Current status of sperm functional genomics and its diagnostic potential of fertility in bovine (Bos taurus).

With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events. Human spermatozoal transcriptome profiling has been carried out on a large number of individuals to predict the semen quality. A study in human indicated that the outcome of some idiopathic couples seeking reproductive care could be helped using transcriptomic profiling of spermatozoa. Such studies have a direct impact on the bovine dairy industry, wherein AI is practiced. Limited studies in bovine spermatozoal transcriptome profiling have revealed that the spermatozoa contain various classes of RNA, like in human. Approximately 13,000 bovine genes yield a series of spermatozoal transcripts, of which most are fragmented in nature. Their abundance is indicative of the timing of events associated with spermatogenesis, e.g., PRM1, IGF1, BMP2; sperm function, TSSK6, CRISP, HSFY2; fertility, UBE2D3, Integrin-β, LDC-1; and embryonic development, miR34c-5p, BCL2L11, BRCA1. The most abundant translated bovine transcripts are BSP3 and SPATA18, and are involved in regulation of germ cell development and the maintenance of chromatin integrity during spermatogenesis respectively. The presence of transcripts associated with placental development, e.g., placental associated glycoproteins (PAGs) have suggested their possible influence beyond early embryonic development. Changes in transcript levels like RPL31 and PRKCE that increase, and PRM1 that decreases, during cryopreservation need to be defined in order to optimize cryopreservation and fertility yield. Spermatozoal transcriptome profiling with validation studies are warranted in large numbers of animals to elucidate their significance for selecting fertile bulls for the breeding program. Abbreviations: AI: artificial insemination; BSE: breeding soundness evaluation; cfs-mRNA: cell-free seminal mRNA; piRNA: PIWI-interacting RNA; tRNA: transfer RNA; fg: femtogram; TPM: transcripts per million reads; RPKM: reads per kilobase million; rRNA: ribosomal RNA; mt-RNA: mitochondrial RNA; lncRNA: long non-coding RNA; sncRNA: small noncoding RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; miRNA: microRNA; snaR: small NF90-associated RNAs; SINES: short interspersed nuclear elements; LINES: long interspersed nuclear elements; MER: medium reiterated sequence; F1 offspring: filial 1 offspring; PAGs: placental associated glycoproteins; TCP: Transcription factor T complex protein; BSP3: bovine seminal plasma protein 3; SCNT: somatic cell nuclear transfer; qPCR: quantitative (real-time) polymerase chain reaction; SSH: suppression subtractive hybridization; SNP: single nucleotide polymorphism; 2-DE: 2 dimensional gel electrophoresis; LC-MS/MS: liquid chromatography-tandem mass spectrometry.