29 30 31 32 33 34 35 ABSTRACT 3637 Artificial insemination with cryopreserved sperm is a major assisted reproductive 38 technology in many species. In horses, as in humans, insemination with cryopreserved 39 sperm is associated with lower pregnancy rates than those for fresh sperm, however, 40 direct effects of sperm cryopreservation on the development of resulting embryos are 41 largely unexplored. The aim of this study was to investigate differences in gene 42 expression between embryos resulting from fertilization with fresh or cryopreserved 43 sperm. Embryos were obtained at 8, 10 or 12 days after ovulation from mares 44 inseminated post-ovulation on successive cycles with either fresh sperm or frozen-45 thawed sperm from the same stallion, providing matched embryo pairs at each day.46 RNA was isolated from two matched pairs (4 embryos) for each day, and cDNA 47 libraries were built and sequenced. Significant differences in transcripts per kilobase 48 million (TPM) were determined using (i) genes for which the expression difference 49 between treatments was higher than 99% of that in the random case (P < 0.01), and (ii) 50 genes for which the fold change was 2, to avoid expression bias in selection of the 51 candidate genes. Molecular pathways were explored using the DAVID webserver, 52 followed by network analyses using STRING, with a threshold of 0.700 for positive 53 interactions. The transcriptional profile of embryos obtained with frozen-thawed sperm 54 differed significantly from that for embryos derived from fresh sperm on all days, 55 showing significant down-regulation of genes involved in biological pathways related to 56 oxidative phosphorylation, DNA binding, DNA replication, and immune response.57 Many genes with reduced expression were orthologs of genes known to be embryonic 58 lethal in mice. This study, for the first time, provides evidence of altered transcription in 59 embryos resulting from fertilization with cryopreserved spermatozoa in any species. As 60 sperm cryopreservation is commonly used in many species, including human, the effect 61 of this intervention on expression of developmentally important genes in resulting 62 embryos warrants attention. 63 64 65 67 INTRODUCTION 68 69 Cryopreservation is a common procedure in assisted reproductive technology, in both 70 humans and the animal breeding industry [1-3]. Cryopreserved sperm are routinely used 71 for artificial insemination (AI), in vitro fertilization (IVF) and intracytoplasmic sperm 72 injection (ICSI). However, it is clear that sperm cryopreservation methods are currently 73 sub-optimal, as pregnancy rates with cryopreserved sperm are lower than those with 74 fresh sperm in humans and horses [4], among other species. Cryopreservation leads to 75 extensive damage of sperm cell membranes and causes metabolic and functional 76 alteration of sperm [5, 6], particularly of their mitochondria [7-9]. Cryopreservation 77 may alter sperm DNA [10]; recently, specific cryodamage to sperm genes and 78 transcripts have been reported [11,...