The great increase in successful linkage studies in a number of higher eukaryotes during recent years has essentially resulted from major improvements in reference genetic linkage maps, which at present consist of short tandem repeat polymorphisms of simple sequences or microsatellites. We report here the last version of the Genethon human linkage map. This map consists of 5,264 short tandem (AC/TG)n repeat polymorphisms with a mean heterozygosity of 70%. The map spans a sex-averaged genetic distance of 3,699 cM and comprises 2,335 positions, of which 2,032 could be ordered with an odds ratio of at least 1,000:1 against alternative orders. The average interval size is 1.6 cM; 59% of the map is covered by intervals of 2 cM at most and 1% remains in intervals above 10 cM.

A comprehensive genetic map of the human genome based on 5,264 microsatellites

Medical genetics was revolutionized during the 1980s by the application of genetic mapping to locate the genes responsible for simple Mendelian diseases. Most diseases and traits, however, do not follow simple inheritance patterns. Geneticists have thus begun taking up the even greater challenge of the genetic dissection of complex traits. Four major approaches have been developed: linkage analysis, allele-sharing methods, association studies, and polygenic analysis of experimental crosses. This article synthesizes the current state of the genetic dissection of complex traits—describing the methods, limitations, and recent applications to biological problems.

Genetic Dissection of Complex Traits

The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)n blocks was estimated to be 3.6 x 104 and the number of (GT)n blocks to be 2.3 x 104 per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated microsatellites, it was found that wheat microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.

Abundance, variability and chromosomal location of microsatellites in wheat.

We have exploited "progeny testing" to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of > 150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score > or = 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding.

/pdf/mapping-quantitative-trait-loci-controlling-milk-production-4lbsiq1rc0.pdf

Mapping Quantitative Trait Loci Controlling Milk Production in Dairy Cattle by Exploiting Progeny Testing

We report a bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens and serum proteins. The 2990-cM map consists of a sex-specific, X chromosome linkage group and 29 sex-averaged, autosomal linkage groups with an average interval size of 2.5 cM. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. Orientation and chromosomal assignment of all the linkage groups, except BTA20 and BTA22, was provided by 88 markers that were assigned previously to chromosomes. This map provides sufficient marker density for genomic scans of populations segregating quantitative trait loci (QTL) and subsequent implementation of marker-assisted selection (MAS) mating schemes.

/pdf/a-second-generation-linkage-map-of-the-bovine-genome-tjfwrf9bst.pdf

A second-generation 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 linkage map of the bovine genome

Oligonucleotide primers for the polymerase chain reaction (PCR) that enable genus-specific detection of members of the genus Salmonella were developed. The primers amplify a 496-bp genetic sequence of members of the genus Salmonella. Amplification of DNA extracted from all other genera of the family Enterobacteriaceae and various other gram-positive aerobic and anaerobic bacteria yielded negative results. Applications of the PCR using these genus-specific primers are discussed.

https://journals.sagepub.com/doi/pdf/10.1177/104063879300500311

Genus-Specific Detection of Salmonellae using the Polymerase Chain Reaction (PCR)

OBJECTIVE To compare the sensitivity of polymerase chain reaction (PCR) with microbiological culture for detecting salmonellae in equine fecal samples and equine environmental swab specimens. DESIGN Samples and specimens were tested by PCR and microbiological culture. SAMPLE POPULATION A fecal sample from each of 152 horses admitted consecutively to the clinic for evaluation by the outpatient service, 282 fecal samples from 110 hospitalized horses that had been submitted to the clinical microbiology laboratory, and 313 environmental swab specimens were examined. PROCEDURE Each sample and specimen in the study was tested, using PCR and microbiological culture. Results of PCR and culture were compared. RESULTS Significantly (P < 0.001) more fecal samples were positive by PCR than by microbiological culture. 26 of 152 (17.1%) fecal samples collected from horses admitted by the outpatient service were positive by PCR and none was positive by culture. 71 of 110 hospitalized horses were identified as positive by PCR, compared with 11 horses identified as positive by culture. All culture-positive horses were positive by PCR. Of the 11 culture-positive horses, 10 (90.9%) were identified as PCR positive after testing of the first sample submitted, compared with 7 (63.6%) by culture. All PCR-positive horses were detected after a total of 3 samples/horse were submitted, whereas as many as 5 samples/horse was required to identify all culture-positive horses. 8 of 313 environmental specimens were positive by PCR, and none was positive by culture. CONCLUSION The PCR method reported here was more sensitive, more rapid, and required submission of fewer samples or specimens than did microbiological culture for detecting salmonellae.

Comparison of polymerase chain reaction and microbiological culture for detection of salmonellae in equine feces and environmental samples.

The natural resistance-associated macrophage protein gene is associated with Crohn's disease.

Summary

Polymerase chain reaction (PCR) primers designed to amplify the octapeptide repeat region of the bovine prion gene were used to test the association of genotypes with bovine spongiform encephalitis (BSE) in 56 BSE-affected and 177 unaffected animals. Three alleles (A, B, C) were detected as single-strand conformation polymorphisms (SSCPs) and two alleles (1,2 representing six or five copies of the octapeptide repeat respectively) were detected as amplified double-strand fragment length polymorphisms (AMFLPs). Observed genotypes of SSCPs and AMFLPs were analysed by x-square. The SSCP genotypes of nuclear family members of animals with BSE and BSE-affected animals were different (P 0.469). No AMFLP genotypic differences were detected between BSE-affected animals, their relatives, unrelated animals of the same breed or animals of different breeds (P > 0.05). These data suggest that BSE-affected animals and their relatives are more likely to have the AA SSCP genotype than unrelated animals of the same breed or animals of different breeds.

Holly L. Neibergs

Papers

A genetic linkage map of the bovine genome

Genus-Specific Detection of Salmonellae using the Polymerase Chain Reaction (PCR)

Comparison of polymerase chain reaction and microbiological culture for detection of salmonellae in equine feces and environmental samples.

The natural resistance-associated macrophage protein gene is associated with Crohn's disease.

Polymorphism analysis of the prion gene in BSE-affected and unaffected cattle.