Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle

Authors: CANOVAS, ANGELA - University Of California; REVERTER, ANTONIO - Commonwealth Scientific And Industrial Research Organisation (CSIRO); DEATLEY, KASEY - New Mexico State University; ASHLEY, RYAN - New Mexico State University; COLGRAVE, MICHELLE - Commonwealth Scientific And Industrial Research Organisation (CSIRO); FORTES, MARINA - University Of Queensland; ISLAS-TREJO, ALMA - University Of California; LEHNERT, SIGRID - Commonwealth Scientific And Industrial Research Organisation (CSIRO); PORTO-NETO, LAERCIO - Commonwealth Scientific And Industrial Research Organisation (CSIRO); RINCON, GONZALO - University Of California; SILVER, GAIL - New Mexico State University; Snelling, Warren; MEDRANO, JUAN - University Of California; THOMAS, MILTON - Colorado State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2014
Publication Date: 7/21/2014
Citation: Canovas, A., Reverter, A., DeAtley, K.L., Ashley, R.L., Colgrave, M.L., Fortes, M.R., Islas-Trejo, A., Lehnert, S.A., Porto-Neto, L.R., Rincon, G., Silver, G.A., Snelling, W.M., Medrano, J.F., Thomas, M.G. 2014. Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle. PLoS One. 9(7):e102551. DOI: 10.1371/journal.pone.0102551.

Interpretive Summary: Puberty is a complex process of physical changes as animals mature into adults capable of reproduction. To investigate genes affecting puberty, tissues from 8 organs related to reproduction, growth and metabolism were sampled from Brangus heifers. These tissues were analyzed to determine genes expressed at different levels in heifers before and after they reached puberty. Gene expression results were combined with associations between genotypes for over 50,000 genetic markers, located throughout the genome, and measures of age at puberty and pregnancy in heifers. About 1,500 genes were expressed at different levels in heifers before and after puberty, and 950 genes were expressed in only one tissue. A genetic marker associated with puberty or pregnancy was within or close to 19 of the differentially expressed genes. Gene networks developed from gene expression and associations between genotype and puberty phenotypes revealed 7 key transcription factors regulating puberty. This information provides a more complete understanding of interactions among genes affecting puberty, which may be incorporated into selection for earlier puberty.

Technical Abstract: Puberty is a complex physiological event by which animals mature into an adult capable of sexual reproduction. In order to enhance our understanding of the genes and regulatory pathways and networks involved in puberty, we characterized the transcriptome of five reproductive tissues (i.e., hypothalamus, pituitary gland, ovary, uterus, and endometrium) as well as tissues known to be relevant to growth and metabolism needed to achieve puberty (i.e., longissimus dorsi muscle, adipose, and liver). These tissues were collected from pre- and post-pubertal Brangus heifers (3/8 Brahman; Bos indicus x 5/8 Angus; Bos taurus) derived from a population of cattle used to identify quantitative trait loci associated with fertility traits (i.e., age of first observed corpus luteum (ACL), first service conception (FSC), and heifer pregnancy (HPG)). In order to exploit the power of complementary omics analyses, pre- and post-puberty co-expression gene networks were constructed by combining the results from genome-wide association studies (GWAS), RNA-Seq, and bovine transcription factors. Eight tissues among pre-pubertal and post-pubertal Brangus heifers revealed 1,515 differentially expressed and 943 tissue-specific genes within the 17,832 genes confirmed by RNA-Seq analysis. The hypothalamus experienced the most notable up-regulation of genes via puberty (i.e., 204 out of 275 genes). Combining the results of GWAS and RNA-Seq, we identified 25 loci containing a single nucleotide polymorphism (SNP) associated with ACL, FSC, and (or) HPG. Seventeen of these SNP were within a gene and 13 of the genes were expressed in uterus or endometrium. Multi-tissue omics analyses revealed 2,450 co-expressed genes relative to puberty. The pre-pubertal network had 372,861 connections whereas the post-pubertal network had 328,357 connections. A sub-network from this process revealed key transcriptional regulators (i.e., PITX2, FOXA1, DACH2, PROP1, SIX6, etc.). Results from these multi-tissue omics analyses improve understanding of the number of genes and their complex interactions for puberty in cattle.