Animal Molecular Breeding 2024, Vol.14, No.5, 307-317 http://animalscipublisher.com/index.php/amb 311 5 Functional Annotation and Pathway Analysis 5.1 Linking genetic markers to biological functions Genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with milk production traits in dairy cattle. These genetic markers are linked to various biological functions through gene ontology (GO) and pathway enrichment analyses. For instance, significant SNPs identified in Holstein cows were linked to genes such as DGAT1 and PPP1R16A, which are associated with milk yield, fat percentage, and protein percentage (Bakhshalizadeh et al., 2021). Similarly, a meta-analysis of GWAS data revealed significant loci on chromosome 14, implicating genes like DGAT1 and CPSF1 in milk production traits (Taherkhani et al., 2022). These findings highlight the importance of specific genomic regions and their associated biological functions in influencing milk production. 5.2 Pathway analysis of identified genes Pathway analysis of genes identified through GWAS provides insights into the biological mechanisms underlying milk production traits. For example, GO term enrichment analysis has identified pathways such as regulation of cation channel activity, ion channel complex, and phosphoric diester hydrolase activity as significant for milk yield (Bakhshalizadeh et al., 2021). Additionally, pathways related to calcium signaling, metabolic processes, and carbohydrate digestion have been associated with milk coagulation properties and cheese yield (Dadousis et al., 2017b). These pathways are crucial for understanding how genetic variations influence milk production and its components. 5.3 Integrating GWAS with transcriptomic and proteomic data Integrating GWAS findings with transcriptomic and proteomic data enhances the understanding of the genetic architecture of milk production traits. For instance, combining GWAS with gene expression data can identify candidate genes and their regulatory networks. In a study on Thai dairy cattle, genomic regions associated with milk production traits were found to contain genes related to heat tolerance, longevity, and fertility, indicating indirect selection pressures (Buaban et al., 2021). Furthermore, integrating proteomic data can reveal protein interactions and pathways involved in milk production, as demonstrated by the identification of intracellular cell transportation and protein catabolism networks. This integrative approach provides a comprehensive view of the genetic and molecular mechanisms driving milk production in dairy cattle. 6 Case Studies 6.1 Successful GWAS applications in improving dairy breeds Genome-wide association studies (GWAS) have significantly contributed to the improvement of dairy breeds by identifying quantitative trait loci (QTL) associated with key production traits. For instance, a study comparing within-breed and multibreed GWAS in French and Danish dairy cattle demonstrated that multibreed GWAS could enhance the detection and fine mapping of QTL, thereby increasing the power and precision of genetic selection (Berg et al., 2016). Similarly, a meta-analysis of GWAS in Holstein cows across different countries identified numerous QTLs for milk yield, fat percentage, and protein percentage, highlighting the potential of integrating multiple studies to improve genetic evaluations (Bakhshalizadeh et al., 2021). These findings underscore the utility of GWAS in pinpointing genetic variants that can be targeted for breeding programs to enhance milk production traits. 6.2 GWAS in holstein cattle: a comprehensive study Holstein cattle, being one of the most prominent dairy breeds, have been extensively studied using GWAS to understand the genetic basis of milk production traits. A longitudinal GWAS in a Chinese Holstein population identified numerous QTL regions associated with milk yield, fat percentage, and protein percentage, providing insights into candidate genes such as DGAT1, HSF1, and MGST1 (Teng et al., 2023). Another study in Brazilian Holstein cattle identified genomic regions associated with traditional milk production traits under tropical conditions, confirming well-known genes like MGST1 and DGAT1, and discovering novel genes involved in mammary gland repair and immune response (Iung et al., 2019). These comprehensive studies in Holstein cattle have not only validated previously known genetic markers but also uncovered new candidate genes, thereby enhancing our understanding of the genetic architecture of milk production traits.
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