Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean F_IS values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.     

Genetic diversity of Chinese indigenous goat breeds based on microsatellite markers

Eighteen microsatellites were used to investigate the genetic diversity and differentiation of eight Chinese indigenous goat breeds. The results indicated that there is a significant difference of genetic diversity between different loci. Chinese indigenous goat breeds have similar genetic diversity to other Asian goats, but with lower Fst. The clustering of individuals and populations showed that Chinese indigenous goat breeds might have originated from two ancestral populations. The genetic differentiation between populations is consistent with the results of archaeology, mtDNA and RAPD.     

Genetic variability of Lizard canary breed inferred from pedigree analysis

The genealogical data of 471 (whole population: WP) Lizard canaries of an Italian breeder were analyzed to evaluate the genetic variability of the breed. The reference population (RP) comprised 346 living reproductive birds. Average generation interval was 1.61 ± 0.718 for males and 1.72 ± 0.863 for females. The average value of inbreeding (F) and relatedness (AR) in the RP were 15.83% and 22.63%, while the average increase in inbreeding was estimated to be 6.71% per generation (effective population size = 7.49). The results showed the need to reduce the level of inbreeding which would result in significant loss of genetic variation and in significant inbreeding depression.     

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。     

微卫星标记分析福建地方品种猪的遗传多样性

采用8个微卫星座位对福建省5个地方猪种(槐猪、官庄花猪、莆田黑猪、闽北花猪、武夷黑猪)的遗传结构进行了分析,计算了遗传杂合度、有效等位基因数、多态信息含量、Nei氏标准遗传距离。结果表明:8个位点均为高度多态位点;5个猪种群体内的遗传多样性比较高,8个微卫星位点平均杂合度介于0.7006～0.7760之间;多态信息含量在0.6917～0.7609之间;槐猪与武夷黑猪的遗传距离最小0.5531,官庄花猪与闽北花猪的遗传距离最大0.8618。     

Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.     

微卫星标记ILSTS011在3个绵羊品种中的遗传多样性分析

为了分析微卫星标记ILSTS011的遗传多态性,研究以河南省地方绵羊品种大尾寒羊、小尾寒羊和豫西脂尾羊为研究对象,采用聚丙烯酰胺凝胶电泳技术分离微卫星标记的带型.结果表明:在3个绵羊品种中均检测到微卫星标记ILSTS011有3个等位基因,微卫星标记ILSTS011的平均杂合度为0.614 1,平均有效等位基因数为2.614 0,平均多态信息含量为0.551 3.说明ILSTS011为高度多态基因座,可作为有效的遗传标记用于大尾寒羊、小尾寒羊和豫西脂尾羊的遗传多样性分析.     

7个地方鸡种的分子评估

成熟的基因扩增及测序技术,结合比较发达的网络与信息技术,给我们提供了以DNA为基础的系统分类方法.一种新的DNA分类方法--DNA条形编码(DNA Barcoding)技术应运而生.本研究以线粒体细胞色素C氧化酶亚基Ⅰ(cytochrome c oxidase Ⅰ,CD Ⅰ)基因的特定序列作为DNA条形码,对我国7个地方鸡种进行分子评估.研究结果表明:选择的这段CO Ⅰ基因序列有22个突变位点,为13个单倍型,其中11个单倍型为各品种所特有;6个鸡种有其特异位点,这些特异单倍型和特异位点作为DNA条形码可以对其进行分子评估,并可以作为辅助各品种鉴定的依据.7个品种间Kimura双参数遗传距离为0.017～0.389.7个品种的DNA分类和形态学分类基本一致,该基因可以探讨地方鸡种分类问题.     

Genetic structure of pig breeds from Korea and China using microsatellite loci analysis

To understand molecular genetic characteristics of Korean pigs, the genetic relationships of nine pig breeds including two Korean pigs (Korean native pig and Korean wild pig), three Chinese pigs (Min pig, Xiang pig, and Wuzhishan pig), and four European breeds (Berkshire, Duroc, Landrace, and Yorkshire) were characterized from a 16-microsatellite loci analysis. The mean heterozygosity within breeds ranged from 0.494 to 0.703. Across multiple loci, significant deviation from Hardy-Weinberg equilibrium was observed in most pig breeds, except for two Chinese pigs (Min pig and Wuzhishan pig). This deviation was in the direction of heterozygote deficit. Across population loci, 36 of 144 significantly deviated (P < 0.05) from Hardy-Weinberg equilibrium. The mean FST, a measure of genetic divergence among subpopulations, of all loci indicated that 26.1% of total variation could be attributed to the breed difference. Relationship trees based on the Nei's DA genetic distance and scatter diagram from principal component analysis consistently displayed pronounced genetic differentiation among the Korean wild pig, Xiang pig, and Wuzhishan pig. Individual assignment test using a Bayesian method showed 100% success in assigning Korean and Chinese individual pigs into their correct breeds of origin and 100% exclusion success from all alternative reference populations at P < 0.001. These findings indicate that the Korean native pig has been experiencing progressive interbreeding with Western pig breeds after originating from a North China pig breed with a black coat color. Considering the close genetic relationship of Korean pigs to the Western breeds such as Berkshire and Landrace, our findings can be used as valuable genetic information for the preservation and further genetic improvement of the Korean native pig.     

Genetic characterisation and breed assignment in Austrian sheep breeds using microsatellite marker information

Samples from 717 sheep of 11 Austrian sheep breeds were genotyped for 25 microsatellite loci. Twenty‐one loci showing no deviation from Hardy–Weinberg equilibrium were used to calculate pairwise genetic distances (Nei's minimum distance and Reynolds’ distance). All breeds could be clearly distinguished through these genetic distances. The shortest genetic distance was found between Alpines Steinschaf (AS) and Waldschaf (WS). Within the so‐called ‘Steinschaf’ group [AS, Montafoner Steinschaf (MS), Krainer Steinschaf (KS) and Tiroler Steinschaf (TS)] the MS adopted an extreme status with the largest distance to the other breeds in the group. This finding resulted in the decision to consider the MS no longer as subpopulation of Alpines Steinschaf but as an independent breed. A correct breed assignment using a Bayesian approach was possible for only 66% of all individuals belonging to Alpines Steinschaf, but for at least 90% of individuals for all other breeds investigated.     

Genetic variability and relationships in nine South African cattle breeds using microsatellite markers

Tropical Animal Health and Production - Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven...     

Genetic relationships in Swiss sheep breeds based on microsatellite analysis

Genetic relationships between Swiss sheep breeds were estimated on the basis of microsatellite analysis. In addition to the Swiss breeds wild-type Mouflon was included in this investigation. Polymerase chain reaction amplifications of 31 ovine, bovine and caprine microsatellites were performed in a total of 307 animals representing eight populations. The average heterozygosity within each population was high in the domestic breeds (0.60–0.71) and lower in Mouflon 0.45. The average coefficient of gene differentiation G _ST over all loci was 0.17, i.e. a small part of the variability at the 31 microsatellite loci analysed must be ascribed to between-breed variability. Genetic distances between breeds were obtained, which were used to construct a phylogenetic tree. Microsatellites developed from closely related species of cattle and goat are useful for estimating genetic relationships among sheep breeds.     

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 structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms

Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (F_it) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (F_is) amounted to 6.1%. The breeds were moderately differentiated (F_st = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the F_st value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub‐clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub‐clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.     

Genetic variability of three Italian cattle breeds determined by parameters based on probabilities of gene origin

In this study, we have investigated the genetic variability of three Italian cattle breeds, autochthonous of the Tuscany region (Chianina, Maremmana and Mucca Pisana), using the parameters based on probabilities of gene origin: f _e, f _a and N _g. Compared with Chianina (N _g=53.9) and Maremmana (N _g=79.6), Mucca Pisana was found to be the genetically smaller (N _g=10.1) and less diverse population. The genetic variability in Chianina population was lower than in Maremmana probably because of bottlenecks in its pedigree and genetic drift. However, the values found in these breeds were higher than those found in dairy cattle breeds, but lower than those found in beef cattle breeds.     

地方鸡种与隐性白羽鸡遗传变异的AFLP指纹

利用6对AFLP引物组合对我国12个地方鸡种和引进鸡种隐性白羽鸡进行了遗传检测,统计了每个引物组合在各个品种中检测到的多态性条带和特异性条带,计算了13个鸡种的遗传相似系数和遗传距离,并据此构建了UPGMA聚类关系图,分析了所研究鸡种的遗传关系.结果表明:6对AFLP引物组合在13个鸡种中共检测到290条多态性条带,平均每个引物组合产生48.3奈多态性标记,同时在每个品种群体中还检测到了数量不等的特异性条带,其中寿光鸡和东乡黑鸡最多,为9条,旧院黑鸡、兴义矮脚鸡和隐性白羽鸡最少,为1条.13个鸡种聚为4类,其中隐性白羽鸡单独聚为一类,鸡种间的遗传相似系数及聚类结果与各个鸡种的地理分布、现实状况相吻合,从而表明AFLP指纹用于我国地方鸡种的遗传多态性分析、品种鉴定及品种间亲缘关系分析是可行的.     

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.     

Genetic structure of Iranian indigenous sheep breeds: insights for conservation

Tropical Animal Health and Production - Genetic structure and genetic diversity levels of indigenous Iranian sheep breeds are not clear, despite the interest this region has in itself as an...     

Carcase characteristics and qualitative meat traits of three Italian local chicken breeds

1. An experiment involving 60 male chickens reared in an organic production system was carried out in order to investigate carcase characteristics and qualitative meat traits of three slow-growing Italian local breeds of chicken (Ermellinata, Padovana and Pepoi). 2. Chicks were randomly selected at hatch, raised together under the same conditions, slaughtered at 190 d of age, dissected for carcase traits, and meat (breast and thigh) stored for subsequent analysis of quality parameters. 3. Ermellinata (EA) chickens were significantly different from Padovana (PA) and Pepoi (PI) chickens for live, carcase and thigh weights. Breeds were also different for breast muscle protein content (EA > PI and PA), shear force (PA < EA and PI) and cooking loss (PI > PA and EA) values. 4. The CIE system values of lightness (L*), redness (a*), and yellowness (b*) evidenced a distinctive darker meat and lighter skin colour of PA breast meat. 5. Polyunsaturated fatty acids composition of breast meat was similar among the analysed breeds. EA had significantly higher saturated but significantly lower monounsaturated fatty acid contents than the other two breeds.