Genetic factors affecting milk production, growth and reproduction traits in Bos indicus x Bos taurus crosses in Ethiopia

Abstract

English: Five separate studies were conducted to investigate the genetic factors affecting growth, milk production and reproduction traits in Bos indicus x Bos taurus crosses in Ethiopia. The first three studies were based on early growth data collected from the purebred Boran (Bo), Barca (Ba), Horror (Ho) (Bos indicus) and their crosses with the Friesian (F), Jersey (1) and Simmental (S) breeds (Bos taurus). Early growth data were for calves that were representing three purebred Bos indicus and 38 crossbred genotypes and were separated from their dams one day after birth and fed milk from a bucket. The fourth and fifth studies were based on milk and reproduction data collected from cows of two purebreds (Boran and Friesian) and eight crossbred (crosses of Friesian and Jersey with Boran) genotypes. In the first study, five genetic models were evaluated for goodness of fit and estimation of crossbreeding parameters. These models were: 1) Dominance model, 2) Dickerson's model (recombination loss), 3) Additive x dominance interaction model, 4) Dominance x dominance interaction model and 5) Kinghom's model (x). Models 2 to 5 are epistatic models that included all effects in model one plus one type of epistatic interaction based on a two-locus gene model. The models were evaluated using data for birth, weaning, yearling weights and preweaning average daily gain. All five models tested provided high levels of fit, with adjusted R2 values averaging 93% over traits. All the epistatic models fit the data significantly (P<0.05) better than the dominance model for all the traits. Among the epistatic models, Dickerson's model (Model 2) gave significantly (P<0.05) higher R2 values compared to the other epistatic models. Crossbreeding parameters estimated from this model has relatively lower sampling correlations and correspondingly lower standard errors. This model could, therefore, be considered as the most appropriate one for parameter estimation and prediction of performances of untested genotypes for future crossbreeding decisions for the breeds involved in this study. In the second study, breed difference, heterosis and recombination loss were estimated for birth weight (BWT), weaning weight (WWT), preweaning average daily gain (ADG) and yearling weight (YWT), fitting an animal model. Differences between genotypes were significant (P<0.01) for all traits. Genetic group means adjusted for environmental effects ranged from 20 to 30 kg for BWT, 88 to 114kg for WWT, 122 to 157kg for YWT and 358 to 492g for preweaning average daily gain (ADG). The breed additive effect of the F as a deviation from the Bo was significant (P<0.01) and positive for all traits. Relative to the Bo mean, the additional breed additive contribution of the F breed on BWT, WWT, ADG and YWT was 39.3, 16.5, 9.3 and 10.3%, respectively. On the other hand, the breed additive effects of the Ho and J breeds were significantly (P<0.01) negative for all traits. The heterotic effects were significantly negative (P<0.01) for BWT for all F and S crosses, but positive (P<0.01) for all other traits for all types of crosses. The average heterosis estimated within the F, J and S breeds were: -2.1±0.6, 0.2±0.6 (P>0.05) and -2.3±0.6 kg for BWT, 8.8±2.1, 11.8±2.3 and 13.7±2.4 kg for WWT, 60.4±11.3, 64.8±12.3 and 90.6±12.7 g for ADG and 19.8±2.6, 19.5±2.8 and 20.8±2.9kg for YWT, respectively. The recombination effects were significant (P<0.01) for the majority of crosses for all traits. The estimates for the recombination loss were negative for all traits, except for BWT. The average recombination effects estimated within the F, J and S breeds were: 2.6±0.8, 2.9±0.9 and 2.4±1.0 kg for BWT, -13.6±3.2, -4.2±3.4 (P>0.05) and -16.0±4.0 kg for WWT, -88.0±17.1, -39.4±18.4 and -102.2±21.3 g for ADG and -14.4±4.0, -0.1±4.4 (P>0.05) and -17.5±4.9 kg for YWT, respectively. In the third study, variance components and direct and maternal heritabilities were estimated for weight at birth, weaning and yearling and preweaning average daily gain. Data were analysed using six alternative animal models (direct and including or excluding maternal effects). The direct heritability estimates from the "best" model for each trait were: 0.14±0.03 for birth weight, 0.08±0.03 for weaning weight, 0.06±0.02 for preweaning average daily gain and 0.13±0.03 for yearling weight. The direct maternal heritability estimates were small, but significantly different from zero for only birth weight (0.07±0.02), weaning weight (0.04±0.02) and preweaning average daily gain (0.04±0.02). Direct genetic correlations between birth weight and the other three traits were: 0.66±0.08, 0.55±0.19 and 0.50±0.12 with weaning weight, preweaning average daily gain and yearling weight, respectively. The genetic correlation between weaning weight, preweaning average daily gain and yearling weight was high and ranged from 0.82±0.11 to 0.97±0.O1. Small, but non-zero maternal heritabilities estimated for weaning and preweaning average daily gain for artificially reared calves in this study should be interpreted cautiously because of potential bias from unaccounted breed additive and non-additive effects of the dam. Results of this study also showed that estimates of variance components and genetic parameters suitable for general use can be obtained from mixed purebred and crossbred data after appropriately accounting for breed additive and non-additive effects. In the fourth study, breed additive and non-additive effects plus heritabilities and repeatabilities for milk yield per lactation (LMY), milk yield per day (DMY), lactation length (LL), annual milk yield (AMY), annual milk yield per metabolic body weight (AMYBW) and cow weight at calving (BW) were estimated. In addition, genetic, phenotypic and permanent environmental correlations were estimated between AMY and LL, AMY and BW and LL and BW. Data for each trait were analysed, using two equivalent repeatability animal models: first, fitting genotype as a fixed group effect and in the second model substituting genotype with breed additive, heterotic and recombination effects as fixed covariates. Among the genotypes the Bo had the lowest and the F the highest performance for all traits. The least-squares means for the Bo breed were 529±65 kg for LMY, 2.8±0.1 kg for DMY, 193±6 d for LL, 514±61 kg for AMY, 7.8±0.7 for AMYBW and 304±3 kg for BW. Both F and J breed additive effects, measured as a deviation from the Bo breed were significant (P<0.01) for all traits, except for BW of the J. The F and J additive contributions were 2774±89 and 1473±362 kg for LMY, 7.1±0.2 and 4.8±0.8 kg for DMY, 146±8 and 81±7 d for LL, 2345±71 and 1238±319 kg for AMY, 20.6±0.9 and 18.9±4.3 kg for AMYBWand 140±4 and -21±22 kg (P>0.5) for BW, respectively. The heterotic contributions to the crossbred performance were also positive and significant (P<0.01) for all traits, except for BW in the F x Bo crosses. The Fl heterosis expressed as a deviation from the mid-parent values were 22 and 66 % for LMY, 11 and 20% for DMY, 29 and 29% for LL, 21 and 64 % for AMY, 42% (P>0.05) and 42 % for AMYBW and 2% (P>0.5) and 11% for BW for the F x Bo and J x Bo crosses, respectively. The recombination effect estimated for the F x Bo crosses was negative and significant for LMY (-526±192 kg, P<0.01), DMY (- 3.0±0.4 kg, P<0.01)AMY (-349±174, P<0.05) and BW (-68±11 kg, P<0.001). For the J x Bo crosses the recombination loss was only significant and negative for DMY (-2.2±0.7 kg, P<0.05) and BW (-33±17, P<0.05). The direct heritabilities (h2) and repeatabilities (r2) estimated for each trait after correcting for the fixed environmental and breed additive and non-additive effects were 0.24±0.04 and 0.39±0.02 for LMY, 0.19±0.03 and 0.30±0.02 for DMY, 0.13±0.03 and 0.19±0.02 for LL, 0.23±0.04 and 0.37±0.02 for AMY, 0.17±0.05 and 0.39±0.02 for AMYBW and 0.10±0.03 and 0.34±0.02 for BW, respectively. The estimated genetic correlations between AMY and LL, AMY and BW, LL and BW were 0.71±0.08, 0.17±0.18 and 0.23±0.20, respectively. In the fifth study, estimates of breed additive differences, heterosis and recombination loss, as well as heritabilities were obtained for age at first calving (AFC), calving interval (Cl), days open (DO) and number of services per conception (SPC). The genetic parameters were estimated using a repeatability animal model for Cl, DO and SPC and a unitrait animal model for AFC. The overall least-squares means estimated were: 38.3±0.26 months, 435±4 days, 145±10 days and 1.58±0.03 (number) for AFC, Cl, DO and SPC, respectively. The breed additive effects of F and J were only significant (P<0.01) for AFC. Relative to the Bo, both the F and the J additive contributions for AFC were -5.4±0.5 and -5.5±1.9 months, respectively. Crossing the F and J breeds with the Bo breed also resulted in significant heterosis (P<0.05) ranging from I0ta 21% in all traits. The estimated recombination loss was only significant for AFC (2.8±1.0 months) for the F x Bo crosses. Heritability estimates were high for AFC (0.44±0.05) and low for Cl (0.08±0.03), DO (0.04±0.03) and SPC (0.08±0.02). The corresponding estimates for the repeatability (r2 ) were 0.14±0.02 and 0.14±.0.02 for Cl and DO, respectively. The repeatability estimate for SPC was zero.

Afrikaans: Vyf afsonderlike studies is uitgevoer om die genetiese faktore te ondersoek wat groei, melkproduksie en voortplantingseienskappe in Bos indicus x Bos tauruskruisings in Ethiopië affekteer. Die eerste drie studies is op vroeë groeidata wat versamel is van suiwergeteelde Boran (Bo)-, Barca (Ba)-, Horro (Ho)-rasse (Bos indicus) en hul kruisings met Fries (F)-, Jersey (J)- en Simmentaler (S)- rasse (Bos taurus) versamel is gebaseer. Vroeë groeidata was van kalwers wat drie suiwergeteelde Bos indicus en 38 kruisgeteelde genotipes verteenwoordig het en wat een dag na geboorte van hulle moeders geskei is en melk uit 'n emmer gevoer is. Die vierde en vyfde studies is gebaseer op melk- en voortplantingsdata gebaseer wat van koeie van twee suiwergeteelde (Boran en Fries) en agt kruisgeteelde (Boran met Fries en Jersey) genotypes versamel is. In die eerste studie is vyf genetiese modelle geëvalueer vir geskiktheid van passing en beraming van kruistelingsparameters. Hierdie modelle was: 1) dominansiemodel, 2) Dickerson se model (rekombinasie verlies), 3) additiewe x dominansie interaksie-model, 4) dominansie x dominansie interaksie-model en 5) Kinghom se model (x). Modelle 2 tot 5 is epistatiese modelle wat al die effekte in modeilingesluit het, plus een tipe epistatiese inter-aksie gebaseer op 'n tweelocus gene-model. Die modelle is geëvalueer deur gebruik te maak van data vir geboorte-, speen- en jaaroudgewigte, asook voorspeense gemiddelde daaglikse toename. Al vyf modelle wat getoets is het hoë vlakke van passing vertoon, met aangepaste R2 -waardes wat 'n gemiddeld van 93% oor eienskappe bereik het. Al die epistatiese modelle het die data betekenisvol (P<0.01) beter vir al die eienskappe gepas as die dominansiemodel. Vandie epistatiese modelle het Dickerson se model betekenisvol (P<0.01) hoër Ri-waardes getoon, vergeleke met die ander. Kruistelingparameters wat van hierdie model beraam is het relatief laer monsteringkorrelasies en ooreenstemmend laer standaardfoute gehad. Hierdie model kan derhalwe beskou word as die mees geskikte vir parameterberamings en voorspelling van die prestasie van ongetoetste genotipes Vir toekomstige teeltbesluite oor raskruisings wat in hierdie studie betrokke is. In die tweede studie is rasverskille, heterose en rekombinasieverliese Vir geboortegewig (Ggew), speengewig (Sgew), voorspeense gemiddelde daaglikse toename (GDT) en jaaroudgewig (Jgew) deur 'n dieremodel te gebruik beraam. Verskille tussen genotipes was betekenisvol (P<0.01) vir alle eienskappe. Genetiese groepgemiddeldes aangepas vir omgewingseffekte het van 20 tot 30kg gewissel vir Ggew, 88 tot 114 kg vir Sgew, 122 tot 157 kg vir Jgewen van 358 tot 429g vir voorspeense gemiddelde daaglikse toename (GDT). Die ras-additiewe effek van F as 'n afwyking van die Bo, was betekenisvol (P<0.01) en positief vir alle einskappe. Relatief tot die Bo-gemiddelde was die bykomende additiewe bydrae van die F-ras op Ggew, Sgew, GDT en Jgew onderskeidelik 39.3, 16.5, 9.3 en 10.3%. Hierteenoor was die additiewe effekte van die Ho- en J-rasse betekenisvol (P<0.01) negatief vir alle eienskappe. Die heterose-effekte was betekenisvol negatief (P<0.01) vir Ggew vir alle F- en S-kruisings, maar positief (P<0.01) vir alle ander eienskappe vir alle tipe kruisings. Die gemiddelde heterose wat binne die F-, J- en S-rasse beraam is, was onderskeidelik -2.l±0.6, 0.2±0.6 (P>0.05) en -2.3±0.6 vir Ggew, 8.8±2.1, 11.8±2.3, en 13.7±2.4 kg vir Sgew, 60.4±11.3, 64.8±12.3 en 90.6±12.7 g vir GDT en 19.8±2.6, 19.5±2.8 en 20.8±2.9 kg vir Jgew. Die rekombinasie-effekte was betekenisvol (P<O.OI) vir die meerderheid van kruisings vir alle eienskappe. Die beramings van die rekombinasie-verlies was negatief vir alle eienskappe, behalwe vir Ggew. Die gemiddelde rekombinasie-effekte wat beraam is binne die F-, J- en S-rasse was onderskeidelik 2.6±0.8, 2.9±09 en 2.4±1.0 kg vir Ggew, -13.6±3.2, -4.2±3.4 (P>0.05) en -16.0± 4.0 kg vir Sgew, -88.0±17.l, -39.4±18.4 en -102.2±21.3 g vir GDT en -14.4±4.0, -0.l± 4.4 (P>0.05) en -17.5±4.9 kg vir Jgew vir genoemde drie rasse onderskeidelik. In die derde studie is variansiekomponente en direkte en maternale oorerflikhede vir gewig by geboorte, speen en jaaroud en voorspeense gemiddelde daaglikse toename onderskeidelik beraam. Data is deur die passing van ses alternatiewe dieremodelle (direk en met in- of uitsluiting van maternale effekte) ontleed. Die direkte oorerflikheidsberamings van die "beste" model vir elke eienskap was: 0.14±0.03 vir geboortegewig, 0.08±0.03 vir speengewig, 0.06±0.02 vir voorspeense gemiddelde daaglikse toename en 0.13±0.03 vir jaaroudgewig, Die direkte maternale oorerflikheidsberamings was klein, maar betekenisvol verskillend van slegs zero vir geboortegewig (0.07±0.02), speengewig (0.04±0.02) en voorspeense gemiddelde daaglikse toename (0.04±0.02). Direkte genetiese korrelasies tussen geboortegewig en die ander drie eienskappe was onderskeidelik 0.66±0.08, 0.55±0.19 en 0.50±0.12 met speengewig, voorspeense gemiddelde daaglikse toename en jaaroudgewig. Die genetiese korrelasies tussen speengewig, voorspeense gemiddelde daaglikse toename en jaaroudgewig was hoog en het tussen 0.82±0.11en 0.97±0.0l gewissel. Klein, maar nie-zero maternale oorerflikhede wat speengewig en voorspeense gemiddelde daaglikse toename vir kunsmatig-grootgemaakte kalwers in hierdie studie beraam is, moet met omsigtigheid geïnterpreteer word vanweë die potensiële sydigheid van onverklaarde ras-additiewe en -nie-additiewe effekte van die moeder. Resultate van hierdie studie het ook getoon dat beramings van variansie-komponente en genetiese parameters wat geskik is vir algemene gebruik, verkry kan word van gemengde, suiwergeteelde en kruisgeteelde data na behoorlike inagneming van ras-additiewe en -nie-additiewe effekte. In die vierde studie is ras-additiewe en -nie-additiewe effekte beraam, asook oorerflikhede en herhaalbaarhede vir melkopbrengs per laktasie (LMO), melkopbrengs per dag (DMO), lengte van laktasie (LL), jaarlikse melkopbrengs (lMO), jaarlikse melkopbrengs per metaboliese liggaamsgewig (lMOLgew), en koeigewig met kalwing (Lgew). Bykomend is genetiese, fenotipiese en permanente omgewingskorrelasies tussen lMO en LL, lMO en Lgew en LL en Lgew beraam. Data vir elke eienskap is ontleed deur twee ekwivalente herhaalbaarheids-dieremodelle te gebruik: eerstens, deur genotipe as 'n vaste groep-effek te pas en in die tweede model genotipe te vervang deur ras-additiewe, heterose en rekombinasie-effekte as vaste ko-veranderlikes. Van die genotipes het die Bo die laagste en die F die hoogste prestasie vir al die eienskappe gehad. Die kleinste vierkantgemiddeldes vir die Bo-ras was 529±65 kg vir LMO, 2.8±0.1 kg vir DMO, 193±6d vir LL, 514±61 kg vir JMO, 7.8±0.7 vir JMOLgew en 304±3 kg vir Lgew. Beide F en J ras-additiewe effekte, wat gemeet is as 'n afwyking van die Bo-ras was betekenisvol (P<0.01) vir alle eienskappe, behalwe vir Lgew van 1. Die F en J additiewe bydraes was onderskeidelik 2774±89 en 1473±362 kg vir LMO, 7.l±0.2 en 4.8±0.8 kg vir DMO, 146±8 en 81±7 d vir LL, 2345±71 en 1238±319 kg vir JMO, 20.6±0.9 en 18.9±4.3 kg vir JMOLgew en 140±4 en - 21±22 kg (P>0.5) vir Lgew. Die heterose-bydrae tot die kruisteeltprestasie was ook positief en betekenisvol (P0.01) vir alle eienskappe, behalwe vir Lgew in die FxBo kruisings. Die FI heterose, uitgedruk as 'n afwyking van middelouerwaardes was onderskeidelik 22 en 66 % vir LMO, 11 en 20% vir DMO, 29 en 29% vir LL, 21 en 64% vir JMO, 42% (P>0.05) en 42% vir JMOLgew en 2% (P>0.5) en 11% vir Lgew vir F x Bo- en J x Bo- kruisings. Die rekombinasieeffek vir F x Bo kruisings was negatief en betekenisvol vir LMO (-526± 192 kg, P<0.01), DMO (-3.0±0.4kg, P<0.01),JMO (-349±174, P<0.05) en Lgew (-68±11 kg, P<0.001). Vir J en Bo- kruisings was die rekombinasie-verlies slegs betekenisvol en negatief vir DMO (-2.2±0.7 kg, P<0.05) en Lgew (-33±17, P<0.05). Die direkte oorerflikhede (h2) en herhaalbaarhede (r2) wat vir elke eienskap beraam is nadat vir die vaste omgewings- en ras-additiewe en -nieadditiewe effekte gekorrigeer is, was onderskeidelik 0.24±0.04 en 0.39±0.02 vir LMO, 0.19±0.03 en 0.30±0.02 vir DMO, 0.l3±0.03 en 0.l9±0.02 vir LL, 0.23±0.04 en 0.37±0.02 vir JMO, 0.l7±0.05 en 0.39±0.02 vir JMOLgew en 0.10±0.03 en 0.34±0.02 vir Lgew. Die beraamde genetiese korrelasies tussen JMO en LL, JMO en Lgew, LL en Lgew was onderskeidelik 0.71±0.08, 0.17±0.18 en 0.23±0.20. In die vyfde studie is beramings van ras-additiewe verskille, heterose en rekombinasie-verliese, sowel as oorerflikhede gemaak vir ouderdom met eerste kalwing (OEK), kalwings-interval ( Cl) , dae oop (DO) en aantal dekkings per bevrugting (DPB). Die genetiese parameters IS beraam deur 'n herhaalbaarheidsdieremodel vir Cl, DO en DPB en 'n enkeleienskap-dieremodel vir OEK te pas. Die algehele kleinste kwadraatgemiddeldes wat beraam is, was onderskeidelik 38.3±0.26 maande, 435±4 dae, l45±10 dae en 1.58±0.03 (getal) vir OEK, Cl, DO en DPB. Die ras-additiewe effekte van F en J was slegs vir OEK betekenisvol (P<0.01). Relatief tot die Bo, was beide die F en J additiewe bydraes vir OEK onderskeidelik -5.4±0.5 en -5.5±1.9 maande onderskeidelik. Kruising van die Bo met die F- en J-rasse het ook betekenisvolle heterose tot gevolg gehad (P<0.05) wat van 10 tot 21% in alle eienskappe gewissel het. Die beraamde rekombinasie-verlies was slegs vir OEK (2.8±1.0 maande) vir F- en Bokruisings betekenisvol. Beramings van oorerflikheid was hoog vir OEK (0.44±0.05) en laag vir Cl (0.08±0.03), DO (0.04±0.03) en DPB (0.08±0.02). Die ooreenstemmende beramings vir die herhaalbaarhede (r2) was onderskeidelik 0.14±O.2 en 0.14±0.02 vir Cl en DO. Permanente omgewingseffek vir DPB was zero.