采用微卫星标记分析13个中外牛品种的遗传变异和品种间的遗传关系

本研究应用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的10对微卫星引物,结合荧光–多重PCR技术,检测了10个中国地方黄牛品种和3个外来牛品种的基因型。通过计算基因频率、多态信息含量和遗传杂合度,以Nei’s遗传距离和Nei’s标准遗传距离为基础,采用非加权组对算术平均聚类法构建了聚类图,分析了13个牛品种的群体内遗传变异和群体间遗传关系。并以聚类分析和群体结构分析为基础,将13个中外黄牛品种分为三类:Ⅰ类属于普通黄牛品种,包括延边牛、沿江牛、长白地方牛、蒙古牛、阿勒泰白头牛、哈萨克牛、复州牛和西藏牛;Ⅱ类属于含有瘤牛血统的黄牛品种,包括日喀则驼峰牛和阿沛甲咂牛;Ⅲ类属于外来牛品种,包括德国黄牛、西门塔尔牛和夏洛来牛。研究结果为加强我国地方黄牛品种种质特性研究以及地方牛品种资源的保护与利用提供了科学的依据。     

利用微卫星标记分析山东地方鸡品种的遗传多样性

微卫星是近几年来应用较多的一种分子标记,可有效地进行基因鉴定与系谱分析,并可估算群体间的遗传距离。通过选用5个微卫星标记,检测了山东省5个地方鸡种：日照麻鸡、寿光鸡、莱芜黑鸡、济宁百日鸡、鲁西斗鸡以及一个外来鸡种——安卡黄鸡和一个外省地方鸡种——广西黄鸡共7个鸡种的遗传多样性。根据测试结果计算了每个等位基因的频率,以基因频率为基础分析了品种内的遗传变异和品种间的DA遗传距离,并讨论了微卫星多态性在应用于群体遗传变异及亲缘关系等方面的意义。结果表明：共检测到40个等位基因,其中等位基因数最多的位点为。ADL0136(10个);等位基因数最低的位点为ADL0146(5个);而且每个位点的等位基因分布并不均匀,都有一种或几种优势基因存在。在7个品种中,杂合度最低的为寿光鸡,杂合度值为0．3327,因为此鸡种多年来一直由寿光市慈伦种鸡场进行纯繁保种,未与其他鸡种杂交,因此杂合度最小;其他鸡种杂合度也都低于0．4,据分析可能是由于日照麻鸡、济宁百日鸡群体较小;莱芜黑鸡是正在选育的一个品种,个体间遗传关系也不远;安卡黄鸡和广西黄鸡自从引人嘉明公司后,群体近交现象普遍,因此各鸡种杂合度都偏低。由此可见,通过对杂合度的计算,微卫星可以较好地反应群体内的变异。各品种PIC值的变动范围从0．6196(寿光鸡)到0．7027(莱芜黑鸡),PIC值的大小与杂合度的高低体现了较高的一致性。对DA遗传距离的计算表明：日照麻鸡与济宁百日鸡的距离最近,而鲁西斗鸡与其他鸡种距离均较远。用UPGMA法进行聚类分析,结果7个鸡种被聚为3类：山东的4个地方鸡种寿光鸡、日照麻鸡、莱芜黑鸡与济宁百日鸡聚为一类;安卡黄鸡和广西黄鸡聚在一起;鲁西斗鸡独自为一类。这与几个鸡种的分化与选育历史是一致的,因此聚类图能够比较正确地反映7个品种之间的亲缘关系。     

利用微卫星标记分析四川8个地方鸡品种遗传多样性

通过选用30个多态性较好的微卫星标记,检测了四川省8个地方鸡品种：峨嵋黑鸡、泸宁鸡、旧院黑鸡、米易鸡、石棉草科鸡、凉山崖鹰鸡、兴文乌骨鸡、沐川乌骨鸡的遗传多样性。利用等位基因频率计算出各群体的平均遗传杂合度（H）、多态信息含量（PIC）和群体间的DA遗传距离。结果表明：30个微卫星位点中有24个微卫星位点在8个鸡群体中的多态信息含量均为高度多态,可作为有效的遗传标记用于各鸡品种的遗传多样性和系统发生关系的分析。各鸡种的杂合度都较高,平均杂合度范围是0.629~0.681,最高的是泸宁鸡（0.681）,最低的是旧院黑鸡（0.629）。据分析可能是由于交通闭塞,形成了家禽品种的多种多型,而且杂合度的高低与PIC值的大小体现了较高的一致性。对DA遗传距离的计算表明：用UPGMA法进行聚类分析,结果8个鸡品种被聚为3类：Ⅰ类：峨嵋黑鸡、米易鸡、泸宁鸡、旧院黑鸡聚为一类。米易鸡、泸宁鸡先聚在一起,然后又与峨嵋黑鸡在较近的距离聚在一起,然后再与旧院黑鸡聚在一起;Ⅱ类：石棉草科鸡、兴文乌骨鸡、沐川乌骨鸡聚为一类。兴文乌骨鸡、沐川乌骨鸡在较近的距离聚在一起,然后又与石棉草科鸡在较近的距离聚在一起;Ⅲ类：凉山崖鹰鸡独自聚为一类。这与几个鸡品种的来源、分化、选育历史及地理分布是一致的。     

利用微卫星DNA标记研究绒山羊群体遗传多样性

利用7个微卫星标记对4个绒山羊品种共计18个个体的遗传多样性进行了分析和研究。计算了有效等位基因数、遗传杂合度、遗传距离等,分析了群体相关的遗传变异。结果表明,辽宁多绒山羊的有效等位基因数最大,杂合度最高;而辽宁绒山羊的有效等位基因数最小,杂合度最低。奈氏遗传距离表明,库布齐杂种绒山羊和辽宁多绒山羊的亲缘关系最近,而和阿尔巴斯绒山羊的亲缘关系最远。     

三个虹鳟养殖群体遗传结构的微卫星分析

利用20个微卫星标记对3个虹鳟(Oncorhynchus mykiss)养殖群体进行遗传结构分析。结果表明,(1)3个群体检测的平均等位基因数为3·6～4·1,平均观测杂合度为0·5224～0·6328,平均期望杂合度为0·4736～0·5522,平均多态信息含量为0·4354～0·5084,说明这几个群体多态性属于偏高水平,遗传多样性高。通过d值,确定了Hard-Weinberg平衡的偏离情况,发现AY039638、AY039646在3个群体中都表现为不平衡。对3个群体的遗传距离进行了估算,并进行聚类分析,本溪的两个群体先聚为一支,再与渤海群体相聚,显示出明显的地理特征。(2)本溪虹鳟群体在位点AF352770出现部分等位基因消失的现象;AF352754在本溪群体中表现为位点消失,可作为区分本溪群体和渤海群体的分子标记。(3)综合评价3个群体,渤海站虹鳟群体的遗传多样性最高,与前人研究结果一致。     

用6个微卫星座位研究BMY牛和婆罗门牛的遗传多样性和群体遗传结构

 对6个牛微卫星座位的遗传变异及多态性分析,以期了解BMY牛和婆罗门牛的群体遗传结构与育成情况。6个微卫星座位的多态信息含量为在0.524～0.752间,BMY牛、婆罗门牛两个群体的平均期望杂合度和观察杂合度值接近,分别为0.737 6和0.739 6,0.641 2和0.653 7,进入横交固定第二世代的BMY牛期望杂合度值较高,这与我们的育种进展相符。红安格斯的期望杂合度较低(0.460 9)接近日本和牛0.471,暗示红安格斯牛的同质性较高。                       

两广和云贵川等地区黄牛的微卫星标记遗传多样性栽

选择12对微卫星DNA标记,采用荧光-多重PCR技术,对11个中外黄牛品种的等位基因数、基因频率、多态信息含量和遗传杂合度进行分析,以Nei's遗传距离为基础,采用非加权组对算术平均法构建了聚类图。结果表明,11个黄牛品种首先分为中外两大类:Ⅰ类是我国地方黄牛品种,Ⅱ类是3个引进品种,其中8个地方黄牛品种又可分为两个分支,云贵川高原地区的5个品种关岭黄牛、昭通黄牛、宣汉黄牛、凉山黄牛和川南山地牛聚为一支,两广与江西的3个品种涠州黄牛、徐闻牛和吉安黄牛聚为另一支,两分支聚类与品种的地理分布区域相吻合。     

采用微卫星标记分析10个双峰驼群体的遗传变异和群体间的遗传关系

为从分子水平上对我国双峰驼(Camelus bactrianus)群体的遗传多样性、群体间遗传关系、群体遗传分化及近交情况进行全面、系统地研究,为双峰驼种质资源保护和新品种培育提供基础数据,本文利用18对微卫星引物,分析了我国9个双峰驼群体和1个蒙古双峰驼群体的遗传多样性和遗传关系。结果显示:10个群体均具有较高的遗传多样性,共检测到242个等位基因,平均等位基因数为13.44,平均有效等位基因数为4.18,平均观察杂合度(Ho)为0.5528。10个群体间存在显著的遗传分化,有9.6%的遗传变异来自群体间,90.4%的遗传变异来自群体内部的个体间。聚类分析、主成分分析和群体遗传结构分析结果都表明10个群体被分成2个明显的分支,新疆4个群体单独聚为一类,剩下的6个群体聚为一类。这一结果可能与它们的地理分布和群体间的地理屏障有关。     

微卫星标记分析罗非鱼群体的遗传潜力

利用25个微卫星标记,对奥利亚罗非鱼2个群体["夏奥1号"(ZA)、广西群体(GA)]和尼罗罗非鱼4个群体[埃及品系(ZN)、88品系(XN)、广西群体(GN)、美国品系(MN)]进行检测。共检测到7 775个扩增片段,长度在100~400 bp;等位基因数3~8个不等,共计143个等位基因;平均每个基因座扩增得到5.72个等位基因。各群体平均观测杂合度(H o)在0.7253~0.8160之间,平均期望杂合度(He)在0.5146~0.6834之间,平均多态信息含量(PIC)在0.4212~0.6105之间,平均有效等位基因数(A e)在2.20~3.23之间。ZA与GA遗传相似系数最高(0.9130),ZA与ZN遗传相似系数最低(0.4352)。总的说来,4个尼罗罗非鱼群体的遗传潜力较高,2个奥利亚罗非鱼群体的遗传潜力适中。     

黄颡鱼微卫星标记的筛选及三个野生群体的遗传结构分析

为了探明长江中上游流域黄颡鱼野生群体的遗传多样性状况和遗传结构,本研究采用磁珠富集法筛选出10个黄颡鱼微卫星标记,并利用其对长江中上游流域3个黄颡鱼(Pelteobagrus fulvidrac)野生群体(赤水群体、乐山群体、洞庭群体)的遗传结构进行分析。获得65个阳性克隆并测序,得到36个含有微卫星的序列,设计并合成了22对微卫星引物,经筛选得到10对多态性稳定的引物,其中高多态性位点6个,中多态位点3个。每对引物等位基因数2-9个,平均4.8。3个群体(赤水、乐山和洞庭)的平均多态信息含量(PIC)分别为0.5438、0.4568和0.3965,平均有效等位基因(Ne)分别为2.9928、2.5401和2.1713,平均期望杂合度(He)分别为0.6280、0.5277和0.4757,表明这3个群体遗传多样性水平较高,其中赤水群体遗传多样性最高,洞庭群体最低。种群分化指数(Fst)和遗传距离(Ds)分析表明,洞庭群体和乐山群体之间的亲缘关系最近,而与赤水群体的亲缘关系最远。聚类分析显示,乐山群体和洞庭群体聚为一支,赤水群体单独聚为一支。     

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers

Twenty-seven domesticated yellow cattle breeds of China and three introduced cattle breeds were analysed by means of 30 microsatellite markers to determine the level of genetic variation within and among populations as well as the population structure. In all, 480 microsatellite alleles were observed across the 30 breeds with the mean number of alleles per locus of 9.093 for native breeds and 6.885 for the three introduced breeds. Mean F -statistics (0.08) for Chinese native cattle breeds implied that 92% of the total genetic variation was from genetic differentiation within each breed and 8% of the genetic variation existed among breeds. A phylogenetic tree was constructed based on Nei's genetic distances, and three clusters were obtained. According to the tree, the three introduced breeds were distinct from the 27 native breeds. The indigenous cattle breeds were divided into two clusters, one cluster including five humpless breeds and the other cluster containing 22 humped breeds. This study identifies multiple origins of yellow cattle of China from Bos taurus and Bos indicus . Furthermore, population structure analysis implies that there are possibly five independent original domestications for yellow cattle in China. Four of five origins were four different Bos indicus types, mainly in areas of the Chang Jiang, the Zhu Jiang River basin, the Yellow River and the Huai River basin. The other origin was for Bos taurus type of Mongolian descent, mainly located in Northwestern China, the Mongolian plateau and Northeastern China or north of the Great Wall.     

Analysis of genetic diversity and population structure of Chinese yak breeds （Bos grunniens） using microsatellite markers

Nine Chinese yak breeds (Maiwa,Tianzhu White,Qinghai Plateau,Sibu,Zhongdian,Pall,Tibetan High Mountain,Jiulong,and Xin-jiang) and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations,genetic relationship between populations,and population structure for each breed.A total of 206 microsatellite alleles were observed.Mean F-statistics (0.056) for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds.The Neighbor-Joining phylogenetic free was constructed based on Nei's standard genetic dis-tances and two clusters were obtained.The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together.The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one clus-ter includes yaks from Tibet Autonomous Region and Qinghai Province,one cluster combines Zhongdian,Maiwa,and Tianzhu White,and Jiulong and Xinjiang come into the third cluster.Pali was mainly in the first cluster (90%),Jiulong was mainly in the second cluster (87.1%),Zhongdian was primarily in the third cluster (83%),and the other yak breeds were distributed in two to three clusters.The Gayal was positively left in the fourth cluster (99.3%).     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

Genetic relationships of five Indian horse breeds using microsatellite markers

The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.58 ± 0.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's D_A genetic distance of 0.071 and 0.186, respectively. In a Nei's D_A genetic distances based neighbour joining dendrogram of these breeds and a Thoroughbred horse outgroup, the four pony breeds of Spiti, Bhutia, Manipuri and Zanskari clustered together and then with the Marwari breed. All the Indian breeds clustered independently from Thoroughbreds. The genetic relationships of Indian horse breeds to each other correspond to their geographical/environmental distribution.     

The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data

Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.     

Evaluation of the genetic diversity and population structure of Chinese indigenous horse breeds using 27 microsatellite markers

We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou–Luoping pair to 0.064 for the Jingjiang–Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai‐Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis.     

应用微卫星标记分析中国地方鸡种的遗传变异

利用 8个微卫星位点对中国 9个地方鸡种和 1个引进品种进行了遗传检测。计算出了各品种的平均杂合度、平均多态信息含量 (PIC)及品种间的遗传距离 ,并进行了系统聚类。结果表明 :8个微卫星位点上共检测到了5 4个等位基因 ,每个位点上平均为 6 .75个。各位点平均多态信息含量为 0 .5 0 71～ 0 .74 34,均表现出了高度多态性。各群体平均杂合度较高 ,为 0 .5 5 6 4～ 0 .7135 ,说明我国地方鸡种有着较丰富的遗传多样性。地方鸡种间的遗传距离相对较远 ,10个鸡种共分为三大类。研究结果对我国鸡种资源的评估、保存和预测杂种优势具有一定的指导意义     

Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds

The polymorphism of 23 microsatellites in the four main cattle breeds in Belgium (Holstein Friesian, Belgian Blue, Belgian Red Pied and East Flemish) was analysed. Heterozygosity, polymorphism information content, the effective number of alleles, exclusion probability and the probability of genotypic identity for two random individuals were calculated for all microsatellites and all breeds. The Belgian Blue breed is generally a little less polymorphic in comparison with the other three breeds. Estimates of the genetic distances between these breeds confirmed the widely accepted proposition that the Belgian Blue is the most genetically distinct of these breeds. The three other breeds are likely to become one population, given current breeding strategies. Exclusion probabilities in parentage control cases are >0·9999 in all four breeds when all 23 microsatellites are used and >0·98 with only the two most polymorphic multiplexes.