The genetic and environmental modelling of production and reproduction in ostrich females within and across breeding seasons

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Date
2012-01
Authors
Fair, Michael Denis
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University of the Free State
Abstract
English: Pedigree and performance data of a well-documented ostrich breeding resource flock was used to (1) investigate the flock structure, (2) estimate variance and (co)variance components for egg and day-old chick weight (individual traits), (3) estimate genetic and environmental parameters for egg and chick production, mean egg and day-old chick weights and hatchability within breeding seasons (hen traits) and (4) investigate early identification of superior animals using random regression models for repeated measures (longitudinal) data over years. The average level of pedigree completeness of 40 074 birds of a pair-breeding ostrich flock maintained from 1978 to 2005 at the Oudtshoorn Research Farm, South Africa was high (99.3%) in the first generation and the average level of inbreeding (F) was low at 0.51%. The estimated measures of variability were: effective genome equivalents = 47.3, effective number of founders = 59 and the effective number of ancestors = 58. The numbers of ancestors responsible for 100%, 50% and 20% of the variation in the reference population (birds with both parents known), were equal to 254, 21 and 6 respectively. The generation interval in years calculated as the average age of parents when their offspring which were kept for reproduction were born, amounted to 7.72 ± 4.79 years. The linear regressions of rate of inbreeding on year of hatch for the two distinct periods, 1995-2002 and 2003-2005, were 0.08% and -0.07% per year respectively. The estimate of effective population size (Ne) computed via the increase in the individual rate of inbreeding was 112.7 animals. The results of this study indicated that the population under study was at an acceptable level of genetic variability. Pedigree and performance data for 71 147 individual egg records collected between 1991 to 2005 were used to estimate genetic parameters for egg weight (EWT), live day-old chick weight (CWT) and hatchability (H). Heritability estimates (±SE) were 0.12 ± 0.02, 0.14 ± 0.04 and 0.09 ± 0.04 for EWT, CWT and H. Corresponding estimates for maternal genetic effects were 0.27 ± 0.08, 0.38 ± 0.08 and 0.13 ± 0.02. The effects of common environment, permanent environment and breeding paddock were significant but relatively low for all traits. Egg weight and CWT were highly correlated at all levels, while H was mostly independent of the weight traits. These results indicated that genetic improvement in these traits would be feasible. Data involving monthly records of egg production (EP), chick production (CP), hatchability (H), mean egg weight (MEW) and mean day-old chick weight (MCW) were analysed as hen traits. Heritability estimates amounted to 0.04 ± 0.02 for EP, 0.05 ± 0.03 for CP, 0.44 ± 0.04 for MEW, 0.02 ± 0.02 for H and 0.67 ± 0.02 for MCW. Permanent environmental effects as a ratio of phenotypic variance (c2 pe) ranged from 0.08 ± 0.03 to 0.11 ± 0.02 for the first four traits (MCW did not exhibit a significant c2 pe effect). Monthly EP and CP were highly correlated at all levels, ranging from 0.74 for the temporary environmental correlation to unity for the genetic correlation. Hatchability was highly correlated with EP and CP at the genetic level (>0.94). Genetic correlations of EP and CP with MEW and MCW were variable and in some cases antagonistic. Genetic correlations of H with MEW and MCW were positive (0.52 and 0.47, respectively). Results indicate that selection for improved reproduction (reproductive output and product quality traits) is feasible. Selection for production is unlikely to be complicated by unfavourable correlations with H, MEW and MCW. Hen traits defined above were further analysed in single-trait mixed models with a random regression fitted as an intercept for the direct animal (a) and a quadratic polynomial with intercept for the permanent environmental (p) effect peculiar to each hen. Heritability (h2) estimates were moderate and remained relatively constant for EP and CP ranging from 0.13-0.14 and 0.07-0.08 respectively for 3- to 10-year old hens. Quality traits MEW and MCW had moderately high h2 estimates ranging from 0.49-0.61 and 0.37-0.45 respectively. Hatchability had h2 estimates ranging from 0.11-0.13 for the 10 hen-ages. Permanent environment variance ratio for EP, CP, MEW, MCW and H ranges were 0.28-0.42, 0.29-0.41, 0.17-0.33, 0.21-0.35 and 0.14-0.24 respectively. Selection of superior hens from three years onwards seems possible. Hens older than eleven years should be replaced with younger, genetically superior hens which would reduce the generation interval and improve EP and CP genetically, without adversely affecting MEW, MCW and H.
Afrikaans: Stamboom-en prestasie-data van 'n goed gedokumenteerde volstruis telinghulpbron-kudde is gebruik om (1) ondersoek intestel na die kuddestruktuur, (2) beraamde variansie en (ko)variansie komponente vir eier- en dag-oud kuiken-gewigte (eienskappe van die individu), (3) genetiese- en omgewingparameters te beraam vir eierproduksie, kuikenproduksie sowel as vir gemiddelde eier- en dag-oudkuikengewig en uitbroeibaarheid binne teelseisoene (wyfie-eienskappe) en (4) die vroeë identifisering van diere met hoë genetiese meriete deur die gebruik/ ondersoek van toevalsregressiemodelle vir herhaalde metings van rekords oor jare. Die gemiddelde vlak van die stamboomvolledigheid van 40 074 eiers van 'n afgepaarde volstruisbroeitrop, vanaf 1978 tot 2005 op die Oudtshoorn Navorsingsplaas, Suid-Afrika was hoog (99.3%) in die eerste generasie en die gemiddelde vlak van inteling (F) was laag op 0.51%. Die beraamde maatstawwe van variasie was: effektiewe genoom ekwivalente = 47.3, effektiewe aantal stigters = 59 en die effektiewe aantal voorvaders = 58. Die getalle voorvaders verantwoordelik vir 100%, 50% en 20% van die variasie in die verwysingspopulasie (voëls met beide ouers bekend), was onderskeidelik 254, 21 en 6. Die generasie-interval, aangedui in jare, bereken as die gemiddelde ouderdom van die ouers wanneer hulle nageslag wat vir reproduksie doeleindes geselekteer is, gebore word, het 7.70 ± 4.87 jaar beloop. Die lineêre regressies van die tempo van inteling op jaar van uitbroei vir die twee afsonderlike periodes, 1995 - 2002 en 2003-2005, was onderskeidelik 0.08% en - 0.07% per jaar. Die beraming van die effektiewe bevolkingsgrootte (Ne) bereken deur middel van die toename in die individuele koers van inteling was 112.7 diere. Die resultate van hierdie studie het aangedui dat die populasie tans aanvaarbare vlakke van genetiese variansie handaaf. Stamboom- en prestasie-data van 71 147 individuele eierrekords tussen 1991 tot 2005 ingesamel, is gebruik om genetiese parameters te beraam vir eiergewig (EWT), dag-oudkuiken-gewig (CWT) en uitbroeibaarheid (H). Oorerflikheidsberamings (± SE) was onderskeidelik 0.12 ± 0.02, 0.14 ± 0.04 en 0.09 ± 0.04 vir EWT, CWT en H. Ooreenstemmende beramings vir die maternale genetiese effekte was onderskeidelik 0.27 ± 0.08, 0.38 ± 0.08 en 0.13 ± 0.02. Die toevallige effekte van die wyfie se algemene-, en permanente-omgewing sowel as die broeikamp was statisties betekenisvol maar relatief laag vir al die eienskappe. EWT en CWT was hoogs gekorreleer by alle vlakke, terwyl H meestal onafhanklik van die gewig eienskappe was. Hierdie resultate dui daarop aan dat die genetiese verbetering van die eienskappe haalbaar sou wees. Data met betrekking tot maandelikse rekords van eierproduksie (EP), kuikenproduksie (CP) en uitbroeibaarheid (H), gemiddelde eiergewig (MEW) en gemiddelde dag-oudkuiken-gewig (MCW) is ontleed as eienskappe van die hen. Oorerflikheidsberamings was 0.04 ± 0.02 vir EP, 0.05 ± 0.03 vir CP, 0.44 ± 0.04 vir MEW, 0.02 ± 0.02 vir H en 0.67 ± 0.02 vir MCW. Permanente omgewing (c2 pe) as 'n proporsie van fenotipiese variansie het gewissel tussen 0.08 ± 0.03 en 0.11 ± 0.02 vir die eerste vier eienskappe (MCW het nie 'n betekenisvolle c2 pe effek getoon nie). Maandelikse EP en CP was hoog gekorreleerd op alle vlakke, en was tussen 0.74 vir die tydelike omgewingskorrelasie en 1.00 vir die genetiese korrelasie. H was hoogs gekorreleerd met EP sowel as CP op die genetiese vlak (> 0.94). Die genetiese korrelasies van EP en CP met MEW en MCW was wisselend in grootte en soms antagonisties. Die genetiese korrelasies van H met MEW en MCW was positief (0.52 en 0.47). Die resultate dui daarop dat seleksie vir verbetering van reproduksie (reproduktiewe uitset en kwaliteit van die produk eienskappe) haalbaar is. Seleksie vir produksie hoort nie gekortwiek te word deur ongunstige korrelasies tussen H, MEW en MCW. Heneienskappe hierbo beskryf is ook as enkel-eienskap gemengde modelle ontleed, met 'n toevalsregressie gepas as 'n afsnit vir die dier (a) en 'n kwadratiese polinoom met 'n afsnit op die y-as vir die permanente omgewingseffek wat eie is aan elke wyfie. Oorerflikheidsberamings (h2) was matig en relatief konstant vir die EP en CP wat gevarieer het tussen 0.13-0.14 en 0.07-0.08 onderskeidelik vir 3- tot 10-jaaroue wyfies. Die gehalte-eienskappe MEW en MCW het redelik hoë h2 beraamings van tussen 0.49-0.61 en 0.37-0.45 getoon. H se h2 het tuseen 0.11 en 0.13 vir die 10 hen-ouderdomsgroepe gevarieer. Die permanente omgewings variansieverhoudings vir EP, CP, MEW, MCW en H het onderskeidelik tussen 0.28-0.42, 0.29-0.41, 0.17- 0.33, 0.21-0.35 en 0.14-0.24 gevarieer. Seleksie van drie-jaar-oue henne blyk uitvoerbaar te wees. Voëls ouer as 11 jaar hoort met jonger geneties verbeterde wyfies vervang te word. Die generasie interval sou daardeur verlaag word, terwyl EP en CP additiewe genetiese vordering kan toon, sonder noemenswaardige nadelige invloede op MEW, MCW en H.
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Thesis (Ph.D. (Animal, Wildlife and Grassland Sciences))--University of the Free State, 2012, Ostriches -- Breeding, Ostriches -- Reproduction, Livestock productivity -- Statistical methods
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