Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

QTL, Hypothalamic-Transcriptome, And Candidate Gene Query Suggest Bovine Chromosome 2 Influences Heifer Pregnancy

Milton G Thomas¹ , Sunday O Peters¹ , Kadir Kazilkaya^2,3 , Dorian J Garrick² , Rohan L Fernando² , James M Reecy² , Z-L Hu² , Faye D Schilkey⁴ , Robert L Weaber⁵ , Gail A Silver¹

¹  New Mexico State University, Las Cruces, NM, 88003, USA

²  Iowa State University, Ames, IA, 50011, USA

³  Adnan Menderes University, Aydin, 09100, Turkey

⁴  National Center Genome Resources (NCGR), Santa Fe, NM, 87505, USA

⁵  University of Missouri, Columbia, MO, 65211, USA

Delineation of candidate genes will contribute to understanding of genetic pathways that regulate reproduction. A QTL on chromosome 2 associated with the binary trait of yearling heifer pregnancy success (approximately 80%) was detected in Brangus heifers (3/8 Bos indicus x 5/8 Bos taurus; n = 830 from 67 sires) using genotypes from BovineSNP50 Infinium beadchips. Simultaneous associations of all SNP with phenotype were undertaken with GenSel (Bayes C), using a mixture model that treated SNP effects as random with an assumed fraction pi=0.999 having no effect on phenotype. Posterior probability of association (PPA) for each SNP was computed and PPA/(1-pi) > 100 was assumed indicative of QTL association; 1-pi is the prior probability of association. Bioinformatic tools of www.animalgenome.org were used to visualize informative SNP (SNPlotz), QTL published for the region (CattleQTLdb), and potential candidate genes (gBrowse). Ten QTL and 10 annotations were identified in a 4 Mb region flanking the SNP inferring this QTL. Since hypothalamus is a regulatory tissue of the reproductive endocrine axis, transcriptome of this tissue was sequenced using the Illumina Genome Analyzer II and aligned with bovine genome to evaluate presence and level of expression of potential candidate genes among pre and postpubertal heifers through Alpheus®; Three genes with differential hypothalamic-expression were identified. Ontology of these genes included neuron function and cell signaling. Cumulatively, results warrant fine mapping of this region of chromosome 2 to help determine functionality (USDA-AFRI: 2008-35205-18751; 2009-35205-05100; NRSP-8 Bioinformatics).