Variation in a Y-linked single copy gene, AMELY, was shared among modern and lost male Holstein lineages

Authors: YOUSAF, WASIM - Pennsylvania State University; LIU, WANSHENG - Pennsylvania State University; Liu, Ge - George; LEWIN, HARRIS - University Of California, Davis; Blackburn, Harvey; DECHOW, CHAD - Pennsylvania State University

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/10/2024
Publication Date: 6/25/2024
Citation: Yousaf, W., Liu, W., Liu, G., Lewin, H.A., Blackburn, H.D., Dechow, C.D. 2024. Variation in a Y-linked single copy gene, AMELY, was shared among modern and lost male Holstein lineages [abstract]. Journal of Dairy Science. 107(Suppl. 1):406(abstr. 2646).

Interpretive Summary:

Technical Abstract: Modern US Holstein sires trace their Y-chromosome lineage to Round Oak Rag Apple Elevation (Elevation), Pawnee Farm Arlinda Chief (Chief), or Osborndale Ivanhoe (Ivanhoe). Recently, Y lineages lost since 1960 were reconstituted using semen from U-of-Minnesota W Caliban Cuthbert (Cuthbert) and Zimmerman Alstar Pilot (Pilot) which was available through the National Animal Germplasm Program. The Y-chromosome is complex and includes features such as a pseudoautosomal region, a pseudoautosomal boundary (PAB) with a male-specific region that contains repetitive gene families, and X-degenerated (X-D) regions. The objective of this study was to compare Y-chromosome sequence alignment of various Holstein Y-lineages to the ARS-UCD2.0 reference sequence for a single copy gene from the PAB (AMELY; Amelogenin, Y-linked) and a highly conserved single copy gene (SRY; Sex determining region Y) on the distal end of the Y. The reference chrY sequence is a Wagyu bull. Whole genome Illumina pair-ended reads from Elevation and one son, Chief and one son, Ivanhoe, one Cuthbert son, and one Pilot son were aligned to the reference sequence using Bowtie2 (v 2.4.2). Following alignment, we retained SNP with a read depth >=10 and a base call accuracy of >=99.8% (Phred quality score >=27). All bulls shared a G to A substitution at bp 6,936,835 in the AMELY gene; at bp 6,937,734, the initial analysis indicated an A to G substitution for all bulls except Elevation and his son. However, visual inspection of the region revealed that Elevation and son had the same SNP, but the alignments did not meet our depth requirement. No variants were observed for any bull in the SRY gene. The pseudoautosomal region and highly repetitive nature of the Y-chromosome make sequence alignments more difficult than alignment to autosomal sequence. Nevertheless, the analysis identified two potential SNPs in the AMELY gene that appeared to be shared across Holstein Y lineages and indicated that there was no variation of the SRY gene.