• Asian-Australasian Journal of Animal Sciences
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• v.28 no.1
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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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• v.33 no.9
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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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• v.36 no.5
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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.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.83-92
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• 2017

The purpose of this study was to estimate the inbreeding level and effective population size of Korean indigenous chickens. In the study, two variables were considered to evaluate the pedigree completeness: (1) the proportion (%) of animals with complete pedigree, and (2) the proportion of animals with inbreeding coefficients greater than zero. In the proportion of animals having complete pedigree, all strains reached almost 100% completeness in 1~2 years. In the proportion of animals with inbreeding coefficients greater than zero, all strains reached almost 100% completeness in 5~6 years. We considered that the pedigree recoding system is well managed and that the inbreeding coefficient is a reliable measure. Over the past 20 years, the increase of inbreeding coefficients in Korean indigenous chicken strains has been 7.6~10.9%. The S strain showed the most rapid increase of inbreeding coefficient of 8.2% in 10 years. The reason for this rapid increase is considered to be associated with the fact that the numbers of sires and dams involved in reproduction was 115 and 91, respectively, which are lower than those of the other strains. According to average rates of increase in inbreeding coefficients (${\Delta}F$), all strains have ${\Delta}F$ values of 0.39~0.85%, which is lower than 1%, and the effective population size is above 50. The results showed that inbreeding levels were within the acceptable range and that Korean indigenous chicken population scan be regarded as safe from the threat of extinction.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.6
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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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• v.29 no.4
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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.

• Journal of agriculture & life science
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• v.50 no.2
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• pp.107-116
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• 2016

The study was aimed to analyze pedigree structure and inbreeding coefficients for performance tested Holstein cows in Korea. A total of 400,029 Holstein cows data which born between 2002 and 2012 were obtained from Dairy Cattle Improvement Center of National Agricultural Cooperative Federation(NACF). Their related pedigrees, as obtained from Korean Animal Improvement Association(KAIA), consisted of 509,740 animals. Pedigree depth of the cows were traced back to 3 generations earlier. The percentage of cows with fully identified ancestors in various provinces of Korea were 55.18%(Gyeonggi-do), 23.49%(Gangwon-do), 47.83%(Chungcheongnam-do), 53.62%(Chungcheongbuk-do), 56.38%(Gyeongsangbuk-do), 51.35% (Gyeongsangnam-do), 26.58%(Jeollanam-do), 49.41%(Jeollabuk-do), and 56.90%(Jeju-do), whereas, it was about 63.20% as a whole in Korea. The average inbreeding coefficients showed increment across the consecutive years of birth such as, 0.43(2002), 0.44(2003), 0.58(2004), 0.64(2005), 0.78(2006), 0.93(2007), 1.08(2008), 1.23(2009), 1.46(2010), 1.77(2011), and 2.03 (2012). However, this coefficient was 0.93 in overall Korean population. An average generation interval for sire to daughter genetic path was 8.15 years; which was about 4.20 years considering dam to daughter genetic path. The estimated effective population sizes (Ne) were 56.5, 51.3, and 32.2 animals born in 2004, 2009, and 2012, respectively. These results indicated that an increased rate of inbreeding has led to a significant reduction in the Ne over the decade.