Journal Article

Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

Dai, Dongmei, Santos, Daniel J. A., Huang, Hetian, Fang, Lingzhao, Zhang, Yi, Ma, Chong, Cao, Jie, Liu, George E., Ma, Li, Yan, Ze, Freebern, Ellen, Guo, Gang, Si, Jingfang

2020

Overview

Background Ketosis is a common metabolic disease during the transition period in dairy cattle, resulting in long-term economic loss to the dairy industry worldwide. While genetic selection of resistance to ketosis has been adopted by many countries, the genetic and biological basis underlying ketosis is poorly understood. Results We collected a total of 24 blood samples from 12 Holstein cows, including 4 healthy and 8 ketosis-diagnosed ones, before (2 weeks) and after (5 days) calving, respectively. We then generated RNA-Sequencing (RNA-Seq) data and seven blood biochemical indicators (bio-indicators) from leukocytes and plasma in each of these samples, respectively. By employing a weighted gene co-expression network analysis (WGCNA), we detected that 4 out of 16 gene-modules, which were significantly engaged in lipid metabolism and immune responses, were transcriptionally (FDR < 0.05) correlated with postpartum ketosis and several bio-indicators (e.g., high-density lipoprotein and low-density lipoprotein). By conducting genome-wide association signal (GWAS) enrichment analysis among six common health traits (ketosis, mastitis, displaced abomasum, metritis, hypocalcemia and livability), we found that 4 out of 16 modules were genetically (FDR < 0.05) associated with ketosis, among which three were correlated with postpartum ketosis based on WGCNA. We further identified five candidate genes for ketosis, including GRINA, MAF1, MAFA, C14H8orf82 and RECQL4. Our phenome-wide association analysis (Phe-WAS) demonstrated that human orthologues of these candidate genes were also significantly associated with many metabolic, endocrine, and immune traits in humans. For instance, MAFA , which is involved in insulin secretion, glucose response, and transcriptional regulation, showed a significantly higher association with metabolic and endocrine traits compared to other types of traits in humans. Conclusions In summary, our study provides novel insights into the molecular mechanism underlying ketosis in cattle, and highlights that an integrative analysis of omics data and cross-species mapping are promising for illustrating the genetic architecture underpinning complex traits.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abomasum / Animal Genetics and Genomics / Animals / Association analysis / Bioindicators / Biomedical and Life Sciences / Blood / Cattle / Cattle diseases / Cattle Diseases - genetics / Cattle Diseases - metabolism / Dairy cattle / Dairy industry / Density / Diseases / Economic impact / Female / Gene expression / Gene mapping / Gene regulation / Gene sequencing / Genes / Genetic aspects / Genome-Wide Association Study / Genomes / Genomics / GWAS / Holstein / Humans / Hypocalcemia / Immune response / Indicator species / Indicators / Insulin / Insulin secretion / Ketosis / Ketosis - genetics / Ketosis - metabolism / Ketosis - veterinary / Leukocytes / Leukocytes - metabolism / Life Sciences / Lipid metabolism / Lipids / Mapping / Mastitis / Metabolic diseases / Metabolic disorders / Metritis / Microarrays / Microbial Genetics and Genomics / Milk / Modules / Nervous system / Network analysis / Non-human and non-rodent vertebrate genomics / Ontology / Phe-WAS / Physiology / Plant Genetics and Genomics / Postpartum / Proteomics / Research Article / Ribonucleic acid / RNA / RNA-Seq / Transcription / WGCNA