A genetic evaluation of productive herd life in dairy cattle

Abstract

English: The length of productive life is of major economic importance in dairy cattle production. Simple breeding objectives such as selection for increased production in dairy cattle have led to a significant decline in fitness traits. A multi-purpose breeding objective that includes other traits such as length of productive life should be considered. Herd life reflects the ability of a cow to avoid being culled for low production, low fertility, or illness. Herd life can be used in breeding programs if genetic parameters are known. The objectives of the study were to: (1) estimate genetic parameters for functional herd life for the South African Jersey breed using a multiple trait linear model, (2) develop a prototype breeding value for functional herd life for the South African Jersey breed, (3) estimate genetic relationships between functional herd life and conformation traits in the South African Jersey breed and (4) assess inbreeding depression for functional herd life in the South African Jersey breed based on level and rate of inbreeding. A measure of herd life called functional herd life was considered in the current study. Functional herd life refers to herd life adjusted for milk production in the first lactation. In this study functional herd life was defined as survival in each of the first three lactations. Functional herd life was denoted by a 1 if a cow survived and 0 otherwise. Analyses to estimate genetic parameters for functional herd life were carried out as follows. Data and pedigree records on purebred Jersey cows that participated in National Milk Recording and Improvement Scheme were analyzed. Data before editing comprised test-day and lactation yields on milk, fat and protein yields from 252 629 Jersey cows born between 1968 and 2005. After editing, 181 269 cow records from 636 herds recorded over 16 years were available for analysis. Estimates of genetic parameters for herd life were obtained using REML procedures fitting a multiple-trait linear animal and sire models. Heritability estimates (0.02 to 0.03) from the two models were somewhat similar for all lactations. However, heritability estimates for lactations 2 and 3 were slightly higher with the sire model compared to the animal model. The genetic correlation between lactations 1 and 2 from both the sire and animal models was higher than that between lactations 2 and 3. Genetic correlations from the sire model ranged from 0.68 to 0.99 and corresponding estimates from the animal model ranged from 0.76 to 0.99. Genetic parameters obtained in the current study suggest that sufficient genetic variation exist for herd life to allow for genetic improvement and that early selection for functional herd life is feasible. The development of a prototype breeding value for functional herd life for the South African Jersey breed was carried out as follows. Test-day and lactation data on cows that participated in the National Dairy Cattle Improvement Scheme were considered. A multiple-trait linear animal model was used to estimate breeding values using Parameter ESTimation (PEST) software package. A complete (co)variance structure for the additive genetic and residual effects for the three traits were used. These (co)variances were estimated in the first objective. Reliabilities were approximated using the effective number of daughters. Estimated breeding values were scaled so that the average breeding value was a 100. Estimated breeding values for sires ranged from 79 to 114. The rate of genetic progress per year for the period 1985 to 2002 was statistically non-significant (b = 0.02±0.05 per year). The mean reliability was 33.43% and reflective of the low heritability of functional herd life. However, it should be noted that while direct selection for functional herd life could lead to genetic progress, this genetic response could be relatively slow due to the low heritability. The genetic relationship between conformation traits and functional herd life of the South African Jersey population was investigated. Data on conformation traits (n = 46 238) and functional herd life (n = 90 530) on registered South African Jersey cows calving between 1989 and 2008 were obtained from the Integrated Registration and Genetic Information System. Conformation traits were scored using a subjective linear scoring system ranging from 1 to 9, except for foot angle with a maximum score of 8. Conformation traits included stature, chest width, body depth, dairy strength, rump angle, thurl width, rear leg side view, foot angle, fore udder attachment, rear udder height, rear udder width, udder support, udder depth, front teat placement, rear teat placement and front teat length. Genetic correlations between conformation traits and functional herd life were estimated using a series of bivariate analyses. The highest correlations were estimated for udder traits. Significant moderate to high positive genetic correlations between most udder traits and functional herd life (0.23 to 0.63) were estimated. The most important udder traits related to functional herd life were fore udder attachment, rear udder height, and udder depth. Correlations between the majority of body structure and functional herd life were variable. Most of the body structure traits had a low to moderate negative correlation with functional herd life (-0.04 to -0.27). The structural body traits of rump angle and foot angle were estimated to have a moderate positive genetic correlation with functional herd life. The genetic relationships between functional herd life and conformation traits in the South African Jersey breed indicate that conformation traits could be used to enhance the accuracy of genetic evaluation for functional herd life. The effect of inbreeding depression on functional herd life in the South African Jersey population based on individual level and rate of inbreeding was investigated. A pedigree file of the South African Jersey breed (n = 912 638) was obtained from the Integrated Registration and Genetic Information System (INTERGIS). The data included registered, grade and imported animals. The percentages of animals in the pedigree file with two, one and zero parents unknown were 22%, 18% and 60%, respectively. The inbreeding coefficient for each animal (Fi) and the rate of individual inbreeding (ΔFi), as an alternative measure of inbreeding which is adjusted for the depth of known pedigree, were calculated. The effect of inbreeding on functional herd life in each of the first three lactations was estimated using a single trait sire model on data collected from 1985 to 2003. Three analyses for survival in each of the first three lactations were conducted. In the first analysis, in addition to fixed and random effects, an individual inbreeding coefficient (Fi) was fitted as a linear covariate. In the second analysis, the inbreeding coefficient was included as a discrete variable with the following classes of inbreeding: 0 < F ≤ 3.125, 3.125 < F ≤ 6.25, 6.25 < F ≤ 12.5 and F > 12.5. In the third analysis, the individual rate of inbreeding (ΔFi) was included in the model as a linear covariate. The level of inbreeding in the SA Jersey population showed a gradual increase for the period 1985 to 1994, while the period 1995 to 2009 showed a rapid increase. The current mean level of inbreeding (for the year 2010) is 4.85% with a minimum and maximum of 0 and 31.34%, respectively. The rate of inbreeding showed a gradual increase from 0.36% to 0.43% between 1985 and 2003. The average rate of inbreeding is currently (for the year 2010) at 0.55%. There was a significant (P<0.05) unfavourable relationship between inbreeding and functional herd life in the first and second lactation. The effect of inbreeding was more pronounced in the second lactation for both measures of inbreeding. Based on the current level of inbreeding, the reduction in functional herd life in the first lactation can be estimated to be 0.68%. The corresponding estimate for the second lactation is 1.70%. These results indicate that the current level or rate of inbreeding has reached levels that are detrimental to functional herd life. Therefore, individual inbreeding coefficient should be considered when breeding decisions are made by the Jersey breeders in addition to genetic merit.

Afrikaans: Die produktiewe leeftyd van melkkoeie is van groot ekonomiese belang in melkbeesproduksiestelsels. Eenvoudige teeltdoelwitte, soos seleksie vir verhoogde produksie in melkbeeste, het tot ‘n betekenisvolle afname in fiksheidseienskappe gelei. ‘n Veeldoelige teeltdoelwit, wat ander eienskappe soos die lengte van produktiewe lewe insluit, behoort oorweeg te word. Kuddeleeftyd weerspieël die vermoë van koeie om nie weens lae melkproduksie, lae vrugbaarheid of siekte uitgeskot te word nie. Kuddeleeftyd kan, indien die genetiese parameters bekend is, in teeltprogramme gebruik word. Die doelwitte van die studie was om: (1) genetiese parameters vir funksionele kuddeleeftyd vir Suid-Afrikaanse Jerseys te beraam, deur van ‘n meervoudige-eienskap-liniêre model gebruik te maak, (2) ‘n prototipe teeltwaarde vir funksionele kuddeleeftyd vir Suid-Afrikaanse Jerseys te ontwikkel, (3) die genetiese verwantskappe tussen funksionele kuddeleeftyd en bouvormeienskappe vir Suid- Afrikaanse Jerseys te bepaal en (4) die afname in funksionele kuddeleeftyd in die Suid- Afrikaanse Jerseys populasie is gebaseer op die vlak- en tempo van inteling. In die huidige studie is kuddeleeftyd beskryf as funksionele kuddeleeftyd. Funksionele kuddeleeftyd verwys na kuddeleeftyd wat vir eerste laktasiemelkproduksie aangepas is. In hierdie studie is funksionele kuddeleeftyd gedefinieer as oorlewing gedurende elkeen van die eerste drie laktasies. Funksionele kuddeleeftyd is met ‘n 1 aangedui indien ‘n koei die laktasie oorleef het en met ‘n 0 (nul) indien nie. Om die genetiese paramaters vir funksionele kuddeleeftyd te beraam, is die beramings as volg uitgevoer: Die melkproduksie- en stamboomrekords van suiwergeteelde Jerseykoeie wat aan die Nasionale Melkaantekening en Verbeteringskema deelgeneem het, is in die analise gebruik. Voor die redigering van die data, het dit bestaan uit die toetsdag- en laktasierekords vir melk-, vet- en proteïenproduksie van 252 629 Jersey koeie wat tussen 1968 en 2005 gebore is. Na die redigering was produksierekords van 181 269 Jerseykoeie in 636 kuddes oor ‘n 16-jaar tydperk vir ontleding beskikbaar. Beramings van genetiese parameters vir kuddeleeftyd is verkry deur middel van REML-prosedures deur die passing van meervoudige-eienskap liniêre diere- en vaarmodelle. Oorerflikheidswaardes soos beraam deur beide modelle, was grootliks dieselfde vir alle laktasies, naamlik 0.02 tot 0.03. Die oorerfliksheidsberamings vir laktasie 2 en 3 was egter ietwat hoër vir die vaarmodel in vergelyking met die dieremodel. Die genetiese korrelasie tussen laktasies 1 en 2 vir beide die vaar- en dieremodel was hoër as diè tussen laktasies 2 en 3. Die genetiese korrelasies van die vaarmodel het vanaf 0.68 tot 0.99 gevarieer en die ooreenstemende beramings van die dieremodel het gewissel vanaf 0.76 tot 0.99. Die genetiese parameters wat in dié studie verkry is, dui daarop dat voldoende genetiese variasie ten opsigte van kuddeleeftyd bestaan om genetiese vordering te behaal en dat vroeë seleksie van funksionele kuddeleeftyd haalbaar is. Die ontwikkeling van ‘n prototipe teeltwaarde vir funksionele kuddeleeftyd vir Suid- Afrikaanse Jerseys is as volg uitgevoer: Toetsdag- en laktasierekords van koeie wat aan die Nasionale Melkaantekening en Verbeteringskema deelgeneem het, is vir die ontleding gebruik. ‘n Meervoudige-eienskap-liniêre dieremodel is gebruik om teeltwaardes met behulp van die Parameter ESTimation (PEST) sagtewarepakket te beraam. ‘n Volledige (ko)variansie struktuur is vir die additiewe genetiese- en residuele-effekte vir die drie eienskappe gebruik. Dié (ko)variansies is in die eerste doelwit beraam. Betroubaaarhede is gekorrigeer deur die effektiewe getal dogters te gebruik. Beraamde teeltwaardes is gerangskik met 100 as die gemiddelde teeltwaarde. Beraamde teeltwaardes van bulle het tussen 79 en 114 gewissel. Die tempo van die jaarlikse genetiese vordering, vir die periode 1985 tot 2002, was statisties niebetekenisvol (b = 0.02±0.05 per jaar). Die gemiddelde betroubaarheid was 33.43% en weerspieël die lae oorerflikheid van funksionele kuddeleeftyd. Dit moet egter in gedagte gehou word dat, hoewel direkte seleksie vir funksionele kuddeleeftyd tot genetiese vordering mag lei, die genetiese vordering relatief stadig sal wees weens die lae oorerflikheid van die eienskap. Die genetiese verband tussen bouvormeienskappe en funksionele kuddeleeftyd is vir die Suid-Afrikaanse Jersey populasie bepaal. Data oor die bouvormeienskappe (n = 46 238) en funksionele kuddeleeftyd (n = 90 530) van geregistreerde Suid-Afrikaanse Jerseykoeie wat tussen 1989 en 2008 gekalf het, is vanaf die Integreerde Registrasie en Genetiese Informasie Stelsel (INTERGIS) verkry. Bouvormeienskappe is gepunt volgens ‘n subjektiewe liniêre punteskaal wat tussen 1 en 9 varieer met die uitsondering van hoefhelling wat ‘n maksimum punt van 8 het. Die volgende bouvormeienskappe is ingesluit: skofhoogte, borsbreedte, liggaamsdiepte, suiwelsterkte, kruishelling, kruisbreedte, agterbeen syaansig, hoefhelling, vooruieraanhegting, agteruierhoogte, agteruierbreedte, mediale ligament, uierdiepte, voorspeenplasing, agterspeenplasing en voorspeenlengte. Genetiese korrelasies tussen bouvormeienskappe en funksionele kuddeleeftyd is deur ‘n reeks twee-eienskap ontledings bepaal. Die hoogste korrelasies is tussen funksionele kuddeleeftyd en uiereinskappe verkry. Die positiewe en betekenisvolle genetiese korrelasies tussen die meeste uiereinskappe en funksionele kuddeleeftyd was matig tot hoog. (0.23 tot 0.63). Die belangrikste uiereienskappe wat met funksionele kuddeleeftyd verband gehou het, was vooruieraanhegting, ageruierhoogte en uierdiepte. Die korrelasies tussen die meeste eienskappe ten opsigte van liggaamstruktuur en funksionele kuddeleeftyd was varierend. Die meeste eienskappe het ‘n lae tot matige negatiewe korrelasie met funksionele kuddeleeftyd getoon (-0.04 tot -0.27). Die ontleding het getoon dat strukturele bouvormeienskappe soos kruishelling en hoefhelling ‘n matige positiewe genetiese korrelasie met funksionele kuddeleeftyd het. Die genetiese verband tussen funksionele kuddeleeftyd en bouvormeienskappe vir Suid-Afrikaanse Jerseys dui daarop dat bouvormeienskappe gebruik kan word om die akkuraatheid van genetiese evaluasies van funksionele kuddeleeftyd te verhoog. Die effek van die vlak- en tempo van inteling op die afname in funksionele kuddeleeftyd is vir Suid-Afrikaanse Jerseys beraam. ‘n Stamboom lêer van die Suid-Afrikaanse Jerseyras (n = 912 638) is vanaf INTERGIS verkry. Die datalêer het geregistreerde, graad en ingevoerde diere ingesluit. Die aantal diere in die stamboomlêer met twee, een en geen onbekende ouers nie, was 22%, 18% en 60%, onderskeidelik. Die inteeltkoëffisient van elke dier (Fi) en die tempo van indiwiduele inteling (ΔFi), as ’n alternatiewe inteeltmaatstaf, aangepas volgens bekende stamboominligting, is beraam. Die effek van inteling op funksionele kuddeleeftyd in elkeen van die eerste drie laktasies is bereken deur ‘n enkel-eienskap vaarmodel toe te pas op data wat tussen 1985 en 2003 ingesamel is. Drie ontledings vir oorlewing is uitgevoer in elkeen van die eerste drie laktasies. In die eerste ontleding, benewens vaste en ewekansige effekte, is ‘n indiwiduele inteeltkoëffisient (Fi) as ‘n liniêre ko-variansie gepas. In die tweede ontleding is die inteeltkoëffisient as ‘n diskrete veranderlike ingesluit, met die volgende klasse van inteling: 0 < F ≤ 3.125, 3.125 < F ≤ 6.25, 6.25 < F ≤ 12.5 en F > 12.5. In die derde ontleding is die indiwiduele tempo van inteling (ΔFi) in die model as ‘n liniêre ko-variansie ingesluit. Die vlak van inteling in die Suid-Afrikaanse Jersey populasie het vanaf 1985 tot 1994 ‘n geleidelike toename getoon, terwyl ‘n vinniger toename vanaf 1995 tot 2009 waargeneem is. Die huidige (vir 2010) gemiddelde vlak van inteling is 4.85% met ‘n minimum en maksimum waarde van 0 en 31.34% onderskeidelik. Die tempo van inteling het ‘n geleidelike toename vanaf 0.36% tot 0.43% tussen 1985 en 2003 getoon. Die huidige gemiddelde tempo van inteling (vir 2010) is 0.55%. Daar was ‘n betekenisvolle ongunstige verband tussen inteling en funksionele kuddeleeftyd vir eerste en tweede laktasie. Die effek van inteling was meer waarneembaar in die tweede laktasie vir beide inteeltmaatstawwe. Gebaseer op die huidige vlak van inteling, kan die vermindering in funksionele kuddeleeftyd vir eerste laktasie, as 0.68% bereken word. Die ooreenstemende beraming vir tweede laktasie is 1.70%. Hierdie resultate toon dat die huidige vlak of tempo van inteling vlakke bereik het wat nadelig is vir funksionele kuddeleeftyd. Die indiwiduele inteeltkoëffisient moet dus tesame met genetiese meriete, deur Jersey telers in ag geneem word wanneer teeltbesluite geneem word.