Investigating the genetic background of sensor-based activity and rumination traits in North American Holstein cattle

Behavioral traits are important in differentiating sick from healthy animals or identifying efficient animals by analyzing daily activity and comparing them to a threshold. Activity and rumination time have been shown to be indicators of health and have favorable correlations with traits such as milk production and fertility. Therefore, the primary aims of this thesis were to estimate genetic parameters and variance components for rumination time and activity traits derived from different sensors in North American Holstein cattle and assess their genetic relationship with production traits. We also aimed to identify genomic regions, candidate genes, and metabolic pathways associated with activity and rumination traits in North American Holstein cattle. Records were collected from 20,220 cows in an AfiMilk system and 4,289 cows in a Lely system. There were five activity traits recorded in the AfiMilk system (maximum activity per hour, daily steps, average session activity, rest time, and rest bout), and three activity traits recorded in the Lely system (activity AM, activity PM, and activity total). Rumination time was only recorded in the Lely system. All activity and rumination traits were first analyzed on a per-parity basis. Rest bout had the highest heritability and highest favorable, or positive, correlation with milk yield, as well as the largest number of SNPs (single nucleotide polymorphism) and candidate genes, with most of them being related to milk production and health. In general, heritability estimates decreased as parity number increased for activity total, activity AM, rumination time, average session activity, and maximum activity per hour. Selection based on genomic breeding values based on first-parity records is likely to result in high correlated responses as most traits were highly correlated across parities. A total of 48 SNPs were identified for all traits. There were eleven SNPs shared between activity and inactivity traits (maximum activity per hour, activity AM, activity total, rest bout, rest time, activity PM, and average session activity) which could allow one SNP be used to select for multiple traits. Candidate genes for rumination time were related to milk production and fertility, while candidate genes for activity traits were mostly related to health and fertility. This study highlights the genetic background of activity and rumination traits in Holstein cattle and provides a foundation for future behavioral studies in dairy cattle by providing insights into the genetic parameters, genomic regions, and candidate genes associated with each activity and rumination trait.