A 4 Mb high resolution BAC contig on bovine chromosome 1q12 and comparative analysis with human chromosome 21q22

Abstract

The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb single contig of 92 BAC clones on BTA 1q12. The contig covers the region between the genes KRTAP8P1 and CLIC6. This genomic segment in cattle is of special interest as it contains the dominant gene responsible for the hornless or polled phenotype in cattle. The construction of the BAC contig was initiated by screening the bovine BAC library with heterologous cDNA probes derived from 12 human genes of the syntenic region on HSA 21q22. Contig building was facilitated by BAC end sequencing and chromosome walking. During the construction of the contig, 165 BAC end sequences and 109 single-copy STS markers were generated. For comparative mapping of 25 HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC end sequence comparisons against the human genome sequence revealed significant matches to HSA 21q22 and allowed the in silico mapping of two new genes in cattle. In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped within the bovine BAC contig, of which 16 genes have been cloned and mapped for the first time in cattle. In contrast to the existing comparative bovine–human RH maps of this region, these results provide a better alignment and reveal a completely conserved gene order in this 4 Mb segment between cattle, human and mouse. The mapping of known polled linked BTA 1q12 microsatellite markers allowed the integration of the physical contig map with existing linkage maps of this region and also determined the exact order of these markers for the first time. Our physical map and transcript map may be useful for positional cloning of the putative polled gene in cattle. The nucleotide sequence data reported in this paper have been submitted to EMBL and have been assigned Accession Numbers AJ698510–AJ698674.

A 2.5‐Mb contig constructed from Angus, Longhorn and horned Hereford DNA spanning the polled interval on bovine chromosome 1

“…(2005a). No rearrangements of genes within this interval were found, which is in agreement with Drögemüller et al. (2005a) but in contrast to earlier results based on RH mapping and early assemblies of the human genome sequence (Rexroad et al.…”

“…Alignment of STSs and BESs to the human genome sequence (Build 36.1) using blastn (Altschul et al. 1990) allowed us to anchor 22 annotated human genes from the corresponding region on HSA21 to our physical map, including seven genes not anchored by Drögemüller et al. (2005a).…”

“…A 4‐Mb contig spanning the polled critical interval (from KRTAP8P1 to CLIC6 ) was previously published based on Holstein BAC clones from the RPCI‐42 library (Drögemüller et al. 2005a).…”

A radiation hybrid map of river buffalo <i>(Bubalus bubalis)</i> chromosome 1 (BBU1)

“…Comparison of SLC25A4 on the cytogenetic map with RH map is not shown as this marker is not localized to a band on 1p. The highlighted interval (4 Mb) of BTA1 map indicates the gene order based on Drögemüller et al (2005) and Wunderlich et al (2006). * : SH2D4A, DEFB1, DLGAP2, CLN8, and POU1F1 are assigned to contigs unplaced on BTA build 3.1.…”

Independent Polled Mutations Leading to Complex Gene Expression Differences in Cattle

“…The polled locus ( P ) has previously been mapped on the proximal end of BTA 1 [8] – [13] corresponding to a region on HSA 21 [14] . The apparent causative mutation for polledness in various beef or dual-purpose cattle breeds with a Celtic origin has been described as a structural sequence variant, a complex insertion-deletion affecting an intergenic region of BTA 1 [15] .…”