• Asian-Australasian Journal of Animal Sciences
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• 제28권1호
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• pp.25-36
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• 2015

The complex analysis of the pedigree records of Czech Landrace (CLA), Czech Large White-dam line (CLWd), Czech Large White-sire line (CLWs), Duroc (DC), and Pietrain (PN) was performed to determine trends of genetic diversity (GD), and to find the main sources of the GD loss. The total size of the pedigree was 132,365, 391,151, 32,913, 13,299, and 7,160 animals in CLA, CLWd, CLWs, DC, and PN, respectively. Animals born in the years 2011 through 2013 were assumed as the reference population. The average pedigree completeness index for one generation back was 95.9%, 97.4%, 91.2%, 89.8%, and 94.2% for appropriate breeds. Number of ancestors explaining 100% of gene pool was 186, 373, 125, 157, and 37 in CLA, CLWd, CLWs, DC, and PN, respectively. The relative proportion of inbred animals (58%, 58%, 54%, 47%, and 25%), the average inbreeding (2.7%, 1.4%, 2.5%, 3.6%, and 1.3%) and the average co-ancestry (3.1%, 1.6%, 3.3%, 4.2%, and 3.3%) were found over the past decade in analysed breeds. The expected inbreeding under random mating increased during the last 10 years in CLWs and PN and varied from 1.27% to 3.2%. The effective population size computed on the basis of inbreeding was 76, 74, 50, 35, and 83 in 2012 in CLA, CLWd, CLWs, DC, and PN, respectively. The shortest generation interval (1.45) was observed for CLWd in sire to son selection pathway. The longest generation interval obtained PN (1.95) in sire to daughter pathway. The average relative GD loss within last generation interval was 7.05%, 4.70%, 9.81%, 7.47%, and 10.46%, respectively. The relative proportion of GD loss due to genetic drift on total GD loss was 85.04%, 84.51%, 89.46%, 86.19%, and 83.68% in CLA, CLWd, CLWs, DC, and PN, respectively. All breeds were characterized by a high proportion of inbred animals, but the average inbreeding was low. The most vulnerable breeds to loss of GD are DC and PN. Therefore, a breeding program should be more oriented to prevent the increase of GD loss in these breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제33권9호
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• pp.1369-1377
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• 2020

Objective: The main objectives of the present study were to assess the genetic diversity, population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis. Methods: Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with the use of F_i or ΔF_i as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep. Results: Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37, and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio f_e/f_a obtained in the study was 1.21, which is an indicator of bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree. Conclusion: Study suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended for the herd.

• Animal Bioscience
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• 제36권5호
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• pp.692-703
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• 2023

Objective: The main goals of this investigation were to i) assess the population structure and genetic diversity and ii) determine the efficiency of the ongoing breeding program in a closed flock of Angora rabbits through pedigree analysis. Methods: The pedigree records of 6,145 animals, born between 1996 to 2020 at NTRS, ICAR-CSWRI, Garsa were analyzed using ENDOG version 4.8 software package. The genealogical information, genetic conservation index and parameters based on gene origin probabilities were estimated. Results: Analysis revealed that, 99.09% of the kits had both parents recorded in the whole dataset. The completeness levels for the whole pedigree were 99.12%, 97.12%, 90.66%, 82.49%, and 74.11% for the 1st, 2nd, 3rd, 4th, and 5th generations, respectively, reflecting well-maintained pedigree records. The maximum inbreeding, average inbreeding and relatedness were 36.96%, 8.07%, and 15.82%, respectively. The mean maximum, mean equivalent and mean completed generations were 10.28, 7.91, and 5.51 with 0.85%, 1.19%, and 1.85% increase in inbreeding, respectively. The effective population size estimated from maximum, equivalent and complete generations were 58.50, 27.05, and 42.08, respectively. Only 1.51% of total mating was highly inbred. The effective population size computed via the individual increase in inbreeding was 42.83. The effective numbers of founders (f_e), ancestors (f_a), founder genomes (f_g) and non-founder genomes (f_ng) were 18, 16, 6.22, and 9.50, respectively. The fe/fa ratio was 1.12, indicating occasional bottlenecks had occurred in the population. The six most influential ancestors explained 50% of genes contributed to the gene pool. The average generation interval was 1.51 years and was longer for the sire-offspring pathway. The population lost 8% genetic diversity over time, however, considerable genetic variability still existed in the closed Angora population. Conclusion: This study provides important and practical insights to manage and maintain the genetic variability within the individual flock and the entire population.

• 한국가금학회지
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• 제44권2호
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• pp.83-92
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• 2017

본 연구에서는 가금연구소에서 집단의 혈통 구조 및 근친 수준을 평가하기 위하여 근교계수와 유효집단크기를 추정하였으며, 추정한 근교계수의 신뢰 정도를 제시하기 위하여 혈통의 품질로써 1) 아비 어미를 모두 아는 개체의 비율과 2) 근교계수가 0이 아닌 개체의 비율을 태어난 부화 년도와 계통에 따라 제시하였다. 아비 어미를 모두 아는 개체의 비율에서 대부분 계통이 1~2년 사이에 거의 100%에 도달하였으며, 근교계수가 0이 아닌 개체의 비율에서 기초집단인 0세대부터 5~6년 사이에 비율이 100%에 가깝게 도달하는 것을 보면 가금연구소 혈통기록 시스템이 잘 이루어졌으며, 이 논문에서 추정한 근교계수가 신뢰할 수 있음을 나타낸다. 각 계통의 평균 근교계수에서는 20세대 동안 7.6~10.9%의 근교계수 상승도를 보였다. 세대당 가장 높은 근교계수 상승도를 보인 계통은 S계통으로 10세대 동안 8.2%의 근교계수 상승도를 보였으며, 평균 번식에 참여한 아비 어미의 수가 다른 계통에 비해 낮은 것이 원인인 것으로 사료된다. 평균 근교계수 변화량(${\Delta}F$)으로 추정한 유효집단크기를 보면 모든 계통에서 평균 근교계수 변화량이 0.39~0.85%로 1% 이하로 관리되는 것을 보이며, 따라서 유효집단크기도 모든 계통에서 50 이상의 값을 보였으며, 현 교배 관리에서 토종 닭 집단이 단시간에 근친퇴화나 집단의 멸종으로부터의 위험으로부터 안전하다고 사료된다. 그리고 유효집단크기를 유지하기 위하여, 즉 유전적 다양성을 유지하기 위하여, 적정 수의 아비 어미가 번식에 참여해야 된다고 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제26권6호
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• pp.755-765
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• 2013

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD), Landrace (CL) and Yorkshire (CY) swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.

• Asian-Australasian Journal of Animal Sciences
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• 제29권4호
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• pp.464-470
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• 2016

The objective of this study was to investigate the accuracy of imputation from low density (LDC) to moderate density SNP chips (MDC) in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244) from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570), GGP26K (n = 540) and GGP80K (n = 134) chips. After checking for single nucleotide polymorphism (SNP) quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Animals were divided into two groups, a reference group (n = 912) and a test group (n = 332). The SNP markers chosen for the test group were those located in positions corresponding to GeneSeek GGP9K (n = 7,652). The LDC to MDC genotype imputation was carried out using three different software packages, namely Beagle 3.3 (population-based algorithm), FImpute 2.2 (combined family- and population-based algorithms) and Findhap 4 (combined family- and population-based algorithms). Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed SNP markers to overall imputed SNP markers. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94%) than Findhap (84.64%) and Beagle (76.79%). Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. Most chromosomes that showed either high (73%) or low (80%) imputation accuracies were the same chromosomes that had above and below average linkage disequilibrium (LD; defined here as the correlation between pairs of adjacent SNP within chromosomes less than or equal to 1 Mb apart). Results indicated that FImpute was more suitable than Findhap and Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by increasing the completeness of pedigree information.

• 농업생명과학연구
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• 제50권2호
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• pp.107-116
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• 2016

본 연구는 우리나라의 Holstein 능력검정 암소집단의 혈통자료를 이용하여 근교계수 및 혈통구조를 분석함으로써 Holstein 집단의 유전적 다양성 정도를 알아보고자 실시하였다. 2002년부터 2012년 사이에 태어난 Holstein 400,029두에 대한 능력검정 자료 및 509,740두에 대한 혈통정보를 이용하여 분석하였다. 국내 지역별로 혈통완성도를 분석한 결과, 선조 3대까지의 조상을 알고 있는 개체의 비율은 경기, 강원, 충남, 충북, 경북, 경남, 전남, 전북, 제주 및 우리나라 전체에 대해 각각 55.18, 23.49, 47.83, 53.62, 56.38, 51.35, 26.58, 49.41, 56.90 및 63.20%로 나타났다. 한편, 출생년도 별 평균근교계수는 2002년부터 2012년까지의 년도별 평균 및 전체에 대해 각각 0.43, 0.44, 0.58, 0.64, 0.78, 0.93, 1.08, 1.23, 1.46, 1.77, 2.03 및 0.93%로 추정되었다. 또한 아비에서 딸소까지 평균 세대간격은 8.15년으로 나타났으며, 어미에서 딸소까지 평균 세대간격은 4.20년으로 나타났다. 근교계수 및 세대간격을 이용하여 추정한 국내 능력검정 젖소 집단의 유효집단크기는 2004, 2009 및 2012년에 대해 각각 56.5, 51.3 및 32.2두로 추정되어 시간이 지남에 따라 유효집단의 크기가 감소하는 것으로 추정되었다.