Supplemental file for Genomic and transcriptomic analyses enable the identification of important genes

<strong>Background: </strong>Subcutaneous fat deposition has many important roles in dairy cattle, including immunological defense and mechanical protection. Previous studies have revealed its polygenic nature and large environmental influence. Therefore, the main objectives of this study were to identify key candidate genes regulating subcutaneous fat deposition in high-producing Holstein cows through the integration of genomic and transcriptomic datasets. A total of 1,654 Holstein cows genotyped for 139,376 single nucleotide polymorphisms (SNP) were used to perform a genome-wide association study (GWAS) aiming to identify SNPs and genes associated with subcutaneous fat deposition (skinfold thickness over the neck, the last rib and the rear udder, and body condition score). Subsequently, gene co-expression network analyses were conducted based on RNA-sequencing data of 35 cows and de-regressed estimated breeding values (EBV) of subcutaneous fat deposition. Lastly, differentially expressed mRNA, lncRNA, and differentially alternative splicing genes for subcutaneous fat deposition were obtained for 12 Holstein cows with extreme and divergent phenotypes for subcutaneous fat deposition traits. 
<strong>Results: </strong>Forty-six protein-coding genes were identified as candidate genes regulating subcutaneous fat deposition in Holstein cattle based on the GWAS for the four traits evaluated. Eleven overlapping genes were identified based on the analyses of differentially expressed genes and weighted gene co-expression network analyses. Furthermore, the candidate genes identified based on the GWAS, weighted gene co-expression network analyses, and analyses of differentially expressed genes were significantly enriched for pathways involved in metabolism, oxidative phosphorylation, thermogenesis, fatty acid degradation, and glycolysis/gluconeogenesis pathways. 
<strong>Conclusions: </strong>Based on the integration of all findings, the <em>NID2</em>, <em>STARD3</em>, <em>UFC1</em>, <em>DEDD</em>, <em>PPP1R1B</em>, and <em>USP21</em> genes are considered to be the most important candidate genes influencing subcutaneous fat deposition traits in Holstein cows. This study provides novel insights into the regulation mechanism underlying fat deposition in high-producing Holstein cows, which will be useful when designing management and breeding strategies.   
<strong>Background: </strong>Subcutaneous fat deposition has many important roles in dairy cattle, including immunological defense and mechanical protection. Previous studies have revealed its polygenic nature and large environmental influence. Therefore, the main objectives of this study were to identify key candidate genes regulating subcutaneous fat deposition in high-producing Holstein cows through the integration of genomic and transcriptomic datasets. A total of 1,654 Holstein cows genotyped for 139,376 single nucleotide polymorphisms (SNP) were used to perform a genome-wide association study (GWAS) aiming to identify SNPs and genes associated with subcutaneous fat deposition (skinfold thickness over the neck, the last rib and the rear udder, and body condition score). Subsequently, gene co-expression network analyses were conducted based on RNA-sequencing data of 35 cows and de-regressed estimated breeding values (EBV) of subcutaneous fat deposition. Lastly, differentially expressed mRNA, lncRNA, and differentially alternative splicing genes for subcutaneous fat deposition were obtained for 12 Holstein cows with extreme and divergent phenotypes for subcutaneous fat deposition traits. 
<strong>Results: </strong>Forty-six protein-coding genes were identified as candidate genes regulating subcutaneous fat deposition in Holstein cattle based on the GWAS for the four traits evaluated. Eleven overlapping genes were identified based on the analyses of differentially expressed genes and weighted gene co-expression network analyses. Furthermore, the candidate genes identified based on the GWAS, weighted gene co-expression network analyses, and analyses of differentially expressed genes were significantly enriched for pathways involved in metabolism, oxidative phosphorylation, thermogenesis, fatty acid degradation, and glycolysis/gluconeogenesis pathways. 
<strong>Conclusions: </strong>Based on the integration of all findings, the <em>NID2</em>, <em>STARD3</em>, <em>UFC1</em>, <em>DEDD</em>, <em>PPP1R1B</em>, and <em>USP21</em> genes are considered to be the most important candidate genes influencing subcutaneous fat deposition traits in Holstein cows. This study provides novel insights into the regulation mechanism underlying fat deposition in high-producing Holstein cows, which will be useful when designing management and breeding strategies.