Genetic evaluation of functional longevity in South African Holstein cattle using a proportional hazards model

Imbayarwo-Chikosi, Venancio Edward (2015-12)

Thesis (PhD)--Stellenbosch University, 2015.

Thesis

ENGLISH ABSTRACT: Improvement and selection of superior animals for longevity is a viable complimentary strategy for increasing functional longevity of Holstein dairy cattle. Genetic evaluation of animals for functional longevity is a prerequisite for improvement of the trait. This study was carried out to determine non-genetic factors that influence functional longevity in South African Holstein cattle, as well as to estimate genetic parameters for functional longevity, estimate sire breeding values, and to establish the contribution of conformation traits to the risk of cows being culled from dairy herds. Analyses were carried out using records of 166 222 daughters of 2 051 sires from 1 545 herds in six regions of South Africa. The regions were the Western Cape, Eastern Cape, Northern Cape, Free State, Kwa-Zulu Natal and the combined Gauteng & North Western Provinces. Data were analysed using a piecewise Weibull sire-maternal grandsire model in which the baseline hazard was assumed to change at 270 and 380 days in milk as well as at drying-off. The fixed effects model comprised of the time-independent effect of age at first calving, the combined time-dependent effects of region x year of calving, number of lactations x within-herd milk production class, year of calving x within-herd protein and year of calving x fat percentage production class. Model also had the combined time-dependent effect of herd size x annual herd size change. The random herd-year and sire effects were later included in the model for the estimation of sire and herd-year variance components. Analyses indicated a decline in the survival function, an indicator of functional longevity, among cows that calved for the first time in 2000, 2004 and 2008. Cows that delivered their first calf in 2000 had better survival functions that those that calved for the first time in 2004 and 2008. All fitted effects significantly contributed to the risk of a cow being culled from a herd. Within-herd milk production made the largest contribution to the risk of a cow being culled from a herd. Survival was best in the Northern Cape and worst in Eastern Cape. The risk of being culled was the highest for cows in the second stage of lactation (271- 380 days), when the entire lactation period was considered. High producing cows were more likely not to be culled from a herd than poor producing cows. Cows were more likely to be culled for low protein production percentage than within-herd fat production percentage. The risk of being culled was low for heifers calving at 20 to 25 months of age. The higher risk of culling among cows with multiple lactations indicated the culling policy of dairy farmers to retain a higher number of younger cows than older cows in herds. A decrease in herd size was indicative of a high culling rate. Effective heritability was 0.109. Breeding values ranged from 2.12 for the best cows to -4.80 for the worst cows. This implied that the best and the worst cows were 2.12 times and 4.80 more likely to be culled from herds than the average cow respectively. Genetic trends for functional longevity indicated a marginal decline in sire estimated breeding values. This corresponded with the phenotypic decline in the survivor function observed in cows that calved in 200, 2004 and 2008. All udder, rump, body, feet and leg type traits, with the exception of rear leg side, significantly influenced functional longevity. Farmers culled cows mainly of extremely poor type with a tendency to retain animals with poor to very good structure. Udder traits contributed the most to the risk of a cow being culled. Cows were more likely to be culled for poor scores received for rear teat placement, rear udder height and fore udder attachment, than for any of the other conformation type traits. The contribution of angularity to the risk of being culled was also high, indicating a preference for highly angular bodied cows. Conformation type traits can therefore be used as indicator traits for functional longevity in Holstein cattle, especially when selection and culling is done based on very poor scores for udder traits. The study indicated that genetic improvement in functional longevity can be achieved with the evaluation and selection of dairy sires. There is therefore a wide scope for including functional longevity in the selection objectives for South African Holstein cattle. There is a need to develop appropriate models to ensure that the national dairy industry can benefit from using a Weibull piecewise model.

AFRIKAANSE OPSOMMING: Die verbetering en seleksie van voortreflike diere vir langlewendheid is 'n lewensvatbare en aanvullende strategie vir die verhoging van die funksionele langlewendheid van Holstein melkbeeste. Die genetiese evaluasie van melkproduserende diere ten opsigte van hierdie eienskap is ʼn voorvereiste om verbetering in die eienskap moontlik te maak. Die studie is uitgevoer om nie-genetiese faktore wat die funksionele langlewendheid van Suid-Afrikaanse Holsteins beïnvloed te bepaal, om genetiese parameters vir langlewendheid en vaar teeltwaardes vir dié eienskap te bepaal en ook om die bydrae van bouvorm eienskappe tot die waarskynlikheid van koeie om uitgeskot te word, te bepaal. ʼn Databasis bestaande uit rekords van 166 222 dogters van 2 051 vaars, wat in ses streke in Suid-Afrika (Wes-Kaap, Oos-Kaap, Noord-Kaap, Vrystaat, KwaZulu-Natal en die gekombineerde Gauteng en Noord-Wes Provinsies) voorgekom het, is vir die studie gebruik. Data is ontleed met behulp van 'n stuksgewyse Weibull vader-moeder grootvader model, waarin die basislyn risiko aanvaar is om te verander op 270, 380 dae na kalwing en by afdroog van die melkkoeie. Die vaste effek model het die tyd-onafhanklike effek van ouderdom met eerste kalwing en die tyd-afhanklike effekte van streek en jaar van kalwing, aantal laktasies en binne-kudde melkproduksie klas, binne-kudde proteïen en vet persent produksie klasse volgens jaar van kalwing, asook die gekombineerde tyd-afhanklike effek van kuddegrootte en jaarlikse verandering in kudde grootte, ingesluit. Die ewekansige trop-jaar en vaar effekte is later opgeneem in die model vir bepaling van die vaar- en kudde-jaar variansie komponente. Ontledings het aangedui dat daar 'n algemene afname in die oorlewingsfunksie, wat ʼn aanduiding van funksionele langlewendheid is, was in koeie wat vir die eerste keer in 2000, 2004 en 2008 gekalf het. Koeie wat vir die eerste keer in 2000 gekalf het, het ʼn hoër waarde vir die oorlewingsfunksie gehad as koeie wat onderskeidelik in 2004 en 2008 gekalf het. Alle vaste effekte het betekenisvol tot die waarskynlikheid van ʼn koei om uitgeskot te word, bygedra. Binne-kudde melkproduksie het die grootste bydrae tot die waarskynlikheid van ʼn koei om uitgeskot te word, gemaak. Wanneer die totale laktasieperiode in ag geneem is, was daar gevind dat koeie wat in die tweede fase van laktasie (271-380 dae) die hoogste risiko ervaar het om uitgeskot te word. Hoë produseerders, wanneer hulle met lae produseerders vergelyk is, was minder geneig om uitgeskot te word. Koeie was meer geneig om uitgeskot te word vir lae proteïen produksie persentasie as binne-kudde vet produksie persentasie. Die waarskynlikheid om uitgeskot te word, was laag vir verse wat op ʼn ouderdom van 20 tot 25 maande gekalf het. Die hoër risiko van uitskot van koeie met veelvuldige laktasies het aangedui dat melkboere geneig was om meer jonger koeie te behou en ouer koeie uit te skot. ʼn Afname in kuddegrootte was aanduidend van ʼn hoë uitskotpersentasie. Die effektiewe oorerflikheid was 0.109, met teelwaardes wat van 2.12 vir die hoogste produserende koeie tot -4.80 vir die laagste produserende koeie, gewissel het. Hierdie waardes het dus aangedui dat hoë produseerders en swak produseerders onderskeidelik ʼn 2.12 en 4.80 groter kans gehad het om uitgeskot te kan word. Genetiese tendense vir funksionele langlewendheid het aangedui dat daar 'n marginale afname in vaar beraamde teelwaardes vir funksionele langlewendheid was. Dit het ooreengestem met die waargenome fenotipiese afname in die oorlewingsfunksie wat in 2000, 2004 en 2008 gekalf het. Alle bou-tipe eienskappe (uier, agterkwart, liggaam, voet en been), met die uitsondering van die agterbeen kant, het funksionele langlewendheid betekenisvol beïnvloed. Boere het koeie hoofsaaklik op uiters swak boutipe uitgeskot, met 'n neiging om diere wat as ʼn swak tot uiters goeie bouvorm geklassifiseer is, te behou. Uier eienskappe het die meeste tot die waarskynlikheid van ʼn koei om uitgeskot te word, bygedra. Koeie met ʼn lae gradering vir agterste speen plasing, agter-uier hoogte en voor-uier aanhegting se waarskynlikheid om uitgeskot te word, was groter. Die bydrae van hoekigheid tot die waarskynlikheid van ʼn koei om uitgeskot te word was hoog, wat ʼn aanduiding van ʼn voorkeur vir 'n baie growwe hoekigheid was. Bouvorm tipe eienskappe kan dus gebruik word as indikator eienskappe vir funksionele langlewendheid in Holstein melkbeeste, veral wanneer in ag geneem word dat die meeste melkboere seleksie op grond van swak gradering van uier eienskappe doen. Die studie het aangedui dat genetiese verbetering in funksionele langlewendheid teweeg gebring kan word met die evaluering en seleksie van Holstein vaars. Daar is dus ʼn geleentheid vir die insluiting van funksionele langlewendheid in die seleksie doelwitte vir Suid-Afrikaanse Holstein beeste. Daar is ʼn behoefte om toepaslike modelle te ontwikkel wat met die toepassing daarvan, sal verseker dat die plaaslike melkbedryf sal kan voordeel trek deur die gebruik van 'n stuksgewyse Weibull model benadering.

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