An improved method for discriminating between Japanese Nagoya chickens and others

Recently, we reported a method for identifying the Nagoya, a Japanese chicken breed. Here we describe an improved method suitable for use in conventional laboratories. Five microsatellite markers fixed in the Nagoya breed were amplified by multiplex polymerase chain reaction (PCR). The PCR products were digested with CEL I nuclease and electrophoresed in a ready‐made gel. The fragment‐length polymorphisms of each marker were detected clearly in the gel, and the resultant exclusion probabilities were almost equal to that in our previous data. This method can be used in laboratories without a DNA sequencer for routinely discriminating between the Nagoya breed and other chickens.     

Characterization of two microsatellites in chicken monoamine oxidase A

We surveyed two polymorphic microsatellites in a candidate gene for fear response, monoamine oxidase A ( MAOA ), in chicken. Two hundred and eighty chickens from five breeds (Nagoya, Mikawa, White Leghorn, White Plymouth Rock, and Rhode Island Red) were investigated. A thymine (T) repeat and an adenine (A) repeat were found on MAOA intron 4 ( CMin4T ) and intron 9 ( CMin9A ), respectively. Nine alleles ( 127-bp to 166-bp ) in CMin4T and six alleles ( 184-bp to 198-bp ) in CMin9A were detected. A 128-bp allele in CMin4T was observed in the Nagoya breed only, implying a highly useful marker for discriminating the Nagoya breed from other breeds. In addition, the Mikawa breed had the fixed 127-bp and 198-bp alleles in CMin4T and CMin9A , respectively. The Nagoya breed chickens show densely cowardly behavior, but the Mikawa breed chickens do not show the same behavior. The current results may indicate that MAOA is an informative candidate gene for breed difference.     

利用微卫星标记分析5个家兔品种内的遗传多样性

本研究利用微卫星标记分析了我国5个家兔品种内的遗传多样性。结果表明:在5个品种中,新西兰兔有效等位基因数最多,为6.545 5;加利福尼亚兔有效等位基因数最少,为3.000。比利时兔平均多态信息含量和平均杂合度最大,分别为0.570 4和0.823 3;加利福尼亚兔平均多态信息含量和平均杂合度最小,分别为0.499 7和0.589 7。     

Genetic characterization of Barbari goats using microsatellite markers

Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining. The number of alleles ranged from 4 to 11, with allele sizes ranging from 88 to 220 bp. The distribution of allele frequencies was between 0.0104 and 0.5208. Polymorphism information content varied from 0.5563 to 0.8348. The population was not in Hardy-Weinberg equilibrium for all except two microsatellite loci (ILSTS044 and ILSTS060). The observed heterozygosity ranged from 0.8478 to 1.0000 while the expected heterozygosity ranged from 0.6208 to 0.8509. Based on the results of the present study, there is a good scope for exploiting the genetic variability in the Barbari goats for further improvement of performance.     

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DNA标记与鸡肉品质性状的相关分析

本研究测定了隐性白羽和仙居鸡参考家系F2代500羽个体的26个微卫星座位的多态性,分析微卫星标记与鸡肉品质性状之间的相关性,结果发现:位于2号染色体上的标记ADL212分别与pH值和嫩度显著相关;位于3号和5号染色体上的微卫星标记MCW 004和MCW 223与肉色显著相关;与胸肌失水率显著相关的微卫星标记分别为:位于2号染色体的MCW 264和ADL212以及5号染色体的MCW 223和9号染色体的ADL211。     

利用微卫星分子标记研究我国16份披碱草遗传多样性

利用微卫星(Microsatellite)分子标记对我国16份披碱草Elymus dahuricus进行遗传多样性研究。研究共筛选了38对引物,其中18对引物有扩增条带,占总数的47.4%,具有多态性并且扩增效果较好的引物有6对,占总数的15.8%。用筛选出的这6对引物对供试的16份材料进行微卫星分析,6对引物共检测出26个等位基因,平均每对引物所产生的平均等位基因数为4.3个位点;利用微卫星分子标记数据,对其居群遗传分化进行研究,结果表明:披碱草77.36%的遗传变异出现在居群内,因此,披碱草的遗传多样性主要存在于居群内;对16份披碱草进行聚类分析,构建了亲缘关系树状图,16份供试材料大致分为5类。     

微卫星标记与鸡蛋品质性状关系的研究

本试验分别对60周龄文昌鸡和新扬州鸡进行了蛋品质的测定,测定了8个性状为:蛋重、蛋壳重、蛋壳厚度、蛋壳强度、哈氏单位、蛋形指数、蛋黄重、蛋黄颜色。通过统计软件,对各蛋品质性状进行了相关分析,并通过选用20对微卫星标记,筛选出了与哈氏单位、蛋重有关的分子遗传标记。结果表明:与60周龄新扬州鸡的哈氏单位有关的标记为2号染色体上MCW239和4号染色体上的ADL260,与60周龄新扬州鸡的蛋重有关的标记为2号染色体上的ADL176和MCW239,与60周龄新扬州鸡蛋壳强度有关的标记Z染色体上的LEI229;而与60周龄文昌鸡哈氏单位相关的有2号染色体的的ADL176、MCW239和4号染色体的MCW240,与60周龄文昌鸡蛋重相关的是4号染色体上的标记LEI119,与60周龄蛋壳强度相关的标记为Z染色体上的MCW246和LEI229。     

Genetic characterization of the Blonde d'Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations

This study was conducted to evaluate the genetic diversity of Blonde d'Aquitaine, a well-muscled native French beef breed, and to understand the relationships between Blonde d'Aquitaine, Limousin and Salers. We also compared these three beef breeds to the Holstein dairy breed. For this purpose, a set of 16 microsatellite markers were investigated. The obtained results show that Blonde d'Aquitaine has a high level of genetic diversity. Our study shows also that the French beef breeds have genetic differentiation among them, with approximately 9% of the total variation owing to breed differences. Our results show also that Blonde d'Aquitaine and Salers populations are genetically more similar to each other than to the Limousin.     

Genetic closeness of Zanskari and Spiti ponies of India inferred through microsatellite markers

The Zanskari and Spiti ponies were characterized for genetic variation using a set of 25 equine microsatellite markers. The DNA was isolated from the 42 blood samples of Zanskari and 32 blood samples of Spiti ponies collected from their respective breeding tracts. The DNA was amplified by polymerase chain reaction at the studied microsatellite loci and amplified product was resolved for alleles by denaturing urea-polyacrylamide gel electrophoresis. The allelic frequency data so obtained was statistically analyzed using POPGENE computer program. The PCR product size-range varied from 84 to 102 at locus HTG6 to 238 to 244 at locus UCDEQ425. The observed number of alleles ranged from four to nine with a mean (± standard deviation) of 5.80 ± 1.32 alleles per locus in Zanskari and 5.40 ± 1.04 alleles per locus in Spiti ponies. The mean observed heterozygosity was found to be 0.61 ± 0.06 and 0.56 ± 0.09 for Zanskari and Spiti ponies, respectively. The Nei's standard and unbiased genetic distance were found to be 0.11 and 0.09, respectively, indicating close genetic relatedness of Zanskari and Spiti ponies.     

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco‐zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations – a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F‐statistics revealed negligible genetic differentiation (F_ST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south‐north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.     

Genetic characterization of the Burlina cattle breed using microsatellites markers.

The present study was a contribution on the genetic characterization of the Burlina local cattle breed, and an approach to understanding the relationships between Burlina, Holstein Friesian and Brown Swiss which represent the majority of the dairy cattle reared nowadays in North-East Italy. The obtained results helped to clarify the genetic diversity and distinctiveness of Burlina population. In particular, the low genetic distance between Burlina and Holstein Friesian and the assignment of a moderate percentage of Burlina animals to Holstein Friesian suggested that crosses between them took place in the past, while crosses with Brown Swiss seemed to be less frequent. However, analyses of marker genotypes, showed a cluster with only Burlina individuals, which demonstrates the genetic distinctness of this breed. The Burlina breed showed the highest variability among the analysed breeds and its inbreeding coefficient was low. The data contribute to the feasibility of a conservation and selection programme for this breed and the results are useful for the implementation of a conservation strategy that should aim to conserve animals where the contribution from foreign breeds is as small as possible.     

利用微卫星标记分析泸水中华蜜蜂遗传多样性

利用21对微卫星标记对云南泸水中华蜜蜂群体遗传多样性进行分析,共检测到121个等位基因,等位基因数目从2-12不等。平均等位基因数为5.76;所有位点的平均期望杂合度（He）和平均多态信息含量（PIC）值分别为0.6752和0.6192。表明泸水中华蜜蜂群体遗传多样性较为丰富。     

The legacy of Columbus in American horse populations assessed by microsatellite markers

Criollo horse populations descend from horses brought from the Iberian Peninsula over the period of colonization (15th to 17th century). They are spread throughout the Americas and have potentially undergone genetic hybridization with other breeds in the recent past. In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of “all other Criollo breeds” had the closest genetic relationship with breeds originating from the Iberian Peninsula, specifically with the Celtic group. For the whole set of Criollo breeds analysed, the estimated genetic contribution from other breeds was approximately 50%, 30% and 20% for the Celtic, Iberian and Arab-Thoroughbred groups, respectively. The spatial distribution of genetic diversity indicates that hotspots of genetic diversity are observed in populations from Colombia, Ecuador, Brazil, Paraguay and western United States, possibly indicating points of arrival and dispersion of Criollo horses in the American continent. These results indicate that Criollo breeds share a common ancestry, but that each breed has its own identity.     

Analysis of genetic variability in the Czech Dachshund population using microsatellite markers

The primary goal of this study was to analyse genetic variation within and among six Dachshund varieties in the Czech Republic using 10 microsatellites from StockMarks^® Paternity Polymerase Chain Reaction (PCR) Typing kit. A total of 632 Dachshunds were sampled – 99 Standard Smooth-haired, 72 Standard Long-haired, 272 Standard Wire-haired, 42 Miniature Smooth-haired, 73 Miniature Long-haired and 74 Miniature Wire-haired. Average observed heterozygosity and polymorphic information content ranged in particular Dachshund varieties between 0.58–0.70 and 0.57–0.64, respectively. Subsequent analysis of the population structure ( F -statistics; Nei's genetic identity) showed that Standard Dachshunds shared allele frequencies most closely with their miniature equivalents, and smooth coat type is closer to Wire-haired coat type than to the Long-haired one. Analysis of molecular variance revealed that 11.81% of the total variance occured among varieties. The value of combined exclusion probability (0.9955) validated usefulness of this panel of microsatellites for parentage verification in all analysed populations. We carried out 234 parentage verifications with 1.28% cases where parentage did not match.     

Application of bovine microsatellite markers for genetic diversity analysis of European bison (Bison bonasus)

In this study, the cross‐amplification of a commercial multiplex set of 11 cattle (Bos taurus) microsatellites was tested on a panel of 35 European bison (Bison bonasus) individuals. After polymerase chain reaction optimization, all loci cross‐amplified successfully in investigated bisons. Number of alleles and observed and expected heterozygosity per locus are in the range of 2–4, 0.086–0.629 and 0.288–0.621 respectively. The availability of a heterologous set of multiplexed microsatellite markers derived from cattle opens an avenue for collecting profound genetic data for efficient conservation management strategies of the European bison.     

Interval mapping of growth quantitative trait loci in Japanese Black beef cattle using microsatellite DNA markers and half-sib regression analysis

A confirmatory scan for the regions of bovine chromosome 1 segregating the quantitative trait loci (QTL) influencing birthweight, weaning weight, yearling weight, and preweaning and postweaning average daily gains was performed by genotyping half‐sib progeny of four Japanese Black sires using microsatellite DNA markers. Data were analyzed by generating an F‐statistic every 1 cM on a linkage map by the regression of phenotype on the probabilities of inheriting an allele from the sire after adjusting for the fixed effects of sire, sex, parity and season of birth as well as age as a covariate. Permutation tests at chromosome‐wide significance thresholds were carried out over 10 000 iterations. A significant QTL for birthweight at 114 cM was detected in the sire 2 family. This identification of a birthweight QTL in Japanese Black cattle may be useful for the implementation of marker‐assisted selection.     

A simple and efficient method for extraction of PCR-amplifiable DNA from chicken eggshells

Recently, we reported a method for discriminating a Japanese brand of chicken, the Hinai-jidori. As an application of this method for discriminating Hinai-jidori eggs, we here report an efficient method for extracting maternal DNA from eggshells. Eggshell powder was completely decalcified with EDTA solution, and then DNA was isolated by conventional phenol-chloroform extraction and ethanol precipitation. The efficiency of DNA recovery from eggshells was 50-fold higher than that of a previously reported method. The recovered DNA could be used for PCR, and 10 markers for identifying the Hinai-jidori chicken were detected. The genotypes of the Hinai-jidori exactly matched those of the Hinai-dori breed. Using this method, Hinai-jidori and Hinai-dori eggs could be distinguished from the eggs of Rhode Island Reds. This is the first report of a technique that can be used to discriminate the eggs of Hinai-jidori from those of other chickens, and it can also be utilized to validate the labeling of Hinai-jidori eggs in the market.     

Evaluation of genetic richness among Vietnamese native pig breeds using microsatellite markers

We have elucidated genetic relationships of Vietnamese native pigs (VNP) using preliminarily collected samples by a single‐nucleotide polymorphism (SNP) array. In order to confirm our previous results and compare with the results of a previous study using microsatellite (MS) markers, we aimed to characterize genetic diversity and population structure in wider varieties (24 breeds from 21 Provinces) of VNP across the country using 20 polymorphic MS markers recommended by ISAG/FAO (International Society for Animal Genetics/Food and Agriculture Organization) for diversity study. In this study, we collected 1,136 DNA samples of the VNPs and three exotic breeds. Our results revealed that the average number of alleles and allelic richness across the loci in VNPs were 10.0 and 7.6, which were higher than those of exotic breeds. Genomic components among VNPs were subjected to the sampling locations. Interestingly, Co Binh Thuan showed remarkable genetic feature compared to the other VNPs, because the habitation of Co Binh Thuan was relatively far from the other breeds. The results of this study provided useful information for exploitation, conservation, and development trends of the VNP breeds. More recently, African swine fever caused significant damage to most of the VNP populations. Therefore, our findings will help a reconstruction scheme of the VNP genetic resources.