Genetic Analyses of South African Terminal Sire Sheep Breeds
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GENETIC ANALYSES OF SOUTH AFRICAN TERMINAL SIRE SHEEP BREEDS by Oliver Tendayi Zishiri Thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Agriculture (Animal Sciences) at Stellenbosch University Faculty of AgriSciences Department of Animal Sciences Supervisor: Professor S.W.P. Cloete Co-supervisor: Professor K. Dzama Dr J.J. Olivier Date: March 2009 DECLARATION By submitting this thesis electronically, I declare that the entirety of the work contained is my own, original work, and that I have not previously in its entirety or in part submitted it for obtaining any qualification. Date…………………………………………… Copyright © 2009 Stellenbosch University All rights reserved ii Abstract Genetic analyses of South African terminal sire sheep breeds Candidate : Oliver Tendayi Zishiri Study leader : Professor S.W.P. Cloete Co-study leaders : Professor K. Dzama Dr. J.J. Olivier Department : Animal Sciences Faculty : Agricultural and Forestry Sciences Degree : MSc Agric Fluctuations and a general decline in the ratio between wool and meat prices resulted in marked changes in the South African sheep industry. Commercial producers now exploit other mechanisms such as terminal crossbreeding of Merino-type with meat type breeds or dual-purpose breeds to attain short-term benefits resulting from price fluctuations between wool and mutton without compromising the wool-producing capacities of ewe flocks. Most components of lamb production have low heritability. However, heterosis can be achieved by mating wool-type breeds with specialist meat breed rams. Genetic improvement of livestock depends on defining breeding objectives, estimation of genetic parameters and accurately identifying the right animals to be used for future breeding. Genetic parameters for traits of economic importance in terminal sire sheep breeds that could be used on Merino-type ewes in commercial operations in South Africa had not been published for the national flock apart from a preliminary study having been conducted by Olivier et al. (2004). Selection objectives were poorly defined due to lack of parameter estimates for variance and covariance components. Against this background, this study obtained pedigree information and live weight data from the National Small Stock Improvement Scheme for the Dormer, Ile de France and Merino Landsheep and estimated non-genetic factors and genetic parameters influencing early growth traits. Genetic and phenotypic trends for early growth traits were constructed for the three breeds to monitor genetic progress. Non-genetic factors influencing early growth traits in the Dormer, Ile de France and Merino Landsheep were estimated using data obtained from the National Small Stock Improvement Scheme of South Africa. The original data sets for the Dormer, Ile de France and Merino Landsheep consisted of the following number of records respectively: 52 202, 35 553 and 7 772. However, pre-weaning weights were available for the Ile de France and Merino Landsheep breeds only and post-weaning weights were available only for the Dormer breed. The data sets were complicated to such an extent that smaller data sets had to be generated to analyse for fixed effects. The traits that were analysed were birth weight, pre-weaning weight, weaning weight and post-weaning weight. The fixed effects, identified as having a significant effect (P < 0.01) on early growth traits were sex of lamb, birth type, age of dam, contemporary groups, age at which the trait was recorded and month of birth and year of birth iii in the Merino Landsheep breed. Although some significant interactions were found, they were subsequently ignored owing to their very small effects. In all three breeds, male lambs were significantly (P < 0.001) heavier than female lambs and single-borne lambs were significantly heavier at birth than multiple borne lambs. The age of dam had a significant curvilinear regression on all early growth traits in all three terminal sire sheep breeds. It was concluded from the study that the influence of non-genetic factors on early growth traits should be adjusted for or eliminated statistically in genetic evaluations to get accurate genetic parameter estimations. (Co)variance estimates for birth weight, weaning weight and post-weaning weight were obtained for the Dormer breed using restricted maximum likelihood procedures (REML). Direct heritabilities (h2) in single-trait analyses were 0.21 ± 0.03, 0.23 ± 0.02 and 0.29 ± 0.05 for birth weight, weaning weight and post-weaning weight, respectively. Direct heritabilities of 0.28 ± 0.04, 0.55 ± 0.06 and 0.32 ± 0.02 for birth weight, weaning weight and post-weaning weight respectively were obtained using three-trait analysis. Direct maternal genetic effects (m2) were excluded from the analyses because of the failure to partition maternal effects into maternal genetic and maternal permanent environmental effects (m2 and c2). This culminated as a consequence of poor data and population structures emanating from the loss of genetic links across flocks due to the random entrance and exit of flocks from the recording scheme. Maternal permanent environment was estimated at 0.15 ± 0.02, 0.13 ± 0.02 and 0.20 ± 0.03 for birth weight, weaning weight and post-weaning weight respectively using single-trait analysis. The correlation between direct effects and maternal effects (ram) was excluded from the analyses due the structure of the data. Genetic, phenotypic and environmental correlations between early growth traits were low to moderate. The medium to high heritability estimates for early growth traits obtained in the study led to the conclusion that Dormer sheep can successfully be used in terminal crossbreeding programs to improve meat production characteristics. Direct heritability estimates were 0.31 ± 0.14, 0.09 ± 0.02 and 0.14 ± 0.003 for birth weight, pre-weaning weight and weaning weight respectively using single-trait analysis for the Ile de France breed. Maternal effects were significant for all the traits studied despite the failure to properly partition them into their components due to the loss of genetic linkages across generations emanating from poor data structure. Genetic, phenotypic and environmental correlations were estimated using three-trait analysis and were found to be low to moderate for early growth traits. Direct genetic and maternal permanent environmental ratios were also computed and they did not differ much from the results obtained using single-trait analyses. The reasonable genetic parameter estimates obtained in the study led to the conclusion that the Ile de France can be selected to use as sires in crossbreeding programs. Genetic parameters were estimated for early growth traits in the Merino Landsheep breed. REML estimates of birth weight, pre-weaning weight and weaning weight were obtained using animal models in single-trait analyses. The direct heritability estimate for birth weight was 0.23 ± 0.13 using an animal model with additive direct genetic effects and dam permanent environmental effects as the only random factors. The dam permanent environmental effect for birth weight amounted to 0.10 ± 0.07. Direct heritability for pre-weaning weight was 0.36 ± 0.05 and the dam permanent environmental effect 0.56 ± 0.03. Weaning weight was estimated using an animal iv model that contained direct additive effects and dam permanent environmental effects. The direct heritability estimate for weaning weight was 0.17 ± 0.03. Maternal genetic effects were estimated to be 0.02 ± 0.01. Genetic and phenotypic trends were constructed for early growth traits in the Dormer, Ile de France and Merino Landsheep breeds. The traits that were considered were birth weight, pre-weaning weight, weaning weight and post-weaning weight. However, pre-weaning weights were available for the Ile de France and Merino Landsheep breeds only and post-weaning weights were available only for the Dormer breed. The Dormer exhibited significant improvement in the phenotypic and genetic aspects of early growth traits during the 17 years of evaluation (1990-2007). The average predicted direct breeding values of birth weight decreased by 0.055 % during the evaluation period. The predicted direct breeding value for weaning weight increased by 0.12 % during the 17 year period. Post-weaning weight improved by 0.32 % per annum. The Ile de France registered an increase in the predicted breeding value of birth weight which amounted to 0.025 % per annum. Averaged direct breeding values for pre-weaning weight increased at an annual rate of 0.23 %. and that of weaning weight increased by 1.21 %. In the Merino Landsheep the predicted direct breeding value for birth weights decreased by 0.04 % per annum and pre-weaning and weaning weights increased by 0.36 % and 0.10 % respectively. The trends were obviously biased due to inconsistencies in data structure and very few records available for analysis in this breed. In conclusion, it was evident that the additive genetic variation was available for all the early growth traits in all the three breeds. Although adequate genetic variation for substantial genetic progress was available, only modest rates of progress were attained for all the traits in all three breeds. The only possible exception was weaning weight in the Ile de France breed, which improved at > 1 % per annum. At least all changes were in the desired direction. Breeders should be encouraged to record data consistently, as one of the major shortcomings in the data for all breeds were a lack of continuity in the submission of data to the NSIS. More informative analyses ought to be feasible if this requisite could be met. v Opsomming Genetiese analise van die verskillende Suid-Afrikaanse terminale kruisvaarrasse Kandidaat : Oliver Tendayi Zishiri Studieleier : Professor S.W.P. Cloete Mede- Studieleiers : Professor K. Dzama Dr. J.J. Olivier Departement Veekundige Wetenskappe Fakulteit : Landbou en Bosbou Wetenskappe Graad : M.Sc Landbou Die wisselende en algemene afname in die prysverhouding van wol tot vleis het merkbare veranderinge in die Suid-Afrikaanse skaapbedryf teweeggebring.