Fig. 3
From: Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
Regional association plots for DHC in 21 whole genome-sequenced Nellore bulls. a Peak associations were clustered upstream of the ASIP gene. The dashed line that extends upstream of the ASIP gene spans non-coding exons and introns that are not currently annotated in the ARS-UCD1.2 bovine genome assembly (Ensembl release 102). Linkage disequilibrium (LD) levels were calculated against the most significant variant in the region. b Details of the ASIP transcripts that differ in non-coding exons [33,34,35]. Single nucleotide variants (SNV) and small insertion/deletions (INDEL) are displayed as vertical bars, whereas structural variants (SV) are shown as rectangles. The long interspersed nuclear element (LINE) marked as L1-BT (ASIP-SV2) is responsible for a non-coding exon that is recruited by transcripts 2C and 1C2C. The first rectangle in the SV track (ASIP-SV1) is a 1155 bp deletion significantly associated with dark hair in the 21 sequenced animals (\(p\) = 9.12 \(\times\) 10–5)