晋南牛与部分地方黄牛之间遗传多样性分析

旨在利用微卫星技术检测晋南牛、郏县红牛、鲁西牛和秦川牛四大地方黄牛的牛群遗传多样样及遗传结构。采用16个微卫星DNA标记对4个牛群进行检测分析。16个微卫星DNA标记中,除HEL9位点在所有牛群中呈单态外,其他15个位点的有效等位基因数为2~8个,平均有效等位基因数为3.067 6个。BM1818为低度多态(PIC=0.083 0,PIC0.25),其余位点均为高度多态(PIC0.5),其中HUAT24多态性最大(PIC=0.727 5)。4个牛群共检测到80个等位基因,其中晋南牛为63个,郏县红牛为65个,鲁西牛65个,秦川牛68个。在IDVGA46位点,仅有晋南牛有B等位基因,而在TGLA44位点,仅有晋南牛没有B等位基因。4个牛群的平均表观杂合度为0.385 2,平均期望杂合度为0.640 3,平均杂合度为0.578 0。晋南牛在NJ树上单独聚为一支,与鲁西黄牛、郏县红牛及秦川牛的遗传距离分别为0.809 3、0.759 8、0.807 1。结果表明,晋南牛遗传资源独特,群体遗传多样性丰富,是一个生长进化上较为封闭的群体。     

利用微卫星DNA标记分析槟榔江水牛群体遗传特征

槟榔江水牛是近年在我国云南西部发现的第一个本土河流型水牛.为了揭示其群体遗传多样性、群体遗传组成、其与河流型和沼泽型水牛的遗传关系及沼泽型水牛对该水牛的基因渗入等重要遗传背景信息,本研究采用30个微卫星DNA标记对141份槟榔江水牛样品和对照群体24份河流型水牛(摩拉水牛)样品、41份沼泽型水牛(滇东南水牛)样品进行了检测分析.结果,在槟榔江水牛群体中共检测到253个等位基因,其中,54个为3个群体所共享的等位基因,58个为只在槟榔江水牛与摩拉水牛间共享的等位基因,73个为只在槟榔江水牛与滇东南水牛间共享的等位基因,其余68个等位基因为该群体所独有.槟榔江水牛平均等位基因数、平均表观杂合度、平均期望杂合度和多态信息含量等参数均显著高于对照组群体,分别为8.433 3、0.640 5、0.600 9和0.594 7.该水牛群体近交系数FIS值为0.061 9.槟榔江水牛与摩拉水牛间的DA遗传距离为最小(0.114 4),在NJ树上聚为一支;而滇东南水牛与槟榔江水牛和摩拉水牛间的遗传距离较大(分别为0.382 9和0.555 3),其在NJ树上单独聚为一支.群体遗传结构分析显示,槟榔江水牛遗传组分为河流型与沼泽型2种类型水牛混合的模式(当K=2时),整个群体中有相当数量的个体存在沼泽型水牛的遗传渗入(群体中沼泽型水牛遗传组分为0.067 2).结果揭示,槟榔江水牛遗传资源独特,群体遗传多样性丰富,但该群体杂合子缺乏,且存在一定沼泽型水牛的基因渗入.     

闽南黄牛的微卫星多态性研究

：用8个微卫星标记对闽南黄牛的等位基因频率、多态信息含量、杂合度和有效等位基因数等指标进行统计分析,并在此基础上对其进行聚类分析和分类研究。结果：8个微卫星标记在所检测的闽南黄牛群体中都表现出较丰富的多态性,在4个群体8个微卫星座位共有58个等位基因,每个微卫星标记平均检测到7．2个等位基因（3～11）;8个微卫星标记的平均多态信息含量（PIC）为0．6471,各群体的平均多态信息含量（PIC）差并不显著;全部群体平均杂合度为0．2930;各群体平均有效等位基因数为3．37。此表明闽南黄牛在微卫星位点上具有丰富的遗传多样性;根据奈氏标准遗传距离进行UPGMA聚类分析,结果表明4个群体间的遗传变异不大。     

河流型水牛尼里-拉菲和摩拉水牛群体遗传结构分析

为了对摩拉水牛、尼里-拉菲水牛进行合理有效的保护,研究其遗传多样性,掌握其遗传背景,试验利用15个微卫星位点对96个个体(尼里-拉菲、摩拉水牛各48头)进行遗传多样性检测。结果表明:在尼里-拉菲水牛15个微卫星位点上共检测到92个等位基因,平均等位基因为6. 133 3,平均有效等位基因为2. 942 3,平均多态信息含量(PIC)为0. 565 5,平均期望杂合度值为0. 618 4;在摩拉水牛15个微卫星位点上共检测到76个等位基因,平均等位基因为5. 133 3,平均有效等位基因为2. 545 4,平均PIC为0. 493 7,平均期望杂合度值为0. 541 3。说明摩拉水牛、尼里-拉菲水牛群体的遗传多样性比较丰富,尼里-拉菲水牛群体的遗传多样性高于摩拉水牛群体。     

微卫星标记测定湘西黄牛杂交牛的遗传多样性及其与生产性能的相关性研究

通过6对微卫星DNA标记对湘西黄牛及其与安格斯、夏洛来、利木赞和西门塔尔牛的杂交牛进行了遗传多样性分析,以期了解湘西黄牛及其杂交牛的群体遗传结构和育成情况.通过计算多态信息含量(PIC)、平均杂合度(H),评估湘西黄牛遗传变异和各杂交品种间遗传相关.结果表明,6个微卫星座位共检测到52个等位基因,平均等位基因数为8.67个;6个微卫星座位的多态信息含量在0.6858～0.8576间.表现出较为丰富的信息含量;4个杂交品种与湘西黄牛之间的遗传距离为0.1620～0.2554;杂交牛与湘西黄牛间遗传距离与杂种优势率的相关系数为0.9142,平均基因杂合度与杂种优势率的相关系数为0.8517,呈高度正相关.结果表明,有效微卫星标记的利用能有效的测定湘西黄牛杂交牛的遗传多样性,提高其生产性能.     

第四部分大通牦牛、甘南牦牛微卫星变异的比较研究

为深入了解青藏高原高寒牧区优势畜种--牦牛的种质特性,以青海省大通种牛场为试验基点,探讨了在完全放牧条件下,大通牦牛的生长发育规律.结合实际称重,采集循环血样,分析了血液17种生理生化指标动态及其与生长发育的关系.在分子标记层次,以欧洲15个普通牛品种的有关资料为参照,比较研究了大通牦牛群体、甘南牦牛群体和3头野牦牛的13种微卫星座位的变异,揭示了大通牦牛群体遗传结构,为开发利用牦牛遗传资源提供了科学参考资料.(四)大通牦牛、甘南牦牛微卫星变异的比较研究用联合国粮农组织动物遗传学会(ISAG-FAO)推荐的13种普通牛种的微卫星标记、以已分型的15个欧洲普通牛品种的相应资料作参照,研究了大通牦牛(青海环湖型)、甘南牦牛(青藏高原型)和3头野牦牛的遗传多样性.结果表明,牦牛的全部13种微卫星座位的等位基因或多或少与普通牛相应座位的等位基因分布发生重叠,说明两牛种在上述座位的侧翼碱基序列是较为保守的.与普通牛相比,两个牦牛群体的所有座位同样显示了高度多态性.每个座位等位基因数的范围为4～8个,平均5.462个,略低于普通牛平均数6.515个,可能与对普通牛微卫星的选择有关.在两个牦牛群体间,等位基因片段范围、高频等位基因、等位基因数等非常相似.两个牦牛群体的观察基因杂合度平均值分别为0.639和0.665,与其无偏期望基因杂合度平均值0.676和0.651相近.除HEL5(2个群体类型)和BM1824(环湖型)座位外,其余座位皆处于哈德-温伯格平衡状态.两个牦牛群体的Nei's标准遗传距离Ds等于0.032 4,这一数值甚至比15个欧洲普通牛品种中最小的两个品种的标准遗传距离Ds(0.0662)还小一半.在检测的13个座位中,3头野牦牛共发现42个等位基因,野牦牛的等位基因在大通牦牛群体中平均有92.1%的分布,在甘南牦牛群体中有84.7%的分布.上述结果表明,核基因组微卫星层次的遗传变异比线粒体DNA的遗传变异更丰富.牦牛群体遗传多样性丰富、群体间遗传距离较小,反映了现在的家牦牛,依然是一个培育程度很低的"自然群体",牦牛在漫长的进化历程中产生的遗传变异较为保守,频繁的基因交流、较大的畜群规模和随机交配方式,能使群体产生遗传差异的漂变作用难以发挥,是导致牦牛群体间遗传结构较为相近,遗传距离较小的主要原因.通过对13个微卫星座位的研究分析,足以揭示出牦牛与普通牛的种间遗传差异.     

利用微卫星DNA多态性预测半番鸭的杂种优势

为探究微卫星DNA多态性与鸭肉用性能杂种优势的相关关系,选取10对微卫星标记对金定鸭、樱桃谷鸭、F1(樱桃谷鸭×金定鸭)和番鸭进行遗传多样性检测。利用ONEDscan、GENEPOP、Mstools软件对目的基因进行分型,计算遗传多样性参数以及群体间标准遗传距离,并测定半番鸭各杂交组合F1代体重杂种优势。结果表明:在4个鸭群体共检测到52个等位基因,金定鸭、F1(樱桃谷鸭×金定鸭)、樱桃谷鸭与番鸭群体间标准遗传距离分别为0.57678、0.52220、0.46356,樱桃谷鸭与金定鸭遗传距离为0.38949。并根据遗传距离,采用对数曲线模型对半番鸭体重杂种优势进行了预测,χ2检验结果显示,预测结果与实验测定结果无显著性差异,表明本研究建立的根据微卫星DNA多态性预测半番鸭部分生长阶段体重杂种优势是可行的。     

荣昌猪和两种小型猪遗传背景的微卫星分析

荣昌猪是我国优良地方品种,巴马香猪和贵州小型香猪为我国独特小型猪品系。本研究采用美国猪基因组协作计划推荐的19个微卫星标记对荣昌猪、荣昌猪B系、巴马香猪、贵州小型香猪及外来猪种大白猪进行了遗传学检测和分析。结果表明:19个微卫星位点在群体中均表现为多态,每位点等位基因数10~23个。5个猪种中荣昌猪B系的遗传多样性最高,荣昌猪次之;2种小型猪的遗传多样性较低,其中巴马香猪的等位基因数(121个)略大于贵州小型香猪(114个),但其遗传多样性指数(平均期望杂合度0.6535±0.0347)小于贵州小型香猪(0.6919±0.0227),反映了巴马香猪较低的基因杂合度和较小的遗传变异;大白猪的遗传多样性最低。从品系的共有等位基因来看,荣昌猪B系基因背景组成中其亲本品系荣昌猪所占比例(30.22%)要大于大白猪(24.37%);大白猪和其他4个猪群体的共享等位基因数均较低(21.24%~25.12%);巴马香猪和贵州小型香猪之间共有等位基因数最高(45.06%)。采用基于遗传距离的NJ法和基于基因频率的最大似然法进行系统聚类,除了大白猪明显为独立分支及荣昌猪B系表现出较远的聚类关系外,其他3个猪种间的聚类有所不同。     

利用微卫星DNA多态性预测引进肉用绵羊品种杂种优势

旨在利用微卫星DNA在不同绵羊群体中的多态性预测引进肉用绵羊品种与地方绵羊品种的杂种优势。利用23个微卫星基因座对4个国外引进肉羊品种及3个地方绵羊品种的群体多态信息含量、有效等位基因数、杂合度和遗传距离进行遗传检测,并测定引进肉羊与地方肉羊品种的杂交效果。结果,23个微卫星座位在7个绵羊群体中均呈现高度多态,共检测到348个等位基因,平均每个座位等位基因数为15个;多态信息含量在0.532 1~0.936 1,有效等位基因数在2.572 8~9.345 8,平均杂合度在0.549 2~0.936 0,品种平均杂合度在0.714 2~0.829 5,可以用于绵羊遗传多样性的评估。从不同品种看,无角陶赛特的遗传变异最大,而小尾寒羊的遗传变异相对较小;经遗传关系分析,在引进的4个肉羊品种中,与小尾寒羊、蒙古羊及滩羊杂交优势由大到小依次为白萨福克、波德代、无角陶赛特、特克赛尔,与实际杂种优势测定结果一致。利用微卫星DNA多态性预测引进肉用绵羊品种与小尾寒羊、蒙古羊及滩羊的杂种优势是可行的,这将对今后绵羊育种具有重要的应用价值和指导意义。     

新疆地方斗鸡遗传多样性的微卫星分析

本试验利用8个微卫星座位分析了新疆3个地方（吐鲁番、喀什和伊犁）斗鸡群体的等位基因频率、多态信息含量、基因杂合度和有效等位基因数等群体遗传变异参数。结果表明,3个地方斗鸡的8个微卫星座位共检测到77个等位基因,多态信息含量（除伊犁斗鸡ADL0298位点外）均大于0.5,表现高度多态信息,群体间平均遗传距离为0.2866。因此,所选取的微卫星位点可用于新疆3个地方斗鸡的群体遗传多样性分析。     

Genetic diversity analysis of two buffalo populations of northern India using microsatellite markers

The genetic diversity in two buffalo populations of northern India, the Bhadawari and the Tarai was assessed using a set of 22 heterologous (bovine) microsatellite markers. The average number of alleles across all loci in both populations was found to be 4.7, indicating that this set of 22 bovine microsatellite markers could be used to study genetic variation in buffalo species also. The overall polymorphic information content (PIC) value for these markers was 0.54. The average observed and expected heterozygosities for both populations were 0.59 and 0.64, respectively. Common alleles with varying allele frequencies in both populations also represented the genetic variability existing between Bhadawari and Tarai buffaloes. However the θ estimates for population differentiation indicated low levels of differentiation between the two populations. This was further supported by the low genetic distance (0.155) between Bhadawari and Tarai, which was calculated using Nei's standard genetic distance method. The present study on Bhadawari and Tarai populations represents a much‐needed preliminary effort that could be extended to other local buffalo populations of India as well.     

Genetic analysis of Mexican hairless pig populations.

The main Creole pig population in Mexico, the hairless Mexican pig, remains as an unimproved and endangered genetic resource. In order to learn more about the genetic characteristics of this pig population, we assessed the allele frequency of 10 microsatellite loci in 177 unrelated hairless pigs from seven regions at Mexico and in 111 pigs of four commercial breeds (Landrace, Large White, Hampshire, and Duroc). Genetic diversity in each population was estimated by the unbiased average heterozygosity and the allele number. Nei's standard genetic distances and a neighbor-joining dendrogram were used to reveal the genetic relationships among these populations. In this report, we present data showing that the level of the genetic diversity in Mexican hairless pigs is high compared with previous reports, and that they belong to a genetic lineage divergent from commercial breeds. Furthermore, Mexican hairless pigs seem to have developed several genetically distinct lines associated with their geographic location. We conclude that the Mexican Creole pig populations may be a reservoir of genetic diversity that is important to preserve and evaluate as a source of new alleles for the future improvement of commercial pig lines.     

Evaluation of genetic variability and mutation drift equilibrium of Banni buffalo using multi locus microsatellite markers

The present study was conducted to evaluate genetic diversity of Banni buffalo and its relationship/differentiation with Murrah using genotypic data on 24 heterologus bovine specific microsatellite marker loci. A total of 138 alleles were observed with a mean of 5.75 alleles/locus across two populations. The mean observed and expected heterozygosities were found to be 0.441 and 0.572 respectively in Banni buffaloes while it was 0.464 and 0.610 respectively in Murrah buffaloes. The average heterozygosity deficit was significantly positive with substantially higher values observed in Banni (22.3%) and Murrah (24%) buffalo populations. Banni buffalo population, when evaluated for mutation drift equilibrium revealed significant heterozygosity excess under IAM while no such excess was observed under SMM and TPM. The qualitative graphical test revealed a normal L-shaped distribution of allele frequencies indicating the absence of genetic bottleneck in Banni buffaloes. The mean estimates of F-statistics over all the loci were 0.376 for F_IT, 0.187 for F_ST and 0.232 for F_IS respectively. Analysis of molecular variance (AMOVA) revealed 18.95% of the total variation being explained by between breed differences while 14.36% of the variation explained differences between individuals within each breed. Genotype assignment test revealed distinct clustering of Banni and Murrah buffaloes. Genetic distance was estimated using three different methods, the results of which revealed considerable genetic differentiation between these two buffalo populations. The divergence time between Banni and Murrah buffaloes was estimated to be around 7286 years. The results of the present study may be helpful in decision making for conservation programs as Banni buffalo population is on decline.     

Genetic and demographic bottleneck analysis of Indian camel breeds by microsatellite markers

The genetic and demographic bottleneck analysis of Indian camel breeds was carried out utilizing 40 microsatellite markers. Allelic polymorphism was observed at 20 loci in the Indian dromedary breeds. A total of 66 alleles were scored. The average number of alleles, expected heterozygosity and polymorphic information content were, respectively, 3.25?±?0.27, 0.56?±?0.04 and 0.49?±?0.04 in Bikaneri; 3.25?±?0.25, 0.53?±?0.03 and 0.46?±?0.03 in Jaisalmeri; 3.0?±?0.21, 0.53?±?0.04 and 0.45?±?0.03 in Kachchhi and 3.1?±?0.19, 0.51?±?0.03 and 0.44?±?0.03 in Mewari breed. Higher genetic variation was observed in most numerous Bikaneri breed. Genetic distances were least between the breed pair Bikaneri and Jaisalmeri which was closely placed with the Kachchhi breed. The Mewari camels had relatively higher genetic distance from the other three Indian dromedary breeds. The bottleneck analysis revealed the presence of genetic bottleneck in all four breeds of Indian dromedary. However, the qualitative graphical method resulted in normal L-shaped distribution of allele frequencies in Jaisalmeri breeds and shifted mode in Bikaneri, Kachchhi and Mewari breeds. The demographic bottleneck analysis revealed minimum reduction (?9.65 %) in the population of camels in Jaisalmeri breeding tract as compared to that of Bikaneri (?14.18 %), Kachchhi (?27.78 %) and Mewari (?32 %) breeding tracts. Conclusively, the genetic bottleneck analysis could explain the demographic bottleneck in the Indian dromedary populations. Therefore, appropriate conservation and improvement efforts are needed in all four dromedary breeds with immediate attention on Mewari and Kachchhi breeds. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in the Indian dromedary populations.     

Genetic relationship and diversity analysis of Indian water buffalo (Bubalus bubalis)

The water buffalo (Bubalus bubalis) is an important dairy animal on the Indian subcontinent and in Southeast Asian countries. The diversity and differentiation among 12 populations or breeds of buffalo were studied. Data were generated and analyzed from 527 animals belonging to 10 recognized breeds and 2 additional populations of Indian buffalo by using 22 microsatellite loci. Relationships among buffalo breeds and populations were estimated based on genetic distances. The Bayesian analysis grouped 12 populations into 8 distinctive clusters. Geographically close breeds clustered together, except for the Jaffarabadi and Murrah, which were not in geographic contiguity. The Mantel test revealed nonsignificant correlations between genetic and geographic distances. This supports the hypothesis that buffaloes have been domesticated at different places for specific purposes. The phylogenetic relationship based on microsatellite loci supported the breed classification based on body size. The Toda breed, which is considered to be endangered, had genotypes similar to those of the surrounding buffalo populations.     

Biodiversity in Mediterranean buffalo using two microsatellite multiplexes

The present study was carried out to investigate genetic diversity in Nile-Delta and Southern-Egypt buffalo populations in comparison with the Italian buffalo utilizing two microsatellite multiplexes. A total of 104 animals classified into three groups were used, 28, 38 and 38 representing the Nile-Delta, Southern-Egypt and Italian buffalo, respectively. The 15 studied microsatellites were CSSM38, CSSM70, CYP21, CSSM42, CSSM60, MAF65, BM0922, CSSM19, INRA006, ETH02, BM1706, BMC1013, CSSM47, INRA026 and CA004. All studied microsatellites showed allelic polymorphism. Number of polymorphic alleles ranged between 4 alleles (CSSM38, CSSM70 and CYP21) and 11 alleles (CA004). Pairwise Chi-square test for Nile Delta and Southern Egypt showed significant differences in allelic distribution at five loci, CSSM70, CSSM38, BM0922, ETH02 and BM1706. Italian buffalo showed the lowest percentage of observed heterozygotes (65%), while the Southern Egypt showed the highest (71%). Both the Italian and the Delta populations deviated significantly (P < 0.05) from HW equilibrium. Italian buffalo is relatively the most inbred population while the Southern-Egypt buffalo is the only outbred population. High level of genetic differentiation (F_ST estimates) between the Italian group and each of the Delta and Southern-Egypt group (0.083 and 0.076, respectively) was observed while Southern-Egypt group showed a lower level of genetic differentiation with the Delta group (0.014). Italian buffalo had the greatest genetic distance values with the two Egyptian groups (0.25 and 0.23) while much lower values between the Southern-Egypt and the Delta groups (0.06) was observed. Genetic variation between the Italian buffalo and the Egyptian buffalo was detected in 14 (out of 15) microsatellite loci. While a lower level (than that between Egyptian and Italian) of genetic variation between Southern-Egypt and Delta buffalo populations was expressed by 5 loci. It was concluded that the Southern-Egypt buffalo could be considered as distinct population from the Delta buffalo. In addition, Southern-Egypt group, being the only group with non-significant global deviation from HW equilibrium, the most heterozygous, and the only outbred population as well, is expected to respond more favorably to selection.     

Genetic analysis of Mexican Criollo cattle populations

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.     

沼泽型水牛微卫星DNA的遗传多样性分析

为探究中国沼泽型水牛品种或类群的遗传多样性,本研究采用了沼泽型水牛30个微卫星标记结合LabChip芯片检测法对德昌水牛、德宏水牛、温州水牛、贵州水牛、西林水牛、富钟水牛及两个引进品种摩拉水牛、尼里－拉菲水牛等40个样本进行了检测和遗传多样性分析。结果表明,在30个微卫星DNA标记上共发现332个等位基因,平均基因多样性和PIC值分别为0.7808和0.7554。聚类分析结果显示,德宏水牛和德昌水牛先聚为一类,随后与富钟水牛、贵州水牛、温州水牛、西林水牛聚为一类;摩拉水牛与尼里－拉菲水牛聚为一类。本研究证实了所选的30个沼泽型水牛微卫星DNA标记可作为有效的遗传标记用于水牛品种间的遗传多样性分析,同时也丰富了当前的水牛微卫星标记资源。     

Genetic Diversity Analysis of Microsatellite DNA Markers in Swamp Buffalo

This study was aimed to investigate the genetic diversity of swamp buffalo breeds in China.The analysis of genetic diversity was performed in 40 buffalo individuals from 8 buffalo breeds（Dechang buffalo,Dehong buffalo,Wenzhou buffalo,Guizhou buffalo,Xilin buffalo,Fuzhong buffalo,Murrah buffalo and Nili-Ravi buffalo）by 30 microsatellite loci and LabChip chip test method.The results showed that 332 alleles at 30 microsatellite loci were found in 8 buffalo breeds,the average values of gene diversity and PIC were 0.7808 and 0.7554,respectively.Cluster analysis indicated that Dechang buffalo and Dehong buffalo firstly clustered together,followed by Fuzhong buffalo,Guizhou buffalo,Wenzhou buffalo and Xilin buffalo.Moreover,Murrah buffalo and Nili-Ravi buffalo clustered together.Our findings revealed that the 30 microsatellite loci could be used as an effective genetic marker for the analysis of genetic diversity among the buffalo breeds,which enriched the current SSR marker resources in buffalo.