IMPROVING LIVESTOCK CLIMATIC ADAPTATION THROUGH GENOMICS
Creators: name: Freitas, Pedro Henrique Ferreira
Publisher: name: Purdue University Graduate School
Year: 2022
Subjects: Genomics

description: As the effects of climate change become more evident, the development of effective strategies for improving livestock climatic adaptation and the long-term sustainability of animal food production have become key priorities around the world, including in the US. Together with nutrition, infrastructure, and management practices, genetically improving animals is an effective and lasting alternative to simultaneously improve productive efficiency and climatic adaptation of animals. Genetic improvement requires basic understanding of the genomic architecture of the indicator traits of interest and the availability of large-scale datasets. Understanding the role of evolution and selection (both natural and artificial) on shaping animal genomes is of paramount importance for the optimization of breeding programs and conservation of genetic resources. In addition, properly quantifying environmental stress and individual animal responses to thermal stress are still important challenges in breeding programs. Thus, the identification of optimal statistical methods and traits that better capture key biological mechanisms involved in the heat stress response has the potential to enable more accurate selection for thermal tolerant individuals. Therefore, this thesis aimed to investigate complementary topics related to thermal tolerance in livestock species based on genomic information. A total of 946 genotypes from 34 cattle breeds, as well as Datong yak (<em>Bos grunniens</em>) and Bali (<em>Bos javanicus</em>) populations, adapted to divergent climatic conditions, were used to investigate the genetic diversity and unravel genomic regions potentially under selection for thermal tolerance, with a focus on Chinese local cattle breeds and yak. Different signature of selection analyses and a comprehensive description of genetic diversity in 32 worldwide cattle and Datong yak populations was presented. Moderate genetic diversity was observed within each Chinese cattle population. However, these results highlighted the need to adopt strategies to avoid further reduction in the genetic diversity of these populations. Several candidate genes were identified as potentially under selection for thermal tolerance, and important biological pathways, molecular functions, and cellular components were identified, which contribute to our understanding of the genetic background of thermal tolerance in <em>Bos</em> species. Secondly, 8,992 genotyped individuals were used to provide a comprehensive description of genotype-by-environment interaction effects, defining optimal environmental variables based on public weather station data, and critical periods to evaluate heat tolerance for various reproduction, growth, and body composition traits in US Large White pigs. The period of 30 days before the measurement date was suggested to analyze genotype-by-environment interaction for off-test weight, muscle depth, and backfat thickness. While for number of piglets weaned and weaning weight, the suggested period ranged from the last trimester of gestation until weaning. This same population was used to access the genomic predictive ability of heat tolerance based on routinely-measured traits and explore candidate regions involved in the biological mechanisms that underlie heat stress response in pigs. Genotype-by-environment interaction was identified for most of the traits evaluated, and moderate (&gt;0.36 ± 0.05) breeding values prediction accuracy were achieved using genomic information. Lastly, various behavioral, anatomical, and physiological indicators of heat stress were measured in a population of 1,645 multiparous Large White x Landrace lactating sows. This dataset was used to identify the best statistical models and estimate genomic-based genetic parameters for 23 indicators of heat stress, including automatically-measured vaginal temperature, skin surface temperatures, respiration efficiency, respiration rate, panting score, body condition scores, hair density, body size, and ear measurements. All the traits evaluated are heritable, with heritability estimates ranging from 0.04 ± 0.01 to 0.40 ± 0.09. The genetic correlations among these traits ranged from -0.49 (between repeated records of vaginal temperature measured at 0800 hours and caliper body condition score) to 1.0 (between repeated records of vaginal temperature measured at 0800 hours and single record of vaginal temperature measured at 0800 hours; and between repeated records of vaginal temperature measured at 1200 hours and single record of vaginal temperature measured at 1200 hours). These findings indicate that genetic progress for thermotolerance in pigs can be achieved through direct indicators of heat stress in selection schemes. However, special attention is needed due to complex relationship between these traits as evidenced by their genetic correlations. In conclusion, this thesis provides important information to be used when designing breeding strategies for improving thermal tolerance in cattle and pigs, important genomic regions and metabolic pathways that are important for understanding the biological mechanism regulating thermal tolerance, as well as future directions for investigations in the area of livestock climatic adaptation.