Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y

Abstract

When necessary, RNA-sequencing data or polymerase chain reaction (PCR) assays can be used to determine the presence of the chromosome Y (ChrY) in samples. This information allows for biological variation due to sexual dimorphism to be studied. A prime example is when researchers conduct RNA-sequencing of single embryos, or conceptuses, prior to the development of gonads. A recent publication of a complete sequence of the ChrY has removed limitations for the development of these procedures in cattle, otherwise imposed by the absence of a ChrY in the reference genome. Using the sequence of the cattle ChrY and transcriptome data, we conducted a systematic search for genes in the ChrY that are exclusively expressed in male tissues. The genes ENSBIXG00000029763, ENSBIXG00000029774, ENSBIXG00000029788, and ENSBIXG00000029892 were consistently expressed across male tissues and lowly expressed or absent in female samples. We observed that the cumulative values of counts per million were 2688-fold greater in males than the equivalent values in female samples. Thus, we deemed these genes suitable for the sexing of samples using RNA-sequencing data. We successfully used this set of genes to infer the sex of 22 cattle blastocysts (8 females and 14 males). Additionally, the completed sequence of the cattle ChrY has segments in the male-specific region that are not repeated. We designed a pair of oligonucleotides that targets one of these non-repeated regions in the male-specific sequence of the ChrY. Using this pair of oligonucleotides, in a multiplexed PCR assay with oligonucleotides that anneal to an autosome chromosome, we accurately identified the sex of cattle blastocysts. We developed efficient procedures for the sexing of samples in cattle using either transcriptome data or their DNA. The procedures using RNA-sequencing will greatly benefit researchers who work with samples limited in cell numbers which are only sufficient to produce transcriptome data. The oligonucleotides used for the accurate sexing of samples using PCR are transferable to other cattle tissue samples.

Extensive rewiring of the gene regulatory interactions between in vitro–produced conceptuses and endometrium during attachment

“…We used a pipeline published elsewhere ( 84 ) to align sequences produced from EET to the sequence of cattle chromosome Y (GenBank: CM011803.1 ) ( 85 ). Briefly, the fasta sequence of chromosome Y was appended to the cattle genome fasta sequence followed by the creation of an index and alignment of reads using Hisat2 (v 2.2.1) ( 74 ).…”

“…We also used featurecounts to count the reads on chromosome Y using the annotation of chromosome Y provided by Liu et al ( 85 ). Samples that had reads assigned to the genes “ENSBIXG00000029788,” “ENSBIXG00000029774” ( ZRSR2 ), and “ENSBIXG00000029763” ( OFD1 ) were inferred as males ( 84 ) (Fig. S5 ).…”

Pre-Implantation Bovine Embryo Evaluation—From Optics to Omics and Beyond

“…To study lipid-metabolism-associated gene expression in parthenogenetic embryos [199] To study the functional consequences of three critical lineage-specific genes (SOX2, OCT4, and CDX2) [182] sexing of embryos [200] 5500xl Genetic Analyzer, Applied Biosystems, CA, USA…”