Molecular Biotechnology

, Volume 53, Issue 2, pp 217–226

An Integrative Genomic Analysis of the Superior Fecundity Phenotype in QSi5 Mice


  • Jerry Wei
    • Faculty of Veterinary ScienceThe University of Sydney
  • Palaniappan Ramanathan
    • Faculty of Veterinary ScienceThe University of Sydney
  • Peter C. Thomson
    • Faculty of Veterinary ScienceThe University of Sydney
  • Ian C. Martin
    • Faculty of Veterinary ScienceThe University of Sydney
  • Christopher Moran
    • Faculty of Veterinary ScienceThe University of Sydney
    • Faculty of Veterinary ScienceThe University of Sydney

DOI: 10.1007/s12033-012-9530-y

Cite this article as:
Wei, J., Ramanathan, P., Thomson, P.C. et al. Mol Biotechnol (2013) 53: 217. doi:10.1007/s12033-012-9530-y


Laboratory inbred mouse models are a valuable resource to identify quantitative trait loci (QTL) for complex reproductive performance traits. Advances in mouse genomics and high density single nucleotide polymorphism mapping has enabled genome-wide association studies to identify genes linked with specific phenotypes. Gene expression profiles of reproductive tissues also provide potentially useful information for identifying genes that play an important role. We have developed a highly fecund inbred strain, QSi5, with accompanying genotyping for comparative analysis of reproductive performance. Here we analyzed the QSi5 phenotype using a comparative analysis with fecundity data derived from 22 inbred strains of mice from the Mouse Phenome Project, and integration with published expression data from mouse ovary development. Using a haplotype association approach, 400 fecundity-associated regions (FDR < 0.05) with 499 underlying genes were identified. The most significant associations were located on Chromosomes 14, 8, and 6, and the genes underlying these regions were extracted. When these genes were analyzed for expression in an ovarian development profile (GSE6916) several distinctive co-expression patterns across each developmental stage were identified. The genetic analysis also refined 21 fecundity associated intervals on Chromosomes 1, 6, 9, 13, and 17 that overlapped with previously reported reproductive performance QTL. The combined use of phenotypic and in silico data with an integrative genomic analysis provides a powerful tool for elucidating the molecular mechanisms underlying fecundity.


Reproductive performance traitsQuantitative trait lociFecundity genesQSi5mice

Supplementary material

12033_2012_9530_MOESM1_ESM.xls (67 kb)
Additional File 1Candidate gene lists of the 10 co-expression patterns in gestative ovary. (XLS 67 kb)

Copyright information

© Springer Science+Business Media, LLC 2012