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

Frontiers in Genetics
Tingxian DengLiguo Yang

Abstract

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 < 10-4). 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, C2CD...Continue Reading

References

Nov 15, 2001·The Journal of Biological Chemistry·Jarmo LaineMasayuki Noguchi
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Jul 24, 2004·American Journal of Human Genetics·Benjamin M Neale, Pak C Sham
Aug 4, 2004·Cellular and Molecular Life Sciences : CMLS·K A Green, C H Streuli
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
Aug 29, 2006·PLoS Genetics·Anatole GhazalpourSteve Horvath
Nov 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·S HorvathP S Mischel
Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael C OldhamDaniel H Geschwind
Aug 2, 2007·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Tova F FullerSteve Horvath
Jan 30, 2008·Current Opinion in Cell Biology·Jennetta W HammondKristen J Verhey
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Feb 24, 2009·Genetic Epidemiology·Clara C ElbersN Charlotte Onland-Moret
Jul 25, 2009·Nature Reviews. Cancer·Erwin F Wagner, Angel R Nebreda
Feb 19, 2010·Animal Science Journal = Nihon Chikusan Gakkaihō·Takahisa YamadaYoshiyuki Sasaki
Feb 19, 2010·Animal Science Journal = Nihon Chikusan Gakkaihō·Kyoung Hoon KimNobuhiro Kimura
Mar 12, 2010·Nature·Joseph K PickrellJonathan K Pritchard
Jun 10, 2010·International Journal of Cancer. Journal International Du Cancer·Kimako OkaHironobu Sasano
Nov 19, 2010·Nature Reviews. Genetics·Kai WangHakon Hakonarson
Nov 16, 2011·Journal of the Science of Food and Agriculture·Elinor MedhammarBarbara Burlingame
Dec 1, 2011·Cancer Research·Cristina CelluraleRoger J Davis
Jan 17, 2012·American Journal of Human Genetics·Peter M VisscherJian Yang
Jan 27, 2012·BMC Genomics·Saumya WickramasingheJuan F Medrano
Jan 10, 2013·PLoS Computational Biology·William S Bush, Jason H Moore
Jan 15, 2013·G3 : Genes - Genomes - Genetics·Charles R Farber
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Apr 18, 2015·PLoS Computational Biology·Christiaan A de LeeuwDanielle Posthuma
Oct 30, 2015·BMC Genomics·G M F de CamargoH Tonhati

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Citations

Jan 23, 2020·Animal Genetics·Y ZhangJ S F Barker
Nov 25, 2019·Journal of Dairy Science·Jessica Lorena Gonzalez GuzmanHumberto Tonhati

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Datasets Mentioned

BETA
PRJNA480718

Methods Mentioned

BETA
biopsies
RNA-Seq
biopsy
PCR

Software Mentioned

WGCNA
WGCNA R - package
MAGMA
edgeR R - package
house
TopHat
DESeq2 R - package
FastQC
Cytoscape
R scripts

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