利用微卫星标记对4个肉牛品种进行遗传多样性分析

本研究利用10个微卫星标记分析了鲁西黄牛、布莱凯特肉牛、渤海黑牛和日本和牛4个品种185个个体的品种内遗传变异情况及各品种间的亲缘关系,共检测到58个等位基因,每个位点平均观察等位基因数为5.8个,从4(BM1818)到8个(ETH225和TGLA53)不等;有效等位基因数为2.5417～3.5849个;观察杂合度、期望杂合度和多态信息含量变异范围分别为0.2270～0.5459、0.6082～0.7230和0.5482～0.6791,均属高度多态性位点。群体间遗传分化明显,有34.49%的遗传分化来自群体间的变异。以Nei氏遗传距离(D_A)构建UPGMA系统进化树,聚类结果表明,渤海黑牛与鲁西黄牛首先聚为一类,布莱凯特肉牛和日本和牛聚为一类。布莱凯特肉牛的3个微卫星座位10个克隆的PCR扩增片段测序获得的序列已提交GenBank,登录号分别为：GQ368896、GQ368897、GQ368898、GQ368899、GQ368900、GQ368901、GQ368902、GQ368903、GQ368904、GQ368905。10对微卫星座位可作为有效的遗传标记用于4个肉牛品种的遗传多样性和系统发生关系分析。     

利用微卫星标记分析江苏三个地方鸡品种的遗传多样性

利用30个微卫星DNA标记对3个江苏地方鸡品种进行遗传多样性分析，通过计算等位基因频率、多态信息含量、平均杂合度、有效等位基因数和遗传距离，评估各品种内遗传变异和各品种间遗传相关。结果表明：江苏的3个品种在30个微卫星上共发现196个等位基因，其中96个等位基因为三个品种共有，47个等位基因为各品种所特有；3个地方鸡品种的平均杂合度：狼山鸡为0．655，鹿苑鸡为0．681，溧阳鸡为0．687；狼山鸡与溧阳鸡的遗传距离较小，而两鸡与鹿苑鸡的遗传距离较远。     

An evaluation of genetic diversity indices of the Red Bororo and White Fulani cattle breeds with different molecular markers and their implications for current and future improvement options

The genetic diversity of the Red Bororo and White Fulani cattle breeds of Cameroon and Nigeria was assessed with a panel of 32 markers. Estimates for the various indices of genetic diversity, total number of alleles (TNA), mean observed number of alleles (MNA), mean effective number of alleles (MNE), observed heterozygosity (H _ob) and expected heterozygosity (H _ex), were higher at microsatellite loci than at protein loci. Mean H _ex values were above 71% at microsatellite loci in all the breeds and ranged from 37% to 41.6% at milk protein loci and from 40.9% to 45.6% at blood protein loci. The highest TNA and MNA of microsatellites were recorded for the Nigerian White Fulani. MNE of milk protein loci was highest in the Cameroonian Red Bororo, while TNA of blood protein loci was highest in the Cameroonian White Fulani. The high genetic diversity levels indicate the presence of the necessary ingredients for improvement breeding and conservation. Multi-locus estimates of within-population inbreeding (f), total inbreeding (F) and population differentiation (θ) of the breeds were significantly different from zero, except for θ of blood proteins. A high level of gene flow was found between the breeds (5.829). The phylogenetic relationship existing among the four breeds is greatly influenced by location. The high gene flow between the breeds may lead to a loss of genetic diversity through genetic uniformity and a reduction in opportunities for future breed development. We propose an improvement scheme with aims to prevent loss of genetic diversity, improve productivity and reduce uncontrolled genetic exchanges between breeds.     

Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean F_IS=0.05) and genetic differentiation (mean F_ST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic diversity.     

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F_ST). The exact test for Hardy‐Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds.     

微卫星标记BM143在4个山羊品种中的遗传多样性分析

利用经筛选的微卫星引物BM143,对4个山羊品种的BM143基因座进行了多态性分析,研究结果表明,该基因座的等位基因大小在100～123bp范围内,分析检测了各山羊品种该位点的等位基因频率、杂合度、多态信息含量和有效等位基因数。结果表明,该微卫星标记BM143在4个山羊品种中的遗传多态性可以用于山羊遗传多态性的评估,为山羊品种的保存和利用提供了一定的科学理论依据。     

Genetic diversity of Afrikaner cattle in southern Africa

The Afrikaner is an indigenous South African breed of “Sanga” type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding level of 2.7% and a moderate to high degree of variation still persists within the Afrikaner cattle breed, despite the recent decline in numbers of animals.     

Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang

ABSTRACT

1. The genetic diversity and population structure were studied for eight local chicken breeds, including Anjiyan (AN), Hetian Black (HH), Hetian Ma (HM), Aheqi (AH), Baicheng You (BC), Hejing (HJ), Tashkurghan (TS) and Ruoqiang (RQ), in the Southern Xinjiang region of China, using 20 microsatellite markers.

2. Total 336 alleles were obtained from all chicken breeds, with a mean of 16.8 alleles per locus. The polymorphism information content ranged from 0.444 to 0.911, with a mean of 0.729 and almost all of the loci showed significant deviation from Hardy-Weinberg standards. The observed and expected heterozygosity of the eight breeds ranged from 0.5 to 0.677 and from 0.656 to 0.774, with the lowest observed in the AN and the highest in BC breed. The average breed genetic diversity was 0.655 for AN and 0.766 for BC chickens.

3. According to the neighbour-joining (NJ) method, three main clusters were identified in the NJ phylogenetic tree with AN and RQ breeds in one clade, HH and HM breeds in the second clade and TS, HJ, AH and BC breeds in the third clade.

4. Based on STRUCTURE analysis, the most likely cluster number of all breeds was K = 4, whereby HH and HM breeds formed one cluster and AH, BC, HJ and TS formed another, and RQ, AN chicken formed their own distinct cluster. These results indicated that HH and HM breeds had similar genetic background, as did the breeds of AH, BC, HJ and TS. RQ, AN breed had unique genetic backgrounds, distinct from the other breeds. Genetic introgression was detected from AN to HH and HM.

5. The results of the current study can be used as baseline genetic information to implement effective conservation programs and to make better use of these local chicken breeds, especially for the AN, RQ and TS breeds.     

中国6个山羊群体微卫星标记的遗传多样性分析

利用30个微卫星座位，对中国6个群体山羊（阿尔巴斯、二狼山、乌珠穆沁、阿拉善、辽宁绒山羊和陕南白山羊），共计240个个体的遗传多样性进行了分析。计算了各群体的等位基因频率，并以其为基础获得了各群体的平均杂合度（He）、平均多态信息含量（PIC）和平均有效等位基因数（Ne），分别为0．367～0．467、0．533～0．639、2．571～4．915。分析了群体内和群体间的遗传变异，并根据遗传距离，进行了NJ聚类，结果将6个山羊群体分为两大类。为进一步对山羊品种的保存和利用提供科学的依据。     

Genetic variability following selection for scrapie resistance in six autochthonous sheep breeds in the province of Bolzano (northern Italy)

Scrapie is an ovine transmissible spongiform encephalopathy, and its susceptibility is associated with polymorphisms in the prion protein gene (PRNP). Genetic selection is currently the most effective mean for eradication of the susceptible VRQ allele in favour of resistant ARR allele. Maintenance of genetic diversity should be one of the major objectives in breeding programmes, especially in endangered breeds, and genetic information are an excellent alternative to pedigree data where these information are missing. The aim of our study was to determine changes of genetic variability in six native sheep breeds from autonomous province of Bolzano, northern Italy, following simulation of scrapie selection scenarios. A total of 684 rams were investigated for PRNP polymorphisms and for 10 microsatellite loci to estimate genetic variability. Across all loci, a total of 163 alleles were detected with a mean of 10.4 alleles per locus. Average observed (Ho) and unbiased expected (uHe) heterozygosity overall loci were 0.74 and 0.78, respectively, showing a statistically significant deviation from Hardy–Weinberg equilibrium (HWE) in all breeds. This heterozygosity deficit was confirmed by a positive fixation index (Fis), determining a moderate inbreeding in each breed. Simulating a soft selection, where only rams having at least a VRQ allele should be excluded from reproduction, Ho, uHe and Fis values remained almost unchanged, indicating that genetic variability should not be affected by the removal of these individuals. With a mild selection scenario, considering only rams with at least one ARR allele, we observed a decrease in the mean alleles per breed (8.9) and the maintenance of heterozygosity deficiency, except for two breeds, where it was any longer significant. These results showed that selection strategies allowing use of heterozygous as well homozygous ARR rams might be the right compromise to improve resistance to scrapie and to do not dramatically affect genetic variability of these breeds.     

微卫星DNA标记在三个山羊品种中的遗传多态性研究

利用四个微卫星标记对波尔山羊、太行山羊和河北奶山羊的等位基因频率、群体多态信息含量、有效等位基因数和杂合度进行了遗传检测。结果表明：四个微卫星位点在波尔山羊、太行山羊和河北奶山羊三个品种中存在多态性。可以用于山羊遗传多样性的评估；位点OarFCB11变异最大，位点MCM38变异最小，从不同品种来看，太行山羊的遗传变异程度最大，而波尔山羊的遗传变异程度相对较小。     

Microsatellite Analysis of Six Chinese Indigenous Sheep Breeds

This article described the relationship among six Chinese indigenous sheep breeds.There were six microsatellite loci which used to analyze the genetic diversity.Based on the allele frequency of six sheep variations, we calculated the mean heterozygosity (Ho), which were from 0.5446 to 0.7140;The polymorphism information content (PIC) in six sheep breeds were from 0.5211 to 0.7732.Genetic variations within breed were analyzed in the study, and we clustered the UPGMA tree according to the DA genetic distance.The results showed that six breeds had relatively abundant genetic diversity, and MXB had the highest genetic variation, while SW had the lowest genetic variation.The inbreeding coefficient of SW was higher than other breeds, which revealed a higher inbreeding degree in this breed.Phylogenetic tree was constructed using UPGMA, which showed that LZD and MXB were classified as a class, HZK and GF were classified as a class, SIH and SW were classified as a class.The results revealed the genetic structure of breeds correlated with geographical distribution and history of domestication.     

中国6个地方绵羊品种的微卫星分析

为研究中国地方绵羊品种之间的遗传多样性,利用6个微卫星位点,对中国6个绵羊品种群体进行遗传检测,计算了各品种群体的平均杂合度(He)和平均多态信息含量(PIC),同时分析了各品种群体内的遗传变异,进行了UPGMA聚类。结果表明,6个绵羊品种Ho为0.5446~0.7140,PIC为0.5211~0.7732;6个绵羊品种都具有较丰富的遗传多样性,其中岷县黑裘皮羊的遗传变异最高,小尾寒羊的遗传变异最低;小尾寒羊的近交系数最高,揭示该群体内近交程度可能较高。利用UPGMA方法构建了系统发生树,兰州大尾寒羊与岷县黑裘皮羊为一类,哈萨克羊与贵德黑裘皮羊为一类,泗水绵羊与小尾寒羊为一类,表明群体遗传结构与地理分布及其驯化历史相关。     

中国地方鸭品种资源的分子遗传多样性

通过筛选的28个多态性较好的微卫星标记，检测了我国24个地方鸭品种的遗传多样性。利用等位基因频率计算了各群体的遗传参数和群体间的遗传距离，采用邻接法构建了聚类图，并进行了系统发生分析。结果表明：28个微卫星座位在我国家鸭群体中的多态信息含量除APL23和APL79为中度多态外，其他座位均为高度多态座位，可以作为有效的遗传标记用于鸭种之间遗传多样性分析和系统发生关系的分析；我国所有家鸭群体平均杂合度（0．569）低于国内的家鸡和家鹅，其遗传多样性相对贫乏；聚类结果分析表明了各家鸭品种的分子系统发生关系与其育成史、分化及地理分布比较一致。     

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。     

The biodiversity and genetic structure of Balearic sheep breeds

The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was found among the Balearic sheep breeds for the microsatellites scored. The whole mean value of observed heterozygosity amounted to 0.62, whereas the expected heterozygosity value was 0.69, suggesting the presence of a great degree of genetic variability, although a significant deficit of heterozygotes was detected for some markers. Genetic distance estimates showed that Balearic sheep are differentiated from the other Spanish breeds and in particular, from the Merino type. The Ibicenca breed showed the highest distance value from other breeds. The neighbour‐net method of analysis clustered the Roja Mallorquina, Menorquina and Mallorquina breeds. The Structure results clearly demonstrated the genetic differentiation among the four Balearic sheep breeds, with the Ibicenca and Formentera races joined, with slight migration among them. Few external genetic influences from the Spanish mainland breeds were detected.     

利用微卫星标记对7个山羊品种的遗传多样性研究

为了研究小香羊与相邻产区山羊品种之间的亲缘关系,利用7个微卫星位点,以波尔山羊为对照,对中国6个山羊群体进行了遗传检测,计算了各品种群体的等位基因频率、平均杂合度(He)、平均多态信息含量(PIC)和平均有效等位基因数(Ne),同时分析了各品种群体内和群体间的遗传变异,并根据遗传距离进行了NJ聚类。结果表明,各群体的He、PIC、Ne分别为0.778~0.823、0.766~0.809、4.707~5.767;川东黑山羊和川东白山羊聚为一类,乌羊和南江黄羊聚为一类,其次是马头山羊、小香羊,最后是波尔山羊。微卫星标记分析结果与它们的地理分布及品种形成相一致。     

贵州地方山羊品种遗传背景的微卫星分析

用15个牛微卫星位点,以波尔山羊为对照,研究了4个贵州地方山羊品种(贵州白山羊、贵州黑山羊、黔北麻羊、榕江小香羊)的遗传背景。结果:可分析的多态位点6个(BM1258、D1S104、ILSTS030、INRA063、INRABERN192、RM088),占40%(6/15),反应了牛微卫星位点与山羊有较高同源性;贵州地方山羊品种比波尔山羊具有较高的遗传多样性,高低顺序是贵州白山羊>贵州黑山羊>黔北麻羊>榕江小香羊>波尔山羊;群体遗传分化大,群体变异主要存在于品种内,而品种间的变异较小;贵州白山羊与贵州黑山羊遗传距离最近,其次是榕江小香羊、黔北麻羊,与波尔山羊遗传距离最远,这与它们的地理分布及品种形成相符。     

华东27个地方鸡品种(品系)的遗传变异

应用30个微卫星标记对华东27个地方鸡品种（品系）进行了遗传多样性分析，计算了多态信息含量、平均杂合度和遗传距离等遗传参数，并用类平均法进行了聚类分析。结果表明：平均杂合度最高的是河田鸡，为0．6870，最低的是狼山鸡，为0．6170；27个地方鸡品种（品系）的杂合度都较高，反映了这些品种的多种多型；各品种的平均遗传距离反映了各品种分化时间的长短；UPGMA的聚类分析将27个品种（品系）聚为10类：丝绒乌骨鸡、济宁百日鸡、河田鸡、安义瓦灰鸡、仙居鸡、江山乌骨鸡、溧阳鸡、金湖乌风鸡、灵昆鸡、余干乌骨鸡、康乐鸡、萧山鸡、琅讶鸡、淮北麻鸡、淮南三黄鸡为第1类，白耳鸡为第2类，浦东鸡为第3类，崇仁麻鸡与丝羽乌骨鸡为第4类，狼山鸡与寿光鸡为第5类，鹿苑鸡、东乡绿壳蛋鸡、汶上芦花鸡各独自聚为第6、7、8类，鲁西斗鸡与宁都三黄鸡聚为第9类，漳州斗鸡独自聚为第10类。通过微卫星标记对华东27个地方鸡品种（品系）遗传变异的分析说明这些地方品种的遗传多样性极其丰富，各具特色，应促进资源优势向经济优势转化。     

Genetic diversity of Indian native cattle breeds as analysed with 20 microsatellite loci

The aim of the present study was to assess the genetic variation and establish the relationship amongst the three Indian zebu cattle breeds using 20 bovine‐specific microsatellite markers. A total of 136 unrelated DNA samples from Sahiwal (SC), Hariana (HC) and Deoni (DC) breeds of cattle were genotyped to estimate within and between breed genetic diversity indices. The estimated mean allelic diversity was 5.2, 6.5 and 5.9 in SC, HC and DC, respectively, with a total of 167 alleles. The average observed and expected heterozygosity for the population varied from 0.42 (SC) to 0.59 (DC), and from 0.61 (SC) to 0.70 (DC), respectively. Low values of genetic variability estimates were observed in SC when compared with DC and HC, indicating some loss of variability because of its relatively small population size. From global F‐statistics a significant deficit of heterozygotes of 24.2% (p < 0.05) was observed for each one of the analysed breeds whereas the total population had a 32.8% (p < 0.05) deficit of heterozygotes. The F_ST estimates demonstrated that approximately 88.7% of the total genetic variation was because of the genetic differentiation within each breed. Pair‐wise breed differentiation, Nei's standard and D_A genetic distance estimates revealed relatively close genetic similarity between HC and DC in comparison with SC. In the UPGMA‐based phylogenetic tree constructed from the genetic distances, HC and DC were grouped together in one cluster and SC in the other. The estimated time of divergence suggested a separation time of approximately 776 years between DC and HC, and a comparatively longer period (1296 years) between DC and SC.