CpG位点为4、8、9、10、11、12、15,藏猪甲基化频率分别比巴马猪高28.26%、17.39%、26.09%、26.09%、26.09%、23.91%和34.78%。在CpG island2处预测到3个转录因子结合位点（SP2、PPARγ和EGR1）。结果表明,巴马猪和藏猪皮下脂肪组织中UCP3基因mRNA水平的表达差异可能是由于CpG island2的甲基化水平不同所导致,藏猪DNA甲基化水平在一定程度上阻碍了转录因子与启动子调控区域的结合,从而抑制了UCP3基因的表达。     

The comparison of energy metabolism and meat quality among three pig breeds

The objective of this study was to evaluate the effects of muscle‐fibre types and hormones on glycolytic potential and meat quality traits and their association with glycolytic‐related gene expression in three different altitude pig breeds. The pig breeds studied were the Tibetan pig (TP, high altitude), the Liang‐Shan pig (LSP, middle altitude) and the Duroc × (Landrace × Yorkshire) cross (DLY, flatland). The results indicated that TP and LSP had better meat quality than DLY (P < 0.01). The glycolytic potential (GP) increased in the order of TP < LSP < DLY and decreased with time post mortem. DLY had higher glucagon and epinephrine contents than LSP and TP (P < 0.01). The proportions of myosin heavy chain muscle fibers type I in the Longissimus dorsi increased in the order of DLY < TP < LSP, whereas the proportion of type IIb increased in the order of TP < LSP < DLY. The expression of gene PKM2 played an important role in the glycolysis rate of the different genotypes. Compared with the other two pig breeds, the high‐altitude breeds had better meat quality attributes, which may be due to the slow rate of glycolysis metabolism.     

猪TLR2基因Bi-PASA遗传标记的建立及多态性研究

根据人和小鼠TLR2基因序列设计了特异性PCR引物,优化PCR条件后扩增到中国梅山猪、欧洲约克夏猪、PIC-2系及PIC-3系商品猪的TLR2基因690 bp的基因片段,并对其进行序列分析。序列分析结果显示,猪TLR2基因多态性程度低,发现在猪TLR2基因编码区第1 255位点上存在1个单碱基突变位点。利用双向特定等位基因PCR扩增法(B i-PASA)建立了检测猪TLR2基因变异的遗传标记。利用猪TLR2基因的B i-PASA标记,分析了TLR2基因在大河乌猪、撒坝猪和黔邵花猪中的基因频率和多态性。研究建立的B i-PASA遗传标记和基因变异信息,将为进一步分析猪TLR2基因变异与疾病抵抗力及经济性状的相关分析提供基础资料。     

SNP discovery, expression and association analysis for the SDHD gene in pigs

The SDHD gene was examined for single nucleotide polymorphisms (SNP) as well as for expression changes in the Longissimus dorsi muscle of commercial pigs with different potential for growth. Three SNPs, including one previously described in the coding region and two new ones in the 3'-UTR, were found. The normalized expression of SDHD was correlated with growth, meat quality and sensory traits (p < 0.05). For the commercial pigs used in this study, as well as a Berkshire × Yorkshire resource population, the SNPs have been associated (p < 0.05) with: growth, carcass composition, meat quality and sensory traits. Despite the fact that the described SNPs were not significantly associated with the normalized expression values, the SDHD SNPs and expression were associated with growth and meat quality traits in pigs.     

Characterization of MC1R and KIT Genotypes in Luchuan Pig Population

In order to assess the purity of Luchuan pig populations, four South Chinese local pig breeds including Putian Black pig, Yuedong Black pig, Dahuabai pig, Bama miniature pig and three foreign pig breeds including Duroc pig, Yorkshire pig and Landrace pig were studied as controls by sequencing of PCR products, MC1R and KIT genotypes in 56 Luchuan pigs were analyzed in this study. Sequencing results indicated that a splicing mutation (G>A) was presented in the first base in intron 17 of KIT gene in both Yorkshire pig and Landrace pig, in contrast, the wildtype GG of KIT gene was presented in Luchuan pig, four south Chinese local pig breeds and Duroc pig.Compared with Hainan wild boar, South Chinese local pig breeds had two missense mutations 95Val > Met and 102Leu > Pro in the coding region of MC1R gene;Compared with Yorkshire pig, Landrace pig and Duroc pig, South Chinese local pig breeds had 5 to 6 SNPs in MC1R gene 5'UTR, and in addtion, an A base deletion in MC1R gene 3'UTR. Furthermore, we found one litter of Luchuan pig with abnormal coat color.The results showed that the presentation of two distinct MC1R genotypes E^D1 and E^p in both litters and the sow,but only E^D1 in the boar. Considering E^p was derived from Pietrain pig, we preliminarily considered that the genome of the sow might be infiltrated with foreign pig breeds. In summary, we detected the genotypes of the coat color genes KIT and MC1R in eight pig breeds, confirmed the molecular differences of coat color between Chinese local pig breeds and foreign pig breeds, which could be useful for the further investigation of the molecular mechanism of pig coat color.     

香猪SNP位点rs80894395的多态性及其与体尺指标之间的关联研究

为了探究影响香猪生长发育的功能基因,本试验利用Illumina Porcine SNP60K芯片筛选出N-乙酰氨基半乳糖转移酶2(polypeptide N-acetylgalactosaminyltransferase 2,GALNT2)基因内含子10中一个与腹围呈弱相关的单核苷酸多态性(single nucleotide polymorphism,SNP)位点rs80894395。在此基础上应用等位基因特异性PCR(allele-specific PCR,AS-PCR)技术检测520头雌性香猪群体中该位点的基因型,并与43头大白猪、36头柯乐猪相比较。结果表明,从3个猪群体中检测到rs80894395位点的CC、CT和TT3种基因型;其中香猪群体以CT为优势基因型,且基因型与香猪的体重、体长和腹围呈弱的正相关;大白猪群体以CC基因型为主,T等位基因频率较香猪极显著减少(P<0.01);柯乐猪群体中CC与CT基因型频率相等,与香猪和大白猪的基因频率间的差异不显著(P>0.05)。生物信息学分析表明,rs80894395位点可能影响GALNT2基因的剪接过程。rs80894395与香猪的生长发育可能有一定的联系。     

Single nucleotide polymorphisms of the KIT and KITLG genes in pigs

Here, we report the variability in the KIT tyrosine kinase receptor and its ligand KITLG genes by determining single nucleotide polymorphisms (SNPs) in 384 individuals including 11 pig breeds, two synthetic-line cross pigs, two cross breeds, and one Japanese wild boar. SNPs and indels within the coding sequence regions of KITLG and KIT and their 5'-flanking regions were detected by aligning sequences from eight pigs, and subsequently the SNPs were genotyped using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS). Principal component analysis using allele frequencies in the SNP locus showed a distant relationship between Asian and Euro-American pig groups, except for Berkshire and Tokyo X breeds. These breeds were located within the mid-portion of the distribution in the first principal component. The Hampshire breed was distant from the other pig groups on the axis of the second principal component. Haplotype frequencies that were deduced using non-synonymous substitutions of the KIT gene revealed the uniqueness of Landrace, Large White, Middle White, and three-way cross pigs (LWD) and of the Hampshire breed. On the other hand, the haplotypes of KITLG and KIT detected in the Berkshire breed were prevalent in Asian pig groups. This tendency is different from that observed in other Euro-American pig breeds.