Fig 2: Knockout of PTPN12 does not significantly impact BVDV infection in MDBK cells. Panel (A), map of bovine PTPN12 and surrounding genes: blue arrows, genes (open reading frames); vertical blue lines, coding regions (exons); black lines, heterozygous deletions in two alleles of PTPN12 on chromosome 4; red square, homozygous deleted region (33,808 bp); red arrow, exon target of PTPN12 gRNA. Panel (B), RNASeq analyses of relative RNA transcript abundance in MDBK and CRIB cells (trimmed mean of M (TMM) normalization value). Panel (C), western blot of SDS-PAGE for PTPN12 and GAPDH (loading control). Panel (D), Multistep virus growth curve. Cells were infected with BVDV strain NADL (MOI 0.01). Cells were collected and processed 0–96 h post-infection for quantitation of viral RNA using RT-qPCR. Results represent the mean ± standard deviation (n = 3).

Fig 3: Physical maps of the three large homozygous deleted regions in the CRIB cell line. Genome map of ARS-UCD1.2 in the region of the three large homozygous deleted regions. Blue arrows, genes (open reading frames); black lines, overlapping heterozygous deletion alleles; red box, homozygous deleted region. Panel (A) heterozygous deletion alleles of PTPN12 on chromosome 4. Panel (B) heterozygous deletion alleles of GRID2 on chromosome 6. Panel (C) heterozygous deletion alleles of RABGAP1L on chromosome 16. Shown on top of the bovine map are the transcripts annotated for RABGAP1L in the Hereford ARS-UCD1.2 reference genome. Below the map are IsoSeq transcripts from multiple cattle breeds (see Methods). Panel (D), genome map with the full-length bovine RABGAP1L gene as determined using IsoSeq transcripts.