• Asian-Australasian Journal of Animal Sciences
• /
• v.11 no.2
• /
• pp.117-120
• /
• 1998

Relationships of breeding values of sires for first lactation milk yield with pedigree information or indices were examined to identify the optimal criteria of selecting young dairy bulls for future use in artificial insemination (AI). Records of performance data on 1087 crossbred daughters (Holstein - Friesian, Jersey and Brown Swiss with Hariana) of 147 sires, generated at Livestock Production Research (Cattle and Buffaloes) Farm, IVRI, Izatnagar, U.P., during 1972 - 1995 were used to obtain the estimates of sire's breeding values (EBV) using the Best Linear Unbiased Prediction Procedures. The correlations between young bull's EBV and the dam's first lactation milk yield was non-significantly different from zero. However, the young bull's EBV was negatively and significantly related (r = - 0.275 ; P < 0.05) to the dam's best lactation milk yield, suggesting that the selection of young dairy bulls from high yielding elite dams is not a suitable criteria for genetic improvement. The correlations of sire's and paternal grandsire's EBV's with young bull's EBV were high and positive (0.532, 0.844; P < 0.01). The maternal grandsire's EBV was positively but non-significantly related to grandson's EBV. The pedigree index incorporating dam's milk records and sire's EBV's showed a negative and non-significant correlation with young bull's EBV. However, the correlation of a pedigree index $(I_3)$ combining information on sire's and paternal grand-sire's EBV's with young bull's EBV's was considerably high and positive (0.797; P < 0.01). The regression coefficients of young bull's EBV on pedigree index $I_3$, was higher than those on other pedigree information. These results revealed that there was no advantage in basing selection on dam's performance or maternal grand-sire's EBV and that sire's and paternal grandsire's EBV's were reliable pedigree information for selection of young dairy bulls for future use in AI.

• Asian-Australasian Journal of Animal Sciences
• /
• v.33 no.9
• /
• pp.1369-1377
• /
• 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.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.1
• /
• pp.12-18
• /
• 2007

The objective of the study was to compare ranking of Sahiwal bulls selected on the basis of highest lactation milk yield of their dams with their estimated breeding values (EBVs) using an animal model. Data on 23,761 lactation milk yield records of 5,936 cows from five main Livestock Experiment Stations in Punjab province of Pakistan (1964-2004) were used for the study. At present the young A.I bulls are required to be from A-category bull-dams. Dams were categorized as A, B, C and D if they had highest lactation milk yield of ${\geq}$2,700, 2,250-2,699, 1,800-2,249 and <1,800 litres, respectively. The EBVs for lactation milk yield were estimated for all the animals using an individual animal model having fixed effect of herd-year and season of calving and random effect of animal. Fixed effect of parity and random effect of permanent environment were incorporated when multiple lactation were used. There were 396 young bulls used for semen collection and A.I during 1973-2004. However, progeny with lactation yields recorded, were available only for 91 bulls and dams could be traced for only 63 bulls. Overall lactation milk yield averaged 1,440.8 kg. Milk yield was 10% heritable with repeatability of 39%. Ranking bulls on highest lactation milk yield of their dams, the in-vogue criteria of selecting bulls, had a rank correlation of 0.167 (p<0.190) with ranking based on EBVs from animal model analysis. Bulls' EBVs for all lactations had rank correlation of 0.716 (p<0.001) with EBVs based on first lactation milk yield and 0.766 (p<0.001) with average EBVs of dam and sire (pedigree index). Ranking of bulls on highest lactation yield of their dams has no association with their ranking based on animal model evaluation. Young Sahiwal bulls should be selected on the basis of pedigree index instead of highest lactation yield of dams. This can help improve the genetic potential of the breed accruing to conservation and development efforts.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.1
• /
• pp.25-36
• /
• 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.

• Animal Bioscience
• /
• v.36 no.5
• /
• pp.692-703
• /
• 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.

• Journal of Animal Science and Technology
• /
• v.65 no.4
• /
• pp.720-734
• /
• 2023

In Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best linear unbiased prediction [PBLUP], and genomic-BLUP [GBLUP]). The reference population (n = 16,971) was used to estimate breeding values for 481 females as a test population. The accuracy of GBLUP was 0.63, 0.66, 0.62 and 0.63 for carcass weight (CWT), eye muscle area (EMA), back-fat thickness (BFT), and marbling score (MS), respectively. As for the PBLUP method, accuracy of prediction was 0.43 for CWT, 0.45 for EMA, 0.43 for MS, and 0.44 for BFT. Accuracy of PI method was the lowest (0.28 to 0.29 for carcass traits). The increase by approximate 20% in accuracy of GBLUP method than other methods could be because genomic information may explain Mendelian sampling error that pedigree information cannot detect. Bias can cause reducing accuracy of estimated breeding value (EBV) for selected animals. Regression coefficient between true breeding value (TBV) and GBLUP EBV, PBLUP EBV, and PI EBV were 0.78, 0.625, and 0.35, respectively for CWT. This showed that genomic EBV (GEBV) is less biased than PBLUP and PI EBV in this study. In addition, number of effective chromosome segments (M_e) statistic that indicates the independent loci is one of the important factors affecting the accuracy of BLUP. The correlation between M_e and the accuracy of GBLUP is related to the genetic relationship between reference and test population. The correlations between M_e and accuracy were -0.74 in CWT, -0.75 in EMA, -0.73 in MS, and -0.75 in BF, which were strongly negative. These results proved that the estimation of genetic ability using genomic data is the most effective, and the smaller the M_e, the higher the accuracy of EBV.

• Asian-Australasian Journal of Animal Sciences
• /
• v.10 no.6
• /
• pp.614-620
• /
• 1997

Pedigree data were used to predict the performance of 1,166 imported Americas Brahman breeder cattle, composed of 104 bulls and 1,062 heifers with an average age of 24.4 months (range of 17 to 40 months). A total of 13 full sib, 10 maternal half sib, and 228 paternal half sib groups were identified, each with average group size of 2.08, 2.00, and 4.49, respectively. Only 758 (64.9% of total) imported cattle were found to have at least one ancestor with expected progeny differences (EPDs) reported in the Spring 1995 Brahman Sire Summary. Moderate average accuracy values of .71, .69, .52, and .52 for birth weight, weaning weight, yearling weight, and maternal milk, respectively, were noted for EPDs of the ancestors. Prediction equations were derived by multiple regression analysis of available EPDs of sire, paternal grand sire, and maternal grand sire. Based on pedigree indexes that involve various combinations of available ancestral information, the average predicted EPDs (lbs) for imported cattle were $1.76{\pm}0.54$, $14.93{\pm}4.86$, $25.10{\pm}9.50$, and $5.86{\pm}2.08$ for birth weight, weaning weight, yearling weight, and maternal milk, respectively. Significant correlations (p < .05) were also found between sire and son EPDs (+.27) for yearling weight; and between sire and paternal grand sire EPDs for birth weight (+.34), weaning weight (+.51), yearling weight (+.49), and maternal milk (+.55).

• Journal of Animal Science and Technology
• /
• v.52 no.6
• /
• pp.459-466
• /
• 2010

In this study, we suggest an objective standard in selection of candidate horse mates. Korea Racing Authority provided racing records and pedigree information of 44 sires and 954 dams. The datasets were used to predict Racing Indices represented by the averages of earnings earned by offspring for each dam and sire that indicate the racing performance of its domestic progeny. Proportion of wins and second places to the number of taken races and the mean of distances for the won races of a sire were significant factors in linear model with minimum prediction errors. For dam, those factors were the average of earned money per race, number of outstanding broodmares in pedigree, and the comparable index which indicates the relative affinity with its mate. We can use the resultant model for a horse mate by choosing one of the candidates with the largest predicted value for hypothetical offspring.

• Korean Journal of Breeding Science
• /
• v.42 no.5
• /
• pp.525-533
• /
• 2010

In this study, random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) analyses were utilized for evaluation of genetic diversity of 34 Korean bred and introduced apple cultivars. Thirty-seven RAPD primers detected a total of 193 polymorphic bands (36.2%) with an average of 5.6. Twenty-six SSR markers generated a total of 112 alleles with an average 4.3 alleles per locus. Genetic diversity of 34 cultivars estimated by polymorphic information content (PIC) value ranged from 0.536 (CH03d12) to 0.952 (CH04c06) with an average of 0.843. By UPGMA (unweighted pair-group method arithmetic average) cluster analysis with 305 polymorphic bands, the apple cultivars were classified four groups by similarity index of 0.640. The 'Seokwang' was included in group I. Group II consisted of 12 cultivars which have 'Golden Delicious' in their pedigree, with the exception of 'Spur Earliblaze' and 'Jonathan'. Group III included 13 cultivars which have usually 'Fuji' in their ancestry and bud sport of 'Fuji' cultivars. Group IV consisted of 8 cultivars with 'Hongro', 'Gamhong', and 'Saenara'. Similarity values among the tested apple cultivars ranged from 0.529 to 0.987, and the average similarity value was 0.647. The similarity index was the highest (0.987) between 'Hwarang' and 'Danhong', and the lowest (0.529) between 'Seokwang' and 'Hwarang'. The genetic relationships among the 34 studied apple cultivars were basically consistent with the known pedigree.

• Korean Journal of Plant Resources
• /
• v.13 no.1
• /
• pp.1-10
• /
• 2000

Pecan is deciduous tree and belongs to the Julandaceae family. Pecan is an economically important as a nut and timber crop. Heterozygosity is expected to be high for typically cross-pollinated. Yet little is known about the nature of genetic variation within this species. In addition, the pedigree of many pecan cultivars remains unknown or is questionable. In this study, the phylogenetic relationships between 22 pecan cultivars and its analyzed by RAPD (randomly amplified polymorphic DNA). PCR Amplification used 40 randomly selected oligoes as primers. Based on their genetic similarities derived from the RAPD data, the 22 pecan cultivars were classified into different five groups in agarose gel. The 22 pecan cultivars were classified into five sectional groups by UPGMA clustering analysis, too. C. flacra and Black walnut showed the 0.9 of similarity index and Farley, Pawnee showed the 0.85 of similarity index. The 22 pecan cultivars were classified into different five groups by analysis of the 4% polyacrylamide gel fraction. (Group I : 1, 2, 3, 4, 13, 16, 17, 20, 21 Group II : 14,18 GroupIII : 6,12 GroupIV : 5, 11, 15, 19, 22 CroupV : 7, 8, 9, 10) Group V show the 1.0 of similarity index and Farley, Sturya, Clarke, Pawnee show the 0.98 of similarity index and Kiowa, Schley show the 0.92 of similarity index. Results from this study indicated that RAPD can be used to establish the genetic relationships among the 22 pecan cultivars. Similarity coefficients generally agreed with what would be predicted in cultivars with known pedigrees, and we could accurately construct relationships among cultivars. In addition, we have shown that RAPD provides useful information on the origin of unknown cultivars.