A number of molecular genetic maps of the soybean [Glycine max (L.) Merr.] have been developed over the past 10 yr. These maps are primarily based on restriction fragment length polymorphism (RFLP) markers. Parental surveys have shown that most RFLP loci have only two known alleles. However, because the soybean is an ancient polyploid, RFLP probes typically hybridize and map to more than one position in the genome. Thus, the polymorphic potential of an RFLP probe is primarily a function of the frequency of the two alleles at each locus the probe detects. In contrast, simple sequence repeat (SSR) markers are single locus markers with multiple alleles. The polymorphic potential of an SSR marker is dependent on the number of alleles and their frequencies. Single locus markers provide an unambiguous means of defining linkage group homology across mapping populations. The objective of the work reported here was to develop and map a large set of SSR markers. A total of 606 SSR loci were mapped in one or more of three populations: the USDA/Iowa State G. max × G. soja F 2 population, the Univ. of Utah Minsoy × Noir 1 recombinant inbred population, and the Univ. of Nebraska Clark × Harosoy F 2 population. Each SSR mapped to a single locus in the genome, with a map order that was essentially identical in all three populations. Many SSR loci were segregating in two or all three populations. Thus, it was relatively simple to align the 20+ linkage groups derived from each of the three populations into a consensus set of 20 homologous linkage groups presumed to correspond to the 20 pairs of soybean chromosomes. On the basis of in situ segregation or linkage reports in the literature all but one of the classical linkage groups can now be assigned to a corresponding molecular linkage group.

/pdf/an-integrated-genetic-linkage-map-of-the-soybean-genome-9jlaq0vslr.pdf

An Integrated Genetic Linkage Map of the Soybean Genome

Dinucleotide microsatellites have been characterized and used as genetic markers in rice. Screening of a rice genomic library with poly(dG-dA).(dC-dT) and poly(dG-dT).(dC-dA) probes indicated that (GA)n repeats occurred, on average, once every 225 kb and (GT)n repeats once every 480 kb. DNA sequencing of ten randomly selected microsatellites indicated that the numbers of repeats ranged from 12 to 34 and that the patterns of microsatellites in rice were similar to those of humans and other mammals. Primers to these microsatellite loci as well as to four published microsatellite-containing sequences have been designed and degrees of polymorphism has been examined with 20 rice accessions. Multiple alleles, ranging from 5 to 11, have been observed at all the microsatellite loci in 20 rice accessions. Alleles specific to two cultivated subspecies, indica and japonica, were found in some microsatellite loci. Heterozygosity values of all the microsatellite markers were significantly higher than those of RFLP markers, based upon a parallel comparison. Ten microsatellite loci have been genetically mapped to four rice chromosomes. The genomic distribution of microsatellites appears to be random in rice.

Abundance, polymorphism and genetic mapping of microsatellites in rice.

The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at approximately 500,000 years, well before domestication approximately 9,000 years ago. Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major "European" pig breeds. The study is an advance in pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.

https://www.genetics.org/content/genetics/154/4/1785.full.pdf

The origin of the domestic pig: independent domestication and subsequent introgression.

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.

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

/pdf/a-comprehensive-map-of-the-porcine-genome-okb2eg1wfe.pdf

A comprehensive map of the porcine genome.

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (∼16.5 Morgans) than the genetic map of the homogametic sex (female) (∼21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be ∼18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.

The PiGMaP consortium linkage map of the pig (Sus scrofa).

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.

Variation of short tandem repeats within and between species belonging to the Canidae family.

Variable (dG-dT)n.(dC-dA)n sequences in the porcine genome.

Twenty-four PCR primer pairs were designed for the detection of porcine microsatellites. Polymorphism was investigated in 76 unrelated animals from four different breeds: Duroc, Landrace, Hampshire, and Yorkshire. Compared with human microsatellites, a general lower heterozygosity was detected; however, for each microsatellite a significant variation between breeds in number of alleles and heterozygosity was seen. Mean heterozygosity was found to be significantly higher (P<0.01%) in the Yorkshire breed than in the other three breeds. Linkage analyses with the CEPH linkage packet were performed in a backcross family comprising 45 animals, of which 43 had informative meioses. Ten of the microsatellites could be assigned to six different linkage groups, demonstrating that linkage mapping with microsatellites can be carried out with great efficiency in a relatively small number of animals. Four of the linkage groups represent Chromosomes (Chrs) 4, 6, 7, and 8 respectively, while two linkage groups are unassigned.

Characterization of 24 porcine (dA-dC)n-(dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies

1Norwegian Kennel Klub and Department of Morphology, Genetics and Aquatic Biology, Section of Genetics, P.O. Box. 8146 Dep., N-0033 Oslo, Norway ZDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden 3Department of Animal Science and Animal Health, Division of Animal Genetics, The Royal Veterinary and Agricultural University, Btilowsvej, 13, DK-1870, Fredriksberg C, Copenhagen, Denmark ~The Department of Biochemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK 5Centre for Preventive Medicine, Animal Health Trust, PO Box 5, Newmarket, Suffolk CB8 7DW, UK 6Medical Technology and Medicine, Michigan State University, B228 Life Science, East Lansing, Michigan 48824-1317, USA 7Institute of Animal Breeding, University of Berne, Bremgartenstrasse 109 a, 3012 Berne, Switzerland

/pdf/towards-construction-of-a-canine-linkage-map-establishment-3q3gckfo05.pdf

A. K. Winterø

Papers

The PiGMaP consortium linkage map of the pig (Sus scrofa).

Variation of short tandem repeats within and between species belonging to the Canidae family.

Variable (dG-dT)n.(dC-dA)n sequences in the porcine genome.

Characterization of 24 porcine (dA-dC)n-(dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies

Towards construction of a canine linkage map: establishment of 16 linkage groups.