中国7个地方绵羊品种遗传多样性的微卫星分析

利用26个微卫星标记分析了中国7个地方绵羊（Ovis aries）品种的遗传多样性。通过计算基因频率、平均杂合度（H）、多态信息含量（PIC）及有效等位基因数（N_e）,并根据Nei氏标准遗传距离,利用UPGMA法进行了聚类分析,评估其种内遗传变异和品种间遗传关系。结果表明：26个微卫星位点共检测到278个等位基因,Ne 在2.1288-13.3924之间;以等位基因频率为基础,得出位点的平均杂合度在0.0629-0.5903之间,品种平均杂合度在0.3633-0.4489之间。26个位点均为高度多态位点,PIC在0.6628-0.8712之间。聚类分析表明哈萨克羊、阿勒泰羊和巴音布鲁克羊遗传关系最近;然后与白藏羊、黑藏羊聚为一类;湖羊和晋中羊聚为一类。各绵羊品种的聚类关系与其来源、育成史及地理分布基本一致。     

鳜原种群体和养殖群体遗传多样性的微卫星分析

本研究利用20对微卫星引物对鳜(Siniperca chuatsi)原种群体和养殖群体进行遗传多样性分析。结果表明,在鳜原种群体中检测到多态性位点14个,养殖群体11个。在两个群体中共检测到等位基因数96个,其中原种群体检测到等位基因数53个,每个位点的等位基因数在1～7之间,平均有效等位基因数为2.7390;养殖群体检测到等位基因数43个,每个位点的等位基因数在1～6之间,平均有效等位基因数为2.1284。原种群体的平均观察杂合度0.5708,Nei氏期望杂合度0.5295,平均多态信息含量PIC0.5353;养殖群体的平均观察杂合度0.3839,Nei氏期望杂合度0.4011,平均多态信息含量PIC0.5043。因此,与养殖群体相比,鳜原种群体仍有丰富的遗传多样性。本研究可为鳜种质资源的保护、监测和遗传育种提供分子水平上的数据。     

河南地方山羊品种的遗传多样性

采用18个微卫星位点对河南省5个地方山羊品种（牛腿山羊、槐山羊、河南奶山羊、太行黑山羊和伏牛白山羊）的遗传多样性进行了评价.结果表明：18个微卫星位点在5个山羊品种均为高度多态;5个山羊品种的多态信息含量、群体杂合度、有效等位基因数值较高,说明其遗传多样性和各品种内的遗传变异比较丰富;聚类分析显示,牛腿山羊与太行黑山羊的关系较近,与河南奶山羊的关系较远.群体遗传分化系数和群体遗传距离表明,河南省地方山羊的变异主要存在于品种内,品种间的变异相对较小.结合5个山羊品种的实际生态地理分布,提出了避免近交,并有选择地进行品种间杂交的保种模式.     

采用6个微卫星位点研究6个绵羊品种遗传多样性

利用6个微卫星座位对中国乌珠穆沁羊、小尾寒羊、滩羊、昭通绵羊、呼伦贝尔羊和甘肃高山细毛羊6个绵羊品种,共计280个个体进行遗传多样性分析。计算了6个绵羊品种间的多态信息含量、杂合度和遗传距离,并进行了主成分分析和UPGMA聚类。发现了101个等位基因,平均杂合度0.599-0.691,平均多态信息含量0.609-0.680;甘肃高山细毛羊与其他绵羊品种遗传分歧最大,而呼伦贝尔羊与乌珠穆沁羊间的分歧最小。结果表明6个绵羊品种均具有较高的遗传多样性,品种间的遗传关系与其形成历史、分化及地理分布基本一致。     

中国7个地方绵羊品遗传多样性的微卫星分析

利用26个微卫星标记分析了中国7个地方绵羊（Ovis aries）品种的遗传多样性。通过计算基因频率,平均杂合度（H）、多态信息含量（PIC）及有效等位基因数（Ne）,并根据Nei氏标准遗传距离,利用UPGMA法进行了聚类分析,评估其种内遗传变异和品种间遗传关系。结果表明：26个微卫星位点共检测到278个等位基因,Ne在2.1288-13.3924之间;26个位点均为高度多态位点,PIC在0.6628-0.8712之间,聚类分析表明哈萨克羊、阿勒泰羊和巴音布鲁克羊遗传关系最近;然后与白藏羊,黑藏羊聚为一类,湖羊和晋中羊聚为一类,各绵羊各种的聚类关系与其来源,育成史及地理分布基本一致。     

可可西里自然保护区藏羚羊的微卫星多态性研究

藏羚羊是我国特有的珍稀濒危动物,对其开展遗传多样性的研究具有非常重要的科学价值。为了获取足够的遗传信息并进一步研究藏羚羊在核基因水平上的遗传多样性,对来自可可西里地区的75个藏羚羊干皮张样本进行了微卫星遗传多样性研究。研究从来自牛和绵羊的25个微卫星基因座中筛选到9个具有高度多态性的微卫星基因座(MCM38,MNS64,IOBT395,MCMAI,TGLA68,BM1329,BMS1341,BM3501和MB066)。用非变性聚丙烯凝胶电泳检测微卫星的PCR扩增产物,计算了这9个微卫星基因座的等位基因频率、多态信息含量、基因杂合度等指标并估算了种群数量。结果在75只藏羚羊中共检测到85个等位基因,9个微卫星基因座的等位基因数为7~12个,平均每个基因座检测到9.4个等位基因,有效等位基因数为处于4.676~9.169之间,平均为6.519;基因频率分布在0.007~0.313之间,多态信息含量在0.753~0.881之间,平均为0.818;观察杂合度为0.791~0.897,平均为0.844,期望杂合度为0.786~0.891之间,平均为0.838±0.0132,各基因座观察杂合度与期望杂合度比较接近。固定指数为-0.269~-0.097,平均为-0.163。Shannon’s指数为1.660~2.315,平均为1.990。种群数量的估算结果显示这75个体均来自同一种群。结果表明该种群在核基因水平仍具有丰富的遗传多样性。     

茶花鸡群体遗传多样性

茶花鸡是我国具有独特遗传特性的地方家禽品种,为了进一步阐明其群体遗传变异和遗传结构状况,采用了33个家鸡特异性的微卫星标记对该鸡种自然群体中30个个体进行了多态性电泳检测。33个微卫星座位共检测到105个等位基因,所有座位都呈现出多态性,每个座位的等位基因数在2~5个之间,平均每个座位等位基因数3.20个。群体平均杂合度和平均多态信息含量分别为0.612 9和0.527 6。结果表明,茶花鸡自然群体遗传多样性较丰富。     

7个地方山羊品种遗传多样性及遗传结构分析

检测了7个地方山羊群体在15个微卫星位点的遗传多样性和遗传结构,旨为地方山羊群体的保护利用奠定基础。采集燕山绒山羊、辽宁绒山羊、承德无角山羊、济宁青山羊、太行山羊、武安山羊血液样品及内蒙古绒山羊的耳组织,利用微卫星方法分析遗传多样性及遗传结构。结果表明,7个山羊群体的平均有效等位基因数为4.235 8、平均期望杂合度为0.718 8、平均多态信息含量为0.706 8,均具有高度的遗传多样性;总群体平均近交系数为0.088 3,平均遗传分化系数为0.544 2,平均基因流为0.209 4。武安山羊和承德无角山羊的遗传距离最近,太行山羊和燕山绒山羊的遗传距离最远。系统进化树聚类分析表明,燕山绒山羊与辽宁绒山羊聚为一类,济宁青山羊、承德无角山羊、武安山羊、内蒙古绒山羊和太行山羊聚为一类。综上,7个地方山羊群体遗传多样性丰富,群体间遗传分化程度大,基因交流少,受近交程度影响小,具有较高的利用价值和潜力。     

我国地方鸡品种保种群微卫星多态性分析与分子标记档案的建立

利用20个微卫星标记对国家家禽品种资源基因库中保存的11个地方鸡品种保种群进行了遗传检测,计算各群体的等位基因频率、平均基因杂合度、平均多态信息含量及各群体间的遗传距离,并用类平均法进行聚类分析。研究结果表明：20个微卫星标记在11个地方鸡品种保种群共检测到176个等位基因,平均为8.8个,基因频率分布在0.013～0.838之间。检测到等位基因中,有45个等位基因为11个地方鸡品种所共有;11个地方鸡品种平均杂合度在0.6800～0.7432之间。其中藏鸡最高,为0.7432;狼山鸡最低,为0.6800;平均多态信息含量在0.6329～0.7023之间,均大于0.5,表现为高度多态性;11 个鸡品种聚为4类。丝羽乌骨鸡、茶花鸡、仙居鸡、藏鸡、萧山鸡聚为一类,鹿苑鸡、狼山鸡聚为一类,固始鸡、北京油鸡、大骨鸡聚为一类,河南斗鸡单独聚为一类;通过利用20个微卫星基因座检测不同世代群体中等位基因及其频率、群体基因平均杂合度和多态信息含量,建立地方鸡品种保种群微卫星标记档案,并分析世代间的差异,预期可以达到监测保种效果的目的。     

长江中上游两个鲢群体遗传变异的微卫星分析

对长江中上游2个鲢群体使用39个微卫星标记进行了遗传多样性分析, 计算并统计了平均观测等位基因数、平均有效等位基因数、多态信息含量、遗传杂合度、Hardy-Weinberg平衡偏离指数、遗传相似系数、遗传距离等遗传参数。结果表明: 万州鲢和监利鲢群体所检测微卫星位点的平均观测等位基因数分别为6.128和4.974; 平均有效等位基因数分别为4.107和3.395; 多态位点百分率分别为100和94.87; 39个微卫星标记共有等位基因259个, 173个等位基因为两群体所共有; 多态微卫星位点的PIC在0.077~0.865之间变动,平均为0.617; 两群体所检测位点平均观测杂合度为0.834和0.775, 平均期望杂合度为0.713和0.623; 两个群体间的遗传相似系数为0.618, 群体间的遗传距离为0.482。结果显示长江中上游两个鲢群体间存在显著遗传分化, 应隶属于不同的种群。     

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H_O) and expected (H_E) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f₄ statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.     

Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) using microsatellites

Indian goat breeds are recognized as an invaluable component of the world's goat genetic resources. Microsatellite pairs were chosen from the list suggested by International Society for Animal Genetics (ISAG) and amplified in two multiplexes (Set-I: 7 microsatellites and Set-II: 11 microsatellites) for automated fluorescence genotyping to assess bottleneck and analyze genetic variability and genetic distances within and between three goat breeds viz. Zalawadi, Gohilwadi and Surti. The observed number of alleles ranged from 4 (Oar JMP-29) to 15 (ILSTS-030 and -034) with a total of 178 alleles and mean of 9.89 alleles across the three breeds. The overall heterozygosity, PIC and Shannon index values were 0.61, 0.60 and 1.50 indicating high genetic diversity. The maximum observed heterozygosity was found in Gohilwadi and minimum in Surti goat breed. The Nei's standard genetic distance was minimum between Zalawadi and Gohilwadi, and maximum between Gohilwadi and Surti. Non-significant heterozygote excess on the basis of IAM, TPM and SMM models, as revealed from Wilcoxon sign-rank tests, along with a normal ‘L’-shaped distribution of mode-shift test, indicated no bottleneck in Zalawadi and Gohilwadi goat populations, whereas mild bottleneck in the recent past for Surti breed. This research on goat genetic diversity in Gujarat state provides valuable information on Zalawadi, Gohilwadi and Surti goat genetic resources, and will assist in developing a national plan for the conservation and utilization of indigenous goat breeds.     

中国主要地方品种猪血液蛋白遗传多样性研究

实验采用水平板淀粉凝胶电泳技术,对中国地方猪五大类型９个品种,１个引入品种共２０１个个体进行了遗传多样性分析。共分析遗传座痊３０个,其中只有ＭＤＨ、ＰＥＰＢ、Ａ从位具有多在记民生。中国主要地方猪品种的多态座位百分比Ｐ＝０．２００,平均杂２合度Ｈ＝０．０６５,平均等位基因数Ａ＝１．３００。根据基因频率采用ＰＨＹＬＩＰ３．５ｃ民计算Ｎｅｉ氏遗传距离,然后用“ＮＥＩＧＨＢＯＲ”程序分别构建Ｎｅｉｇｈｂｏ     

Genetic Variability of PRNP in Chinese Indigenous Goats

Polymorphism of the prion protein gene (PRNP) is usually associated with scrapie susceptibility or resistance. To determine the variability of PRNP in Chinese indigenous goat breeds, we isolated genomic DNA from goat blood and amplified and sequenced the coding region of the gene. We identified 10 polymorphic sites that gave rise to 28 haplotypes. Clear frequency differences were found between northern and southern breeds and confirmed by genetic distance analysis, except for the Tangshan dairy goat. Phylogeographic analysis supported the idea that northern and southern breeds might be considered separate clusters, except for the Tangshan dairy goat. The finding of significant differences in allele distribution in northern and southern goats, especially if involved in modulating resistance/susceptibility, needs to be carefully considered for the feasibility of selection plans for resistance to scrapie.     

Genetic diversity and population structure in multiple Chinese goat populations using a SNP panel

Information about genetic diversity and population structure among goat breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds. Here, we measured genetic diversity and population structure in multiple Chinese goat populations, namely, Nanjiang, Qinggeda, Arbas Cashmere, Jining Grey, Luoping Yellow and Guangfeng goats. A total of 193 individuals were genotyped for about 47 401 autosomal single nucleotide polymorphisms (SNPs). We found a high proportion of informative SNPs, ranging from 69.5% in the Luoping Yellow to 93.9% in the Jining Grey goat breeds with an average mean of 84.7%. Diversity, as measured by expected heterozygosity, ranged from 0.371 in Luoping Yellow to 0.405 in Jining Grey goat populations. The average estimated pair‐wise genetic differentiation (F_ST) among the populations was 8.6%, ranging from 0.2% to 16% and indicating low to moderate genetic differentiation. Principal component analysis, genetic structure and phylogenetic tree analysis revealed a clustering of six Chinese goat populations according to geographic distribution. The results from this study can contribute valuable genetic information and can properly assist with within‐breed diversity, which provides a good opportunity for sustainable utilization of and maintenance of genetic resource improvements in the Chinese goat populations.     

Genetic characterisation of a domestic dog<Emphasis Type="Italic">Canis familiaris</Emphasis> breed endemic to South African rural areas

Allozyme electrophoresis (horizontal starch gel and PAGE) and histochemical staining techniques were used to study the genetic composition of an endemic southern African domestic dogCanis familiaris Linnaeus, 1758, the Africanis breed. Genetic differentiation was analysed at 21 protein-coding loci. The results were compared to those for three other populations/breeds: representatives of established Western breeds, crossbred dogs of Western descent from rural areas in South Africa, and indigenous Saluki dogs from the Middle East. Nine polymorphic loci were found (Ak-1,-2, Ck, Per, Hb, Po-A-1 to-3 andPo-Tf). Two unique alleles at theCk andPo-A-2 loci separated the Africanis breed from the other groups. There were also significant differences between Africanis and the other breeds in pair-wise comparisons of allelic frequencies at polymorphic loci. An assignment test, fixation index values, gene flow and genetic distance values indicated a closer genetic association between the Africanis and Saluki breeds than with dogs of Western origin. This finding supports archaeological evidence that the endemic Africanis breed was introduced from the Middle East into Africa thousands of years ago, and not through later western influences. The average heterozygosity ranged from 0.106–0.15, with least heterozygosity in the Africanis and most in the rural crossbred group. The percentage of polymorphic loci, the mean number of alleles per locus (biologically more significant than heterozygosity), and conformation of genotypes to Hardy-Weinberg proportions showed no evidence of recent loss of genetic diversity in Africanis. Genetic differentiation and support of archaeological evidence by genetics indicate that the endemic southern African domestic dog breed is unique.     

A study on the Changthangi pashmina and the Bakerwali goat breeds in Kashmir: I. Analysis of blood protein polymorphisms and genetic variability within and between the populations

Blood samples of 483 Pashmina goats and 392 Bakerwali goats were taken from the Ladakh and Jammu provinces, respectively, for characterisation of the breeds by polymorphic enzymes and proteins. Furthermore, the sex, age, body weight and hematocrit of both breeds and the pashmina yield of Pashmina goats were recorded. Polymorphisms of 12 enzymes and proteins (albumin (Al), alkaline phosphatase (Alp), amylase (Amy), NADH-diaphorase 1 (Dia1), vitamin-D-binding protein (Gc), haemoglobin (Hb), hemopexin (Hpx), nucleoside phosphorylase (Np), malic enzyme (ME), phosphohexose-isomerase (PHI), transferrin (Tf), X-protein (X)) in blood plasma and hemolysate were determined using gel electrophoresis. Out of 12 protein systems, 10 were found to be polymorphic. In four systems (Al, Amy, Dia1, Hpx) new phenotypes were detected. To estimate the genetic variability within breeds, the degrees of heterozygosity, deviations from the Hardy–Weinberg-equilibrium (HWE) and F_IS-, F_ST-, and F_IT-values were estimated. In comparison with literature data both breeds show slightly higher variability than other goat breeds, with degrees of heterozygosity ranging from 15 to 25% and 24 to 26% in the Pashmina and Bakerwali goat populations, respectively, and the percentage of polymorphic loci ranging from 50 to 67%. On the other hand, a decrease of variability at some loci can be observed in both breeds. Deviations from HWE in combination with a deficiency of heterozygote genotypes were observed in all sub-populations apart from the Pashmina sub-population ‘Likir’. Genetic differences between the goat breeds could be quantified through calculation of Nei’s genetic distances ranging from 0.002 to 0.080. With exception of the Pashmina sub-population ‘Likir’, lower distance values were found between sub-populations within the respective breeds.     

A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array

Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5–10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.     

Genetic relationship among Mongolian native goat populations estimated by blood protein polymorphism

Several local strains and populations of goats distinguished by morphogenetic and performance characteristics are kept by goat breeders in different natural climatic regions of Mongolia, namely Bayandelger, Ulgii Red, Erchim Black, Dorgon and Zavkhan Buural. The genetic relationships among eight native goat populations in Mongolia at 33 biochemical genetic loci was assessed. A total of 440 animals in eight regional zones were studied. Twelve loci, i.e. the serum transferrin, serum amylase, serum alkaline phosphatase, serum prealbumin-3, cell esterase-D, hemoglobin (Hb) β, hemoglobin (Hb) α-II, cell peptidase-B, cell tetrazolium oxidase, cell esterase-1, cell esterase-2 and cell catalase loci, were found to be polymorphic. The data indicated that Mongolian native goats are not highly differentiated (D=0.0002–0.0038) genetically. To set Mongolian native goats in a larger context, the present data were compared with those on other goat breeds and populations in east and southeast Asia that were previously reported. The average heterozygosity in the Mongolian native goats did not significantly differ from those in other Asian goat populations and breeds. A phylogenetic tree of the gene constitution of the Mongolian native goats and other Asian goat breeds and populations was constructed and revealed that genetically the Mongolian native goats had diverged slightly from the group consisting of Chinese, Japanese, Korean and Indonesian native goats, but markedly from the Indian goat group.