That gene family imprinted in other species (Table 6).DiscussionOur results demonstrated that parthenotes and in vivo fertilised rabbit blastocysts cultured under in vivo UKI 1 conditions differ notably in gene expression. Up till now, few works have analysed transcriptome differences between parthenotes and fertilised embryosTranscriptome of In Vivo Parthenote BlastocystsTable 6. Putative imprinted genes differentially expressed in parthenogenetic late blastocysts identified as family members at Catalogue of Imprinted Genes (http://igc.otago.ac.nz/home.html).Family members genes name Imprinted gene SLC22A2, 256373-96-3 SLC22A3, SLC22A8, SLC22A18S AWT1,WT1-AS IGF2 RB1 L3MBTL PPP1RGA ASB4 KLF14 NAP1L5 UPS29 ZFP264, ZFP127 PEC2, PEC3 NCCR UBE3A TSPAN32 TNFRSF23 ANO1 INPP5F-V2 RASGRF1 COMMD1 HTR2A FBXO40 SNRPN PRIM2 CDKN1C SASH2 doi:10.1371/journal.pone.0051271.t006 CDKN1A, CDKN1B, CDKN3 SASH1 FBXO15, FBXO32, FBXO48 INPP1, INPP4B RASGEF1B, RASGRP3 COMMD3, COMMD5 RASGRP1, RASGRP2 COMMD2, COMMD7, COMMD8 HTRA4 FBXO4, FBXO5, FBXO25, FBXO38, FBXO42 SNRPPA1, SNRPB2 PRIM1 UBE3B, UBE4B TSPAN5, TSPAN12, TSPAN13 TSPAN1N, TSPAN14, TSPAN31 TNFRSF1A ANO6 ASB8 KLF16, KLF12 NAP1L1 USP2, USP4, USP25, USP53 USP7, USP15, USP22, USP28, USP34USP40, USP43, USP46, USP48 ZFP36, ZFP57, ZFP62, ZFP90 PECR NCCRP1 IGF2BP2 RB11A L3MBTL2 L3MBTL1 PPP1CC ASB3 KLF3, KLF4 Upregulated Downregulated SLC22A5, SLC22A17 SWT1 IGF2BP[20,21,22]. However, these works were carried out with parthenote embryos developed in vitro and in vitro cultured fertilised embryos. It is well documented that embryos developed under in vitro environment are still not comparable with in vivo embryos [23], as post-fertilisation culture environment is a determinant for adequate embryonic development [4,24]. For example, one of the most critical time points of preimplantation embryogenesis is the major embryonic genome activation at which the embryo switches from using the mRNA and proteins derived from the maternal genome to those resulting from de novo transcription from the embryonic genome [25]. During that time, availability of transcription factors, which are regulated by cell cycle-dependent mechanisms, is required [26]. These mechanisms are strongly influenced by a change in environmental conditions and subsequently affect the embryonic development, with potentially severe effects on foetal, prenatal and postnatal viability [27]. Corcoran et al. [20] found that a total of 384 genes were differentially expressed between in vivo and in vitro derived blastocysts, the vast majority of them (almost 85 ) being downregulated in in vitro developed embryos. Likewise, the effects of developmental environment on mRNA expression in parthenogenetic embryos have also been described [11] this way. To our best knowledge, this is the first report that compared the genome-wide gene expression profiles between rabbit parthenogenetic blastocysts and fertilised blastocysts developed in vivo. Microarray 
analysis of parthenotes and fertilised embryos developed in vitro indicated differences in expression of 749 genes from mouse with 1.8 fold-changes as a cut-off [20], 24 genes for early embryos and 5 for expanded embryos from bovine with 1.5 fold-changes as a cut-off [22] and 56 genes from buffalo with 1.4 fold-changes as a cut-off [21]. In this study, we observed that 1606, 557 and 199 microarray probe signals were changed in the parthenogenetic blastocyst using a minimum of 1.5, 2.0 and 3.0 fold-changes as a cut-off, respectively.That gene family imprinted in other species (Table 6).DiscussionOur results demonstrated that parthenotes and in vivo fertilised rabbit blastocysts cultured under in vivo conditions differ notably in gene expression. Up till now, few works have analysed transcriptome differences between parthenotes and fertilised embryosTranscriptome of In Vivo Parthenote BlastocystsTable 6. Putative imprinted genes differentially expressed in parthenogenetic late blastocysts identified as family members at Catalogue of Imprinted Genes (http://igc.otago.ac.nz/home.html).Family members genes name Imprinted gene SLC22A2, SLC22A3, SLC22A8, SLC22A18S AWT1,WT1-AS IGF2 RB1 L3MBTL PPP1RGA ASB4 KLF14 NAP1L5 UPS29 ZFP264, ZFP127 PEC2, PEC3 NCCR UBE3A TSPAN32 TNFRSF23 ANO1 INPP5F-V2 RASGRF1 COMMD1 HTR2A FBXO40 SNRPN PRIM2 CDKN1C SASH2 doi:10.1371/journal.pone.0051271.t006 CDKN1A, CDKN1B, CDKN3 SASH1 FBXO15, FBXO32, FBXO48 INPP1, INPP4B RASGEF1B, RASGRP3 COMMD3, COMMD5 RASGRP1, RASGRP2 COMMD2, COMMD7, COMMD8 HTRA4 FBXO4, FBXO5, FBXO25, FBXO38, FBXO42 SNRPPA1, SNRPB2 PRIM1 UBE3B, UBE4B TSPAN5, TSPAN12, TSPAN13 TSPAN1N, TSPAN14, TSPAN31 TNFRSF1A ANO6 ASB8 KLF16, KLF12 NAP1L1 USP2, USP4, USP25, USP53 USP7, USP15, USP22, USP28, USP34USP40, USP43, USP46, USP48 ZFP36, ZFP57, ZFP62, ZFP90 PECR NCCRP1 
IGF2BP2 RB11A L3MBTL2 L3MBTL1 PPP1CC ASB3 KLF3, KLF4 Upregulated Downregulated SLC22A5, SLC22A17 SWT1 IGF2BP[20,21,22]. However, these works were carried out with parthenote embryos developed in vitro and in vitro cultured fertilised embryos. It is well documented that embryos developed under in vitro environment are still not comparable with in vivo embryos [23], as post-fertilisation culture environment is a determinant for adequate embryonic development [4,24]. For example, one of the most critical time points of preimplantation embryogenesis is the major embryonic genome activation at which the embryo switches from using the mRNA and proteins derived from the maternal genome to those resulting from de novo transcription from the embryonic genome [25]. During that time, availability of transcription factors, which are regulated by cell cycle-dependent mechanisms, is required [26]. These mechanisms are strongly influenced by a change in environmental conditions and subsequently affect the embryonic development, with potentially severe effects on foetal, prenatal and postnatal viability [27]. Corcoran et al. [20] found that a total of 384 genes were differentially expressed between in vivo and in vitro derived blastocysts, the vast majority of them (almost 85 ) being downregulated in in vitro developed embryos. Likewise, the effects of developmental environment on mRNA expression in parthenogenetic embryos have also been described [11] this way. To our best knowledge, this is the first report that compared the genome-wide gene expression profiles between rabbit parthenogenetic blastocysts and fertilised blastocysts developed in vivo. Microarray analysis of parthenotes and fertilised embryos developed in vitro indicated differences in expression of 749 genes from mouse with 1.8 fold-changes as a cut-off [20], 24 genes for early embryos and 5 for expanded embryos from bovine with 1.5 fold-changes as a cut-off [22] and 56 genes from buffalo with 1.4 fold-changes as a cut-off [21]. In this study, we observed that 1606, 557 and 199 microarray probe signals were changed in the parthenogenetic blastocyst using a minimum of 1.5, 2.0 and 3.0 fold-changes as a cut-off, respectively.
