• Asian-Australasian Journal of Animal Sciences
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• 제20권1호
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• pp.25-30
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• 2007

The capability of microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in two Indian horse breeds. The strength of these individual assignment methods was also evaluated by increasing the number of loci in increments of five. The probability of identity of two random horses from the two breeds at all twenty five studied loci was as low as $1.08{\times}10^{-32}$ showing their suitability to distinguish between individual horses and their products. In the phylogenetic approach for individual assignment using Nei's genetic distances, 10.81% of horses associated with breed other than the major cluster of the source breed horses when all twenty five microsatellite loci were implemented. Similar results were obtained when the maximum likelihood approach for individual assignment was used. Based on these results it is proposed that, although microsatellite markers may prove very useful for individual identification, their utility for breed assignment of horses needs further evaluation.

• Asian-Australasian Journal of Animal Sciences
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• 제18권11호
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• pp.1529-1534
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• 2005

Individual-breed assignments were implemented in six swine populations using twenty six microsatellites recommended by the Food and Agriculture Organization and the International Society for Animal Genetics (FAO-ISAG). Most microsatellites exhibited high polymorphisms as shown by the number of alleles and the polymorphism information content. The assignment accuracy per locus obtained by using the Bayesian method ranged from 33.33% (CGA) to 68.47% (S0068), and the accumulated assignment accuracy of the top ten loci combination added up to 96.40%. The assignment power of microsatellites based on the Bayesian method had positive correlations with the number of alleles and the gene differential coefficient ($G_{st}$) per locus, while it has no relationship to genetic heterozygosity, polymorphism information content per locus and the exclusion probabilities under case II and case III. The percentage of corrected assignment was highest for the Bayesian method, followed by the gene frequency and distancebased methods. The assignment efficiency of microsatellites rose with increase in the number of loci used, and it can reach 98% when using a ten-locus combination. This indicated that such a set of ten microsatellites is sufficient for breed verification purposes.

• Asian-Australasian Journal of Animal Sciences
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• 제22권9호
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• pp.1234-1240
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• 2009

Gene flow, genetic structure and differentiation of Kutchi, Mehsana and Sirohi breeds of goat from North-Western India were evaluated based on 25 microsatellite markers so as to support breed conservation and improvement decisions. The microsatellite genotyping was carried out using an automated DNA sequencer. The gene diversity across the studied loci for the Kutchi breed varied from 0.57 (ILST 065) to 0.93 (OarFCB 304, OMHC 1, ILSTS 058) with an overall mean of 0.79${\pm}$0.02. The corresponding values for Mehsana and Sirohi breeds were 0.16 (ILST 008) to 0.93 (OMHC 1, ILSTS 058) with an average of 0.76${\pm}$0.04, and 0.50 (ILSTS 029) to 0.94 (ILSTS 058) with an average of 0.78${\pm}$0.02, respectively. The Mehsana breed had lowest gene diversity among the 3 breeds studied. All the populations showed an overall significant heterozygote deficit ($F_{is}$). The Fis values were 0.26, 0.14 and 0.36 for Kutchi, Mehsana and Sirohi goat breeds, respectively. Kutchi and Mehsana were more differentiated (16%) followed by Mehsana and Sirohi (13%).The measures of standard genetic distance between pairs of breeds indicated that the lowest genetic distance was between Kutchi and Sirohi breeds (0.73) and the largest genetic distance was between Mehsana and Kutchi (1.0) followed by Sirohi and Mehsana (0.75) breeds. Mehsana and Kutchi are distinct breeds and this was revealed by the estimated genetic distance between them. All measures of genetic variation revealed substantial genetic variation in each of the populations studied, thereby showing good scope for their further improvement.

• Asian-Australasian Journal of Animal Sciences
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• 제27권5호
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• pp.616-627
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• 2014

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index ($F_{ST}$) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values ($F_{IS}$) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity ($H_E$) or $F_{ST}$, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, $F_{ST}$ and D-scores were used. Only 6 to 8 markers ranking $H_E$, $F_{ST}$ or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, $F_{ST}$ and allelic number of close lineage populations.

• Asian-Australasian Journal of Animal Sciences
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• 제19권7호
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• pp.943-952
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• 2006

The genetic variation in 10 indigenous Caucasian sheep breeds was studied with 14 micro-satellite loci in order to determine the genetic diversity among and between the breeds. Five breeds from Asia, five breeds from Europe and one breed from Africa, were included in order to study any relationships or influences they may have with the Caucasian sheep analyzed. A Karakul population from Uzbekistan was included in the study to see whether there was any Central Asian influence. All the 14 loci were found to be polymorphic in all the breeds, with the exception of ILST0056, which was monomorphic in Imeretian. A total of 231 alleles were generated from all the 688 individuals of the sheep analyzed. The mean number of alleles (MNA) at each locus was 16.5. The total number of alleles detected in all samples ranged from 13 in several loci to 23 in OarJMP029. Out of total 308 Hardy-Weinberg Equilibrium (HWE) tests, 85 gave significant results. After Bonferroni correction for multiple tests, 30 comparisons still remained significant to the experimental levels. The Gala population was the most diverse and Imeretian the least diverse with a MNA of 8.50 and 5.51, respectively. Gene diversity estimates exhibited the same trend and ranged from 0.803 in Gala and 0.623 in Imeretian, but generally there is higher diversity among the Caucasian breeds in comparison to other eference breeds. The closest breeds were Tushin and Bozakh with Da of 0.113 and most distant breeds were $Djallonk{\acute{e}}$ and North Rondalsy with Da of 0.445. Principal Component (PC) analyses were done. PC1 described 14% of the differences. PC2, which described 13% of the differences, further separated the Caucasian breeds from Asian breeds except Karakul and Awasi, and the two British breeds. PC3 described 10% of the differences, allowing better differentiation of the Caucasian breeds. A moderate degree of reliability was observed for individual-breed assignment from the 14 loci using different approaches among which the Bayesian method proved to be the most efficient. About 72% of individuals analyzed were correctly assigned to their respective breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제22권10호
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• pp.1351-1358
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• 2009

Parentage tests using polymorphic DNA marker are commonly performed to avoid incorrect recording of the parental information of livestock animals, and single-nucleotide polymorphisms (SNPs) are becoming the method of choice. In Japanese Black cattle, parentage tests based on the exclusion method using microsatellite markers are currently conducted; however, an alternative SNP system aimed at parentage tests has recently been developed. In the present study, two types of simulations were conducted using the pedigree data of two subpopulations in the breed (subpopulations of Hyogo and Shimane prefectures) in order to examine the effect of actual genetic and breeding structures. The first simulation (simulation 1) investigated the usefulness of SNPs for excluding a close relative of the true sire; the second one (simulation 2) investigated the accuracy of sire identification tests for multiple full-sib putative sires by a combined method of exclusion and paternity assignment based on the LOD score. The success rates of excluding a single fullsib and sire of the true sires were, respectively, 0.9915 and 0.9852 in Hyogo and 0.9848 and 0.9852 in Shimane, when 50 SNPs with minor allele frequency (MAF: q) of 0.25${\leq}$q${\leq}$0.35 were used in simulation 1. The success rates of sire identification tests based solely on the exclusion method were relatively low in simulation 2. However, assuming that 50 SNPs with MAF of 0.25${\leq}$q${\leq}$0.35 or 0.45${\leq}$q${\leq}$0.5 were available, the total success rates including achievements due to paternity assignment were, respectively, 0.9430 and 0.9681 in Hyogo and 0.8999 and 0.9399 for Shimane, even when each true sire was assumed to compete with 50 full-sibs.

• Journal of Animal Science and Technology
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• 제49권5호
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• pp.559-568
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• 2007

최근 들어 유전자 또는 DNA 분절의 반복수 변이 (CNV)에 관한 연구가 다수 수행되었으며, 그 분석 방법 및 기기 또한 다양하게 발달되었다. 본 연구는 Landrace 품종의 KIT 유전자 CNV 탐지를 위하여 다른 분석 방법들에 비하여 정확도가 높은 정량적 OLA 기법(qOLA)을 이용하였다. qOLA와 pyrosequencing assay의 조합하여 분석한 결과를 Landrace 44두에 대한 좌표 분석을 한 결과 I1/I1 또는 I3/i(IBe), I1/I2 또는 I3/IP, I1/I3, I1/IP 또는 I2/i(IBe), I2/I2, I2/IP의 6 genotype으로 분류되었으며, PROC FASTCLUS procedure을 이용한 통계 분석과 좌표 분석을 상호 비교한 결과 genotype의 분류가 100% 일치하였다. 기기간의 차이점을 조사하기 위해 qOLA_3100과 qOLA _3130의 관측치 비교를 실시한 결과 동일한 genotype 분류결과를 얻었다. 또한 정밀성 및 정확도 비교에서 qOLA_3100의 경우 표준편차와 변이계수의 평균이 2.33과 4.10로 qOLA_3130(2.67과 4.81)에 비하여 낮게 나타났다. qOLA 반응전 PCR 산물에 대하여 proteinase K 처리효과를 분석한 결과 pro- teinase K를 처리한 경우 전기영동 분석시 noise peak들이 제거되었으며 각 genotype의 이론적 비율에 보다 정확히 일치하였다.