title: A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome.
abstract: The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development.
authors.affiliation: Department of Genetics, and Southwest National Primate Research Centre, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA. lcox@txbiomedgenetics.org
authors.forename: Laura A
authors.initials: LA
authors.lastname: Cox
authors.forename: Jeremy P
authors.initials: JP
authors.lastname: Glenn
authors.forename: Kimberly D
authors.initials: KD
authors.lastname: Spradling
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Nijland
authors.forename: Roy
authors.initials: R
authors.lastname: Garcia
authors.forename: Peter W
authors.initials: PW
authors.lastname: Nathanielsz
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Ford
mesh_terms: D000818:Animals; D002417:Cattle; D005260:Female; D005318:Fetal Heart / Q000737:chemistry / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011247:Pregnancy; D011272:Pregnancy, Multiple; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D022661:RNA, Untranslated / Q000096:biosynthesis / Q000235:genetics; D016415:Sequence Alignment; D034561:Sheep, Domestic / Q000235:genetics; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated