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Open Access Research article

Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development

Wen Huang1, Brian S Yandell2 and Hasan Khatib1*

Author Affiliations

1 Department of Dairy Science, University of Wisconsin-Madison, Madison, WI 53706, USA

2 Departments of Statistics, Horticulture and Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA

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BMC Genomics 2010, 11:23  doi:10.1186/1471-2164-11-23

Published: 11 January 2010



Early embryonic loss is a large contributor to infertility in cattle. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. The objective of this study was to identify genes differentially expressed between blastocysts and degenerative embryos at early stages of development.


Using microarrays, genome-wide RNA expression was profiled and compared for in vitro fertilization (IVF) - derived blastocysts and embryos undergoing degenerative development up to the same time point. Surprisingly similar transcriptomic profiles were found in degenerative embryos and blastocysts. Nonetheless, we identified 67 transcripts that significantly differed between these two groups of embryos at a 15% false discovery rate, including 33 transcripts showing at least a two-fold difference. Several signaling and metabolic pathways were found to be associated with the developmental status of embryos, among which were previously known important steroid biosynthesis and cell communication pathways in early embryonic development.


This study presents the first direct and comprehensive comparison of transcriptomes between IVF blastocysts and degenerative embryos, providing important information for potential genes and pathways associated with early embryonic development.