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Table_2_Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo.xlsx

By Tingxian Deng (845722), Aixin Liang (4906621), Shasha Liang (6294980), Xiaoya Ma (536145), Xingrong Lu (845724), Anqin Duan (845725), Chunying Pang (845723), Guohua Hua (342698), Shenhe Liu (6182843), Giuseppe Campanile (529389), Angela Salzano (5957189), Bianca Gasparrini (529379), Gianluca Neglia (529380), Xianwei Liang (845728) and Liguo Yang (342702)

Abstract

<p>The mammary gland is the production organ in mammals that is of great importance for milk production and quality. However, characterization of the buffalo mammary gland transcriptome and identification of the valuable candidate genes that affect milk production is limited. Here, we performed the differential expressed genes (DEGs) analysis of mammary gland tissue on day 7, 50, 140, and 280 after calving and conducted gene-based genome-wide association studies (GWAS) of milk yield in 935 Mediterranean buffaloes. We then employed weighted gene co-expression network analysis (WGCNA) to identify specific modules and hub genes related to milk yield based on gene expression profiles and GWAS data. The results of the DEGs analysis showed that a total of 1,420 DEGs were detected across different lactation points. In the gene-based analysis, 976 genes were found to have genome-wide association (P ≤ 0.05) that could be defined as the nominally significant GWAS geneset (NSGG), 9 of which were suggestively associated with milk yield (P < 10<sup>−4</sup>). Using the WGCNA analysis, 544 and 225 genes associated with milk yield in the turquoise module were identified from DEGs and NSGG datasets, respectively. Several genes (including BNIPL, TUBA1C, C2CD4B, DCP1B, MAP3K5, PDCD11, SRGAP1, GDPD5, BARX2, SCARA3, CTU2, and RPL27A) were identified and considered as the hub genes because they were involved in multiple pathways related to milk production. Our findings provide an insight into the dynamic characterization of the buffalo mammary gland transcriptome, and these potential candidate genes may be valuable for future functional characterization of the buffalo mammary gland.</p

Topics: Genetics, Genetic Engineering, Biomarkers, Developmental Genetics (incl. Sex Determination), Epigenetics (incl. Genome Methylation and Epigenomics), Gene Expression (incl. Microarray and other genome-wide approaches), Genome Structure and Regulation, Genomics, Genetically Modified Animals, Livestock Cloning, Gene and Molecular Therapy, buffalo, genome-wide association studies, hub genes, milk yield, RNA-seq, WGCNA
Year: 2019
DOI identifier: 10.3389/fgene.2019.00036.s007
OAI identifier: oai:figshare.com:article/7671089
Provided by: FigShare
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