The single strand conformational analysis of cattle and human single nucleotide polymorphisms may be biased towards specific sequence motifs that minimize local secondary structure of single strand DNA.

Single strand conformational polymorphisms (SSCP) resulting from point mutations were found to be associated preferentially with two DNA sequence motifs. These motifs are (1) three or more of the same base but in which the polymorphism is not due to length variation and (2) a region of polypurine or polypyrimidine bases. These motifs were identified after SSCP alleles from cattle were sequenced. The sequence difference and flanking sequence for each single nucleotide polymorphism are shown. The motifs were also found in SSCP from humans chosen at random from the literature, in which the alleles had been sequenced. There is a low level of complementarity of adjacent bases in these motifs and they should represent regions of low secondary structure in the single stranded DNA. Regions of high secondary structure, such as palindromes, were found in the same sample to have allelic variation that was not detected by SSC analysis. These results give a rule of thumb for selecting the particular part of a DNA fragment to be selected for testing for polymorphisms, but this rule clashes with rules used to design primers to amplify sequences using the PCR, namely, minimise hydrogen bonding within and between primers and reduce self-complementarity.

Differences between the radiation hybrid and genetic linkage maps of bovine chromosome 5 resolved with a quasi-phylogenetic method of analysis.

Two major differences were detected in gene order between the radiation hybrid map and the genetic linkage map of bovine Chromosome (Chr) 5, and these were resolved by analyzing the raw radiation hybrid data by a quasi-phylogenetic method. Seventeen loci were typed on the new cattle whole genome radiation hybrid panel. Most of these loci are framework loci and include AGLA293, BM315, BM6026, BP1, BZRP, CD9, CSSM22, CSSM34, CYP2D@, ETH2, ETH10, ETH152, IGF1, LALBA, SLC2A3, SYT1, and TPI1. BP1 was found to be closer to the centromere than either BM6026 or SYT1 with two standard computer software packages for analyzing radiation hybrid panel data. This is inconsistent with any of the genetic linkage maps as well as their consensus. CYP2D@ was placed between ETH2 and BZRP, and this is also inconsistent with the genetic linkage maps, since CYP2D@ should be the most telomeric of the loci tested in this study. Resolution was reached by analyzing the raw radiation hybrid data for clones that bind some but not all of the loci, and the binding pattern was more consistent with the linkage maps and less consistent with the software-generated radiation hybrid map. The comparative mapping data confirm the relative inversion of gene order of SYT1 compared with humans and mice. A non-polymorphic fragment for CD9 indicates the conservation of gene order for three loci located on human Chr 12p. The genes of bovine Chr 5 conserved on human Chr 12p are located separately from the genes conserved on human Chr 12q. It is recommended that the raw data for radiation hybrid maps be made publicly available so that conflicts in gene order can be evaluated explicity.

Report of the first workshop on the genetic map of bovine chromosome 1.

A report of the first workshop on the genetic map of bovine chromosome 1 (BTA1) is presented. Five laboratories contributed 31,962 informative meioses from 70 loci. Thirty-two loci which had been typed by at least two laboratories were used to construct a framework genetic map with a likelihood ratio support of at least 1000:1 for locus order. The resulting sex-averaged framework map contained 26 loci and spanned 163.6 CM. The lengths of the female and male maps were 159.5 CM and 165.3 CM, respectively, and there was evidence for an expansion in the telomeric one-third of the male map. Of the four cases where order for closely linked loci differed among the maps produced for each of the contributing laboratories, a consensus order was obtained for three in the framework map. The average genetic distance between framework loci on the sex-averaged map was 6.3 CM.

A medium-density genetic linkage map of the bovine genome.

A cattle genetic linkage map was constructed which covers more than 95 percent of the bovine genome at medium density. Seven hundred and forty six DNA polymorphisms were genotyped in cattle families which comprise 347 individuals in full sibling pedigrees. Seven hundred and three of the loci are linked to at least one other locus. All linkage groups are assigned to chromosomes, and all are orientated with regards to the centromere. There is little overall difference in the lengths of the bull and cow linkage maps although there are individual differences between maps of chromosomes. One hundred and sixty polymorphisms are in or near genes, and the resultant genome-wide comparative analyses indicate that while there is greater conservation of synteny between cattle and humans compared with mice, the conservation of gene order between cattle and humans is much less than would be expected from the conservation of synteny. This map provides a basis for high-resolution mapping of the bovine genome with physical resources such as Yeast and Bacterial Artificial Chromosomes as well as providing the underpinning for the interpolation of information from the Human Genome Project.

Report of the first workshop on the genetic map of bovine chromosome 23.

A report of the first workshop on the genetic map of bovine chromosome 23 (BTA23) is given. Five laboratories contributed data from 29 loci, including a total 11586 informative genotypes. The combined pedigrees represented 1930 potentially informative meioses. Eighteen of the 29 loci were common to two or more data sets and were used to construct a framework linkage map of BTA23. Twelve of the 18 could be ordered on the linkage map with a likelihood ratio of greater than 1000:1. Thus, a low resolution consensus map was constructed with a high level of support for order. The sex-averaged, female and male maps span 54.5, 52.7 and 55.8 cM, respectively. Sex-specific differences in recombination frequency were identified for eight pairs of framework loci. Average genetic distance between framework loci on the sex-averaged map is 5.0 cM.

A genetic linkage map of the bovine genome.

A cattle genetic linkage map was constructed which marks about 90% of the expected length of the cattle genome. Over 200 DNA polymorphisms were genotyped in cattle families which comprise 295 individuals in full sibling pedigrees. One hundred and seventy-one loci were found linked to one other locus. Twenty nine of the 30 chromosome pairs are represented by at least one of the 36 linkage groups. Less than a 50 cM difference was found in the male and female genetic maps. The conserved loci on this map show as many differences in gene order compared to humans as is found between humans and mice. The conservation is consistent with the patterns of karyotypic evolution found in the rodents, primates and artiodactyls. This map will be important for localizing quantitative trait loci and provides a basis for further mapping.

A genetic map of index DNA loci on bovine chromosome 21.

Genetic maps of highly polymorphic index DNA loci exist essentially only in humans and some experimental organisms. Here we report the first genetic map of highly polymorphic index DNA loci in livestock for bovine chromosome 21. This map consists of six loci with an average heterozygosity of 82%, each with a minimum of five alleles, spaced at an average genetic distance of 9.7 cM, and covers most of the expected length of the acrocentric bovine chromosome 21. The order of markers along the chromosome is cen-ETH 131-UWCA 4-TGLA 337-TGLA 122-CSSM 18-GMBT 16-tel. There is heterogeneity among the recombination fractions between the sexes.

A genetic map of DNA loci on bovine chromosome 1.

We constructed a genetic map of most of the length of bovine chromosome 1 using the CSIRO and the Texas A&M University cattle reference families. Twelve loci are in a single linkage group, 9 of which are highly polymorphic loci. Four loci are of known biochemical function, alpha-1 crystallin (CRYA1), gamma-s crystallin (CRYG8), superoxide dismutase 1 (SOD1), and uridine monophosphate synthase (UMPS), and these have also been previously mapped in humans. The loci CRYA 1, CSRD 1613, GMBT 7, RM 95, SOD1, and UMPS had been previously assigned to bovine syntenic group U10, while CSRD 1613 and UMPS had also been assigned to chromosome 1 by in situ hybridization. All of the loci show statistically significant linkage to at least one other locus. The conserved loci indicate that there have been major rearrangements during the evolution of bovine chromosome 1 compared to other mammalian chromosomes. The estimate of the total length of the linkage group is 168 cM, which accords well with the predicted length based on chiasmata frequencies for the bovine genome and the relative size of chromosome 1 in the bovine genome.

Linkage relations between A2M, HOX3, INT1, KRAS2, and PAH on bovine chromosome 5.

There is a high level of conservation between human chromosomes and bovine syntenic groups. One such comparison is between human chromosome 12 and bovine chromosome 5, where at least 16 loci have been shown to be conserved in an homologous segment. However, the degree of conservation of order of the loci on bovine chromosome 5 is unknown, and in general the conservation of order in comparisons between humans and cattle can only be speculated. We have estimated the recombination fractions between five of the loci that were previously published as mapping to bovine chromosome 5 by a combination of in situ hybridization and analysis of bovine-rodent somatic cell hybrid lines to determine whether order has been conserved in the homologous segment of bovine chromosome 5 and human chromosome 12. Recombination fractions were estimated in reference pedigrees of cattle. The loci were A2M, GSNL, HOX3, INT1, KRAS2, and PAH. Restriction fragment length polymorphisms for all loci were defined by screening a panel of eight restriction endonucleases. The linkage between loci was estimated using the lod score method, and all possible pairwise comparisons were made. A preliminary map was created by joining together loci that showed the smallest recombination fractions and the largest lod scores. A multipoint analysis was performed to estimate support for the most likely order. This order shows the relative inversion of some of the loci. Moreover, the distance spanned in cattle is less than a quarter the distance spanned in humans. Together, these data indicate that several chromosomal evolutionary events have occurred in the homologous segment shared by humans and cattle.

Bovine and ovine DNA microsatellites from the EMBL and GENBANK databases.

Bovine and ovine microsatellite sequences were extracted from the EMBL and GENBANK databases. When analysed for number of alleles and degree of heterozygosity in the CSIRO cattle reference families, allele numbers range from 1 to 14 with heterozygosities, in the polymorphic systems ranging from 15.8% to 100%. Six (46%) of the 13 bovine systems tested gave specific and polymorphic products in sheep. Similarly 2 of the 4 ovine systems gave specific and polymorphic products in cattle. These data define 11 bovine and 8 ovine microsatellite systems which are associated with known genes and are thus useful for comparative mapping studies.