• Title, Summary, Keyword: Expected Inbreeding

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Studies on Inbreeding and Its Effects on Growth and Fleece Traits of Muzaffarnagari Sheep

  • Mandal, Ajoy;Pant, K.P.;Notter, D.R.;Rout, P.K.;Roy, R.;Sinha, N.K.;Sharma, N.
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.10
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    • pp.1363-1367
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    • 2005
  • A pedigree file of 4,738 records of a purebred flock of Muzaffarnagari sheep, maintained at Central Institute for Research on Goats (CIRG), Makhdoom, for a period of 24 years (1978 to 2001) was used to calculate inbreeding coefficients. The lambtraits studied were birth, 3, 6, 9 and 12 months weights as well as 6 and 12 months fleece yields. The lambs' and ewes' inbreeding coefficients ranged from 0 to 26.4% and 0 to 25%, respectively. The average inbreeding coefficient of lambs was higher than that of ewes in all periods as expected in a closed flock. Fluctuations in lamb and ewe inbreeding were observed in the periods under study. The percentages of animals in the higher inbred categories varied somewhat but generally were relatively constant. The mean rate of inbreeding was 0.63% per generation. The effective population size of the flock was 79.1. On average, an increase of 1% individual inbreeding significantly (p<0.05) reduced weights at birth by 0.010 kg, at 3 month by 0.048 kg, at 6 month by 0.075 kg, at 9 month by 0.129 kg and at 12 month by 0.112 kg. Ewes' inbreeding had non-significant effects on body weight at all ages. Effects of both lambs' and ewes' inbreeding had negative but non-significant effects on fleece weights at 6 and 12 months of age. Thus, inbreeding depression in lambs significantly reduced body weights from birth to 12 months of age but had a negligible effect on fleece yields.

Evaluation of Inbreeding and Genetic Variability of Five Pig Breeds in Czech Republic

  • Krupa, Emil;Zakova, E.;Krupova, Z.
    • 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.

Genetic parameters and inbreeding effects for production traits of Thai native chickens

  • Tongsiri, Siriporn;Jeyaruban, Gilbert M.;Hermesch, Susanne;van der Werf, Julius H.J.;Li, Li;Chormai, Theerachai
    • Asian-Australasian Journal of Animal Sciences
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    • v.32 no.7
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    • pp.930-938
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    • 2019
  • Objective: Estimate genetic parameters, the rate of inbreeding, and the effect of inbreeding on growth and egg production traits of a Thai native chicken breed Lueng Hang Kao Kabinburi housed under intensive management under a tropical climate. Methods: Genetic parameters were estimated for weight measured at four weekly intervals from body weight at day 1 (BW1D) to body weight at 24 weeks (BW24) of age, as well as weight at first egg, age at first egg (AFE), egg weight at first egg, and total number of eggs (EN) produced during the first 17 weeks of lay using restricted maximum likelihood. Inbreeding depression was estimated using a linear regression of individual phenotype on inbreeding coefficient. Results: Direct additive genetic effect was significant for all traits. Maternal genetic effect and permanent environmental hen effects were significant for all early growth traits, expect for BW24. For BW24, maternal genetic effect was also significant. Permanent environmental hen effect was significant for AFE. Direct heritabilities ranged from 0.10 to 0.47 for growth traits and ranged from 0.15 to 0.16 for egg production traits. Early growth traits had high genetic correlations between them. The EN was lowly negatively correlated with other traits. The average rate of inbreeding for the population was 0.09% per year. Overall, the inbreeding had no effect on body weight traits, except for BW1D. An increase in inbreeding coefficient by 1% reduced BWID by 0.09 g (0.29% of the mean). Conclusion: Improvement in body weight gain can be achieved by selecting for early growth traits. Selection for higher body weight traits is expected to increase the weight of first egg. Due to low but unfavorable correlations with body weight traits, selection on EN needs to be combined with other traits via multi-trait index selection to improve body weight and EN simultaneously.

SLA Homozygous Korean Native Pigs and Their Inbreeding Status Deduced from the Microsatellite Marker Analysis

  • Jung, Woo-Young;Lim, Hyun-Tae;Lim, Jae-Sam;Kim, Sung-Bok;Jeon, Jin-Tae;Lee, Jun-Heon
    • Journal of Animal Science and Technology
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    • v.52 no.6
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    • pp.451-457
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    • 2010
  • The porcine MHC (Major Histocompatibility Complex), encoding the SLA (Swine Leukocyte Antigen) genes, is one of the most significant regions associated with immune rejection in relation to transplantation. In this study, three SLA class I (SLA-1, SLA-3, SLA-2) loci and three SLA class II (DRB1, DQB1, DQA) loci were investigated in the previously unidentified Korean native pig (KNP) population that was closely inbred in the Livestock Technology Research Station in Cheongyang, Korea. Total thirteen KNPs from four generations were genotyped for the SLA alleles and haplotypes were investigated using PCR-SSP (Sequence-Specific Primer) method. The results showed that all of these KNPs had Lr-56.30/56.30 homozygous haplotype, indicating high level of inbreeding in the SLA genes. The inbreeding status of these animals was also investigated using microsatellite (MS) markers. From the 50 MS markers investigated, 17 MS markers were fixed in all generations and the fixed alleles are increased as 26 loci for the fourth generation. Two MS markers, S0069 and SW173, were heterozygous for all the animals tested. Observed and expected heterozygosities were calculated and the average inbreeding coefficients for each generation were also calculated. In the fourth generation, the average inbreeding coefficients was 0.732 and this may increase with further inbreeding process. Analysis of the SLA haplotypes and MS alleles can give important information for breeding the pigs for xenotransplantation studies.

Genetic Diversity of Magra Sheep from India Using Microsatellite Analysis

  • Arora, R.;Bhatia, S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.7
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    • pp.938-942
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    • 2006
  • Genetic diversity of Magra - a lustrous carpet wool breed of India, was investigated by means of 25 ovine microsatellite markers proposed by the Food and Agriculture Organization and the International Society for Animal Genetics (FAO-ISAG). All used microsatellites amplified well and exhibited polymorphisms. A wide range of genetic variability was observed as allele number from 3 (BM6506, OarCP20) to 10 (CSSM31), observed heterozygosity from 0.200 (BM6506) to 0.947 (OarHH35), expected heterozygosity from 0.368 (CSSM47) to 0.864 (BM1314) and Polymorphism Information Content (PIC) from 0.347 (CSSM47) to 0.849 (BM1314). This supported the utility of these microsatellite loci in the measurement of genetic diversity indices in Indian sheep too. Various average genetic variability measures viz., allele diversity (5.7), observed heterozygosity (0.597), expected heterozygosity (0.694) and mean PIC (0.648) values showed high genetic variability despite accumulated inbreeding as reflected by the high average inbreeding coefficient ($F_{IS}=0.159$) due to the unequal sex ratio of the breeding animals.

Estimation of Genetic Variation in Holstein Young Bulls of Iran AI Station Using Molecular Markers

  • Rahimi, G.;Nejati-Javaremi, A.;Saneei, D.;Olek, K.
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.4
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    • pp.463-467
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    • 2006
  • Genetic profiles of Iranian Holstein young bulls at the national artificial insemination station were determined on the basis of individual genotypes at 13 ISAG's recommended microsatellites, the most useful markers of choice for parentage identification. In the present study a total of 119 individuals were genotyped at 13 microsatellite loci and for possible parent-offspring combinations. A high level of genetic variation was evident within the investigated individuals as assessed from various genetic diversity measures. The mean number of observed alleles per microsatellite marker was 9.15 and the number of effective alleles as usual was less than the observed values (4.03). The average observed and expected heterozygosity values were 0.612 and 0.898, respectively. The mean polymorphic information content (PIC) value (0.694) further reflected a high level of genetic variability. The average exclusion of probability (PE) of the 13 markers was 0.520, ranging from 0.389 to 0.788. The combined exclusion of probability was 0.999, when 13 microsatellite loci were used for analysis in the individual identification system. Inbreeding was calculated as the difference between observed and expected heterozygosity. Observed homozygosity was less than expected which reflects inbreeding of -3.7% indicating that there are genetic differences between bull-sires and bull-dams used to produce young bulls. The results obtained from this study demonstrate that the microsatellite DNA markers used in the present DNA typing are useful and sufficient for individual identification and parentage verification without accurate pedigree information.

Performance Evaluation of Karan Fries and Karan Swiss Cattle under Closed Breeding System

  • Singh, M.K.;Gurnani, M.
    • Asian-Australasian Journal of Animal Sciences
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    • v.17 no.1
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    • pp.1-6
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    • 2004
  • The 490 and 380 performance records of Karan Fries and Karan Swiss cows developed through crossbreeding followed by inter-se mating were evaluated for production, reproduction performance and disposal rate. Duration of study (1982-92) was grouped into five periods (1982-83; 1984-85; 1986-87; 1988-89; 1990-92) and each year was divided into four seasons (Winter: Dec.-Jan.; Spring: Feb.-March; Summer: April-June; Rainy: July-Sept.; Autumn: Oct.-Nov). Data were also classified according to sire and level of inbreeding. The least squares means of FLY (first lactation yield -305 days), FLL (first lactation length), FSP (first service period), FDP (first dry period), FCI (first calving interval ), MY/FLL (milk yield per day of first lactation length), MY/FCI (milk yield per day of first calving interval), EBV (expected breeding value) and EBE (expected breeding efficiency) were $3,173{\pm}82$ kg, $34611{\pm}$days, $143{\pm}11$ days, $75{\pm}6$ days, $423{\pm}11$ days, $10.6{\pm}0.2$ kg, $8.9{\pm}0.2$ kg, $3,380{\pm}26$ kg, and $88.2{\pm}1.3$% respectively in Karan Fries. Corresponding estimates in Karan Swiss cows were $2,616{\pm}82$ kg, $328{\pm}8$ days, $148{\pm}12$ days, $103{\pm}9$ days, $435{\pm}13$ days, $8.9{\pm}0.2$ kg, $7.2{\pm}0.3$ kg, $2,924{\pm38}$ kg and $86.0{\pm}3.8$% respectively. The effect of sire was significant on FLY, MY/FLL, MY/FCI and EBV in both the herd (p<0.01). The 10 and 15% sires showed superiority (FLY) over herd average of 11 and 7% in Karan Fries and 32 and 21% in Karan Swiss cattle respectively. Inbreeding has adversely and significantly (p<0.05) affected the FLY, MY/FLL, MY/FCI and survivability of Karan Fries females; FDP and disposal through culling of Karan Swiss heifers. The Karan Fries heifers with inbreeding above 12.5% performed 16% lower FLY to herd average. The effect of season of calving was significant on FLL, FSP and FCI (p<0.05) in Karan Fries. Summer calvers ($361{\pm}12$) were have higher lactation length and autumn calvers ($329{\pm}14$) had minimum. Period of calving significantly influenced the FSP, FCI, MY/FLL and MY/FCI in Karan Fries and FLY, MY/FLL and MY/FCI in Karan Swiss. Production efficiency traits in Karan Fries herd witnessed higher yield in the last two periods whereas, Karan Swiss heifers showed fluctuating performance. The findings suggested judicious use of available genetic variability, keeping of inbreeding under safer level and managemental interventions for the consistent improvement of both herds.

Genetic Diversity Analyses of Asian Duck Populations using 24 Microsatellite Markers

  • Sultana, Hasina;Seo, Dongwon;Choi, Nu-Ri;Kim, Yeon-Su;Manjula, Prabuddha;Bhuiyan, Md. Shamsul Alam;Heo, Kang-Nyeong;Lee, Jun-Heon
    • Korean Journal of Poultry Science
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    • v.44 no.2
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    • pp.75-81
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    • 2017
  • A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.

Genetic Diversity Measures of 8 Local Sheep Breeds in Northwest of China for Genetic Resource Conservation

  • Zeng, X.C.;Chen, H.Y.;Hui, W.Q.;Jia, B.;Du, Y.C.;Tian, Y.Z.
    • Asian-Australasian Journal of Animal Sciences
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    • v.23 no.12
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    • pp.1552-1556
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    • 2010
  • The aim of this study was to evaluate, through the use of microsatellite markers, the current genetic diversity and the relationships of 375 individuals from 8 local sheep breeds reared in typical breeding farms in the northwest of China, and moreover, to offer a contribution towards genetic conservation decisions for the studied breeds. The expected heterozygosities and allelic richness for the 8 breeds varied from 0.474 to 0.623 and from 3.8 to 5.4, respectively. All the populations showed a significant deficit in heterozygosity and a relatively low level of genetic diversity. Furthermore, the high positive FIS value (ranging from 0.255 to 0.556) indicated inbreeding to be one of the main causes for high genetic homogeneity and lack of heterozygosity in all breeds. The clustering analysis performed with the DISPAN package showed that Aletai, Kazak, Bashibai and Bayinbuluke were grouped together, and Hetian, Qira black and Duolang were grouped together, which indicated that the relationship among breeds displayed some degree of consistency with their geographical distribution, production and origin. These findings indicate that improved conservation measures must be undertaken to avoid further losses of genetic diversity and minimize inbreeding represented by these breeds.

Molecular Characterisation of Nilagiri Sheep (Ovis aries) of South India Based on Microsatellites

  • Girish, Haris;Sivaselvam, S.N.;Karthickeyan, S.M.K.;Saravanan, R.
    • Asian-Australasian Journal of Animal Sciences
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    • v.20 no.5
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    • pp.633-637
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    • 2007
  • Genetic variation in Nilagiri sheep, the only apparel wool breed in South India was studied using 25 FAO recommended ovine-specific microsatellite markers. The number of observed alleles ranged from 3 to 8 with a mean of 5 across all loci. The size of alleles ranged from 72 to 228 bp. The frequency of alleles ranged from 0.0104 to 0.5781. In total, 125 alleles were observed at the 25 loci studied. The effective number of alleles ranged from 2.18 to 6.49. The mean number of effective alleles was 3.84 across all loci. All the 25 loci were found to be highly polymorphic. The PIC values ranged from 0.4587 to 0.8277 with a mean of 0.6485. Of 25 microsatellites studied, 17 were in Hardy-Weinberg Equilibrium proportions. The observed heterozygosity ranged from 0.4222 to 1.000 with a mean value of 0.7610 whereas the expected heterozygosity ranged from 0.5415 to 0.8459 with a mean value of 0.7213. Except six loci, the other loci revealed negative within-population inbreeding estimates (FIS) indicating excess of heterozygotes in the population of Nilagiri sheep.