The utility of age at puberty and anogenital distance as early-in-life predictors of an animal’s genetic merit for fertility during lactation in New Zealand dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science, AL Rae Centre of Genetics and Breeding, Massey University, Manawatū, New Zealand. EMBARGOED to 30 June 2025.
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Date
2023
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Massey University
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Abstract
Background. The New Zealand (NZ) dairy sector is predominantly pasture-based, with low-cost farm systems heavily dependent upon good alignment between the herd’s feed demand and the seasonal supply of pasture. The feed demand of the herd varies across the season according to lactational performance and the physiological status of the cows. Therefore, management of the timing and spread of reproductive events are critical drivers of farm profit. Cows in NZ normally calve annually between July and September each year to ensure that the peak feed demand of the herd coincides with increased spring pasture growth. Adhering to a strictly annual calving interval is biologically challenging for dairy cows, and at least 10% of the national herd is culled each year due to reproductive failure. Selection for fertility provides a long-term tool that can genetically improve the reproductive performance of the national dairy herd. Gains in reproductive performance can contribute to improved pasture utilization, days in milk, cow longevity and, ultimately, farm profitability. Unfortunately, evaluating traits that represent reproductive success during lactation is challenging. The calving, breeding, and pregnancy date phenotypes required for evaluation typically have low heritabilities and are expressed relatively late in an animal’s life, when cows are at least two years of age. Higher heritability traits that exhibit at least moderate genetic correlations with target fertility traits can have value as predictor traits, especially if they are expressed earlier in life than the target trait itself. Two candidate predictor traits for evaluating genetic merit for fertility during lactation are age at puberty (AGEP) and anogenital distance (AGD).
Objectives. There were four key objectives of this thesis. First, to investigate a cost-effective approach for measuring AGEP for the purpose of genetic evaluation. Second, to estimate the heritabilities of both AGEP and AGD in NZ Holstein-Friesian cattle, and third to estimate the genetic correlations between fertility during lactation and both AGEP and AGD. Finally, I aimed to undertake a Genome-Wide Association Study (GWAS) to identify genomic regions associated with variation in each of these candidate predictor traits.
Materials and Methods. I used data from a study population of 5,010 predominantly Holstein-Friesian and Holstein-Friesian cross Jersey cows, born in 2018 across 54 commercial pasture-based dairy herds. Elevated blood plasma progesterone (BP4) concentrations were used as an indicator of an animal’s puberty status, with animals considered post-pubertal once their BP4 was >1 ng/mL. Each animal was blood tested on three occasions, when the average age of the animals in their herd cohort was around 10, 11 and 12 months of age. These age at first BP4 elevation (AGEP4) phenotypes (n = 4,688) are an example of a censored phenotype, as each animal’s phenotype was only known to fall within a lower or upper bound, rather than being known precisely. Anogenital distance was measured at about 11 months of age (AGD1; n = 4,688) as the distance between the anus and the clitoris using digital calipers. These animals were subsequently followed through first and second lactation, and binary calving (calved in the first 42 d of the seasonal calving period; first n = 4,327; second n = 3,575), breeding (bred within the first 21 d of the seasonal breeding period; first n = 4,111; second n = 3,507) and pregnancy (pregnant within the first 42 d of the seasonal breeding period; first n = 3,939; second n = 3,353) rate traits were recorded. A second measure of AGD was taken when the animals were around 29 months of age (AGD2) in a subset of herds (n=17; 1,956 animals).
Results. Overall, variance parameter and breeding value estimation for AGEP4 were remarkably robust to phenotype censoring, and reducing the blood testing regime down to a single BP4 test per animal may be sufficient for the purpose of genetic analysis. I used Markov chain Monte Carlo (MCMC) techniques applying a single site Gibbs sampler to obtain samples from the posterior distributions of (co)variance parameters between AGEP4, AGD and fertility during lactation. The AGEP4 trait had a moderate heritability with a posterior mean of 0.34 and 90% of estimated samples falling within a credibility interval (90% CRI) of 0.30 to 0.37. The heritabilities of AGD were slightly lower at 0.23 (90% CRI 0.20 to 0.26) and 0.29 (90% CRI 0.24 to 0.34) when measured at 11 months and 29 months of age, respectively. Calving, breeding, and pregnancy rate traits exhibited moderate genetic correlations with AGEP4 (0.11 to 0.60), AGD1 (0.19 to 0.52) and AGD2 (0.46 to 0.63). The GWAS analysis of AGEP identified 1 genomic window on chromosome 5 that was associated with variation in AGEP4. Another 4 regions of decreasing importance, located on chromosomes 14, 6, 1 and 11, were identified with suggestive associations with AGEP4. In addition, 2 regions on chromosome 20 and 13 were suggestively associated with variation in AGD1, but there were no associations with AGD2, possibly because this trait was measured in fewer animals.
Conclusion. I conclude that both AGEP and AGD are moderately heritable traits, which likely have value as early-in-life genetic predictors for reproductive success during lactation in NZ Holstein-Friesian and Holstein-Friesian cross Jersey cattle.
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Embargoed to 30 June 2025
Keywords
Dairy cattle, Fertility, Breeding, Genetics, New Zealand