Abstract
Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure precisely.Examples include time-dependent traits such as reproductive status,or lifespan.Incomplete measures for these traits result in phenotypes that are subject to left-,interval-and right-censoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound respectively.Here we compare three methods for deriving phenotypes from incomplete data using age at first elevation(＞1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example trait.Methods We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein-Friesian or Holstein-Friesian × Jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New Zealand.We used these actual data to simulate 7 different visit sce-narios,increasing the extent of censoring by disregarding data from one or two of the three visits.Three methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation approach.Results Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but esti-mated heritabilities tended to be higher when left censoring was reduced.For sires with at least 5 daughters,the cor-relations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to 0.95.The estimated breed effects also varied by method,but breed differ-ences were smaller as phenotype censoring increased.Conclusion Our results indicate that using some methods,phenotypes derived from one observation per offspring for a time-dependent trait such as AGEP4 may provide comparable sire rankings to three observations per offspring.This has implications for the design of large-scale phenotyping initiatives where animal breeders aim to estimate variance parameters and estimated breeding values(EBVs)for phenotypes that are challenging to measure or prohibi-tively expensive.
基金项目
New Zealand dairy farmers through DairyNZ Inc()
New Zealand Ministry of Business,Innovation and Employment(DRCX1302)
国家科技期刊平台
NSTL
万方数据