Genetic analyses of South African terminal sire sheep breeds

Zishiri, Oliver Tendayi (2009-03)

Thesis (MScAgric (Animal Sciences))--University of Stellenbosch, 2009.

Thesis

ENGLISH ABSTRACT: 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 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 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.

AFRIKAANSE OPSOMMING: Die wisselende en algemene afname in die prysverhouding van wol tot vleis het merkbare veranderinge in die Suid-Afrikaanse skaapbedryf teweeggebring. Kommersïele produsente maak nou gebruik van ander metodes soos terminale kruisteling van Merino-tipe ooie met vleis tipe vaars of dubbel-doel rasse om korttermynvoordele uit die wisselende wol en vleis pryse te behaal, sonder om die wol-produksie potensiaal van die ooi-kudde te benadeel. Die meeste van die lamproduksie eienskappe het ‘n lae oorerflikheid. Nietemin, kan heterose wel behaal word deur die kruisteling van wol-tipe rasse met spesialis vleisramme. Genetiese verbetering van vee is afhanklik van die beskrywing van die teeltdoelwitte, die akkurate beraming van genetiese parameters en die noukeurige identifikasie van die geskikste diere vir toekomstige teling. Genetiese parameters vir ekonomies belangrike eienskappe van terminale ramrasse wat gebruik kan word op Merino-tipe ooie in die kommersiële skaapbedryf in Suid-Afrika is nog nie gepubliseer vir die nasionale kudde nie, behalwe vir ‘n voorlopige studie wat gedoen is deur Olivier et al. (2004). Seleksiedoelwitte is nie duidelik beskryf nie a.g.v ‘n tekort aan akkurate parameterberamings vir (ko)variansie komponente. Hierdie studie het dus stamboominligting en lewende gewig data verkry vanaf die Nasionele Kleinveeverbeteringsskema vir die Dormer-, Ile de France- en die Merino landskaaprasse en nie-genetiese faktore sowel genetiese parameters vir vroeë lamgewigte beraam. Genetiese en fenotipiese tendense vir vroeë lamgewigte is vervolgens opgestel vir drie rasse om genetiese vordering te evalueer. Die oorspronklike datastelle vir die Dormer, Ile de France en die Merino Landskaap het uit die volgende aantal rekords bestaan, onderskeidelik: 52 202, 35 553 en 7 772. Voor-speen gewigte was net beskikbaar vir die Ile de France- en die Merino Landskaaprasse, en na-speen gewigte was net beskikbaar vir die Dormerras. Die beperkings in die datastelle het genoodsaak dat dat kleiner datastelle ontwikkel moes word om die vaste effekte te analiseer. Die eienskappe wat ge-analiseer was, was geboortegewig, voor-speengewig, speengewig en naspeengewig. Die vaste effekte wat vroeë lamgewigte betekenisvol (P < 0.01) beïnvloed het, was geslag van die lam, geboortestatus, ouderdom van die ooi, kontemporêre groep, die ouderdom waarop die eienskap aangeteken is en (in sommige gevalle) die maand en jaar van geboorte. Alhoewel daar sommige betekenisvolle interaksies was, is dit nie in die finale modelle ingesluit nie, omdat dit min tot die verklaarde variasie bygedra het. In al die rasse het ramlammers swaarder (P < 0.001) geweeg as ooilammers. Enkelinge was ook swaarder (P<0.001) as meerlinge. Die ouderdom van die moer van die lam het ‘n beduidende kromlynige invloed op alle vroeë lamgewigte by al drie terminale ramrasse gehad. Die gevolgtrekking van hierdie studie is dat die invloed van nie-genetiese faktore op vroeë lamgewigte in ag geneem moet word, of dat dit moet statisies elimineer word in die genetiese evaluasie om akkurate genetiese beramings te verkry. (Ko)variansie beramings vir geboortegewig, speengewig en na-speengewig is deur gebruik te maak van die “restricted maximum likelihood procedures” (REML) vir die Dormerras verkry. Die direkte oorerflikheid (h2) wat verkry was deur die mees geskikste diere model in ‘n enkel-eienskap analise te gebruik was onderskeidelik 0.21 ±0.02, 0.23 ±0.02 en 0.29± 0.05 vir geboortegewig, speengewig en na-speengewig. Direkte ooreenstemende oorerflikheid wat uit die drie-eienskap analise was 0.28±0.04, 0.55±0.06 en 0.32±0.02 onderskeidelik vir geboortegewig, speengewig en na-speengewig. Direkte maternale genetiese effekte (m2) is uitgesluit vanaf die analise weens die onvermoë om die maternale effekte te verdeel in maternale genetiese effekte en maternale permanente omgewings effekte (m2 en c2). Dit was a.g.v onvolledige data en populasiestrukture wat gelei het tot die gebrek in genetiese bande oor kuddes, wat ontstaan het weens kuddes wat slegs tydelik data tot die skema bygedra het. Maternale permanente omgewingeffekte is geskat op onderskeidelik 0.15±0.02, 0.13±0.02 en 0.20±0.03 vir geboortegewig, speengewig en na-speengewig met die gebruik van die enkel-eienskap analise. Die korrelasie tussen direkte effekte en maternale effekte (ram) is uitgesluit a.g.v die gebrekkige struktuur van die data. Genetiese-, fenotipiese- en omgewingskorrelasies tussen die vroeë lamgewigte was laag tot matig. Die matige tot hoë oorerflikheidberamings vir vroeë lamgewigte uit hierdie studie het gelei tot die gevolgtrekking dat Dormer skape suksesvol gebruik kan word in terminale kruisteel programme om vleisproduksie te verbeter. Direkte oorerflikheid skattings was 0.31±0.14, 0.09±0.02 en 0.14±0.003 vir die geboorte gewig, voor-speen gewig en speen gewig onderskeidelik met die gebruik van ‘n enkel-faktor analise vir dir Ile de France skaap ras. Maternale effekte was beduidend vir al die eienskappe wat bestudeer was , ten spyte van die onvermoë om dit behoorlik te verdeel in hul komponente weens die verlies van genetiese bande dwarsoor die generasies wat uitvloei vanaf ‘n swak data struktuur. Genetiese, fenotipiese en omgewings korrelasies was geskat deur gebruik te maak van ‘n drie-faktor analise en was gevind om laag tot matig te wees vir die vroeë groei eienskappe. Direkte genetiese en maternale permanente omgewings ratios was bereken en dit het nie veel verskil van die resultate verkry deur die enkel-faktor analise. Die aanvaarbare genetiese parameter skattings verkry in hierdie studie het gelei tot die gevolgtrekking dat die Ile de France geselekteer kan word as teelramme in kruisteel programme. Genetiese parameters was geskat vir vroeë groei eienskappe in die Merino Landskaa ras. REML skattings van geboorte gewig, voor-speen gewig en speen gewig was verkry deur diere modelle in enkel-faktor analises. Die direkte oorerflikheid skatting vir geboorte gewig was 0.23±0.13 met die gebruik van die diere model met additiewe direkte genetiese effekte en ooi permanente omgewings faktore as die enigste ewekansige faktore. Die ooi permanente omewings effek vir geboorte gewig was 0.10±0.07. Direkte oorerflikheid vir voor-speen gewig was 0.36±0.05 en die ooi permanente omgewings effek 0.56±0.03. Speen gewig was geskat deur die gebruik van ‘n diere model wat die direkte additiewe effekte en die ooi permanente omgewings effekte bevat het. Die direkte oorerflikheids skatting vir speen gewig was 0.17±0.03. Maternale genetiese effekte was geskat as 0.02±0.01. Genetiese en fenotipiese tendense is verkry vir vroeë lamgewigte in die Dormer-, Ile de France- en Merino Landskaaprasse. Die eienskappe wat oorweeg is, was geboortegewig, voor-speengewig, speengewig en naspeengewig. Voor-speengewigte was net beskikbaar was vir die Ile de France- en die Merino Landskaap rasse en die na-speense gewigte net vir die Dormerras. Die Dormer het beduidende verbetering vertoon in die fenotipiese en genetiese aspekte vir vroeë lamgewigte gedurende die 17 jaar van evaluasie (1990-2007). Die gemiddelde voorspelde direkte teeltwaarde van speen gewig het met 0.12% per jaar gestyg gedurende die 17- jaar periode. Na-speen gewig het met 0.32% per jaar verbeter. By die Ile de France het ‘n toename in die voorspelde teelwaarde van geboortegewig (0.025% per jaar) voorgekom. Gemiddelde direkte teelwaardes vir voor-speengewig het toegeneem teen ‘n jaarlikse tempo van 0.23% en speengewig het met 1.21% per jaar toegeneem. In die Merino Landskaapras het die voorspelde direkte teelwaarde vir geboortegewig met 0.04% per jaar gedaal, terwyl voor-speen- en speengewigte met 0.36% en 0.10% onderskeidelik toegeneem het. Die tendense was ooglopend gekompromiteer weens probleme met die data struktuur, en a.g.v van die relatief min rekords wat beskikbaar was vir die analise in die ras. Dit was duidelik dat die additiewe genetiese variasie beskikbaar was vir al die vroeë groei eienskappe in al die drie rasse. Alhoewel voldoende genetiese variasie vir wesentlike genetiese vordering beskikbaar was, is daar slegs matige vordering verkry vir al die eienskappe in al drie rasse. Die enigste moontlike uitsondering was speengewig in die Ile de France ras, wat met 1.21 % per jaar gestyg het. Alle veranderinge was minstens in die gewensde rigting. Telers word versoek om data deurlopend en akkuraat aan te teken , aangesien een van die groot tekortkominge met die data van al die rasse ‘n tekort aan deurlopendheid in die indiening van die data aan die NISS was. ‘n Meer verteenwoordigende analise sal uitvoerbaar wees, as daar aan al die bogenoemde aanbeveling voldoen kan word.

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