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J Kaukinen

Publications and source records attributed to J Kaukinen.

5 recordsLinked to original sources
PubMed1994

A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism.

Cattle microsatellite clones (136) were isolated from cosmid (10) and plasmid (126) libraries and sequenced. The dinucleotide repeats were studied in each of these sequences and compared with dinucleotide repeats found in other vertebrate species where information was available. The distribution in cattle was similar to that described for other mammals, such as rat, mouse, pig, or human. A major difference resides in the number of sequences present in the bovine genome, which seemed at best one-third as large as in other species. Oligonucleotide primers (117 pairs) were synthesized, and a PCR product of expected size was obtained for 88 microsatellite sequences (75%). Synteny or chromosome assignment was searched for each locus with PCR amplification on a panel of 36 hamster/bovine somatic cell hybrids. Of our bovine microsatellites, eighty-six could be assigned to synteny groups of chromosomes. In addition, 10 other microsatellites--HEL 5, 6, 9, 11, 12, 13 (Kaukinen and Varvio 1993), HEL 4, 7, 14, 15--as well as the microsatellite found in the kappa-casein gene (Fries et al. 1990) were mapped on the hybrids. Microsatellite polymorphism was checked on at least 30 unrelated animals of different breeds. Almost all the autosomal and X Chr microsatellites displayed polymorphism, with the number of alleles varying between two and 44. We assume that these microsatellites could be very helpful in the construction of a primary public linkage map of the bovine genome, with an aim of finding markers for Economic Trait Loci (ETL) in cattle.

Animals↗
PubMed1993

Bovine microsatellites: racial differences and association with SINE-elements.

Patterns of polymorphism at eight microsatellite loci in three cattle races are described: two large commercial breeds and one endangered landrace. Significant interracial allele frequency differences were found at six loci. The mean heterozygosity was slightly higher in the landrace (H = 0.75) than in the others (H = 0.69). The difference is smaller than that found by DNA-fingerprinting. Intrapopulation distributions of microsatellite allele size (dinucleotide repeat number) were generally bimodal, with certain intermediate repeat types lacking. Sequencing of individual alleles revealed some hidden heterogeneity: an allele defined by PCR-product size actually corresponded to different sequence motifs in different races. Two of the microsatellites occurred as tails of SINE-elements. In contrast to some earlier reports, the position of one of the amplification primers within a high-copy-number SINE-element did not disturb microsatellite amplification; even multiplex PCR was possible.

Alleles↗
PubMed1992

Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR.

During a search of polymorphic microsatellites for bovine genome mapping, we found that microsatellites often occur as tails of artiodactyl C-A retroposon elements. In this element, C (85bp) is a tRNA derivative, while A (117bp) is of unknown origin. The A element also occurs as dimer element with a connecting 27bp linker sequence comprising hexanucleotide CACTTT repeats. In 10 clones (45% of those selected deliberately for dinucleotide repeats), the microsatellite motif is associated with the C-A retroposon. In 50% of 44 database artiodactyl C-A sequences, the element also has a microsatellite tail. The microsatellite is usually a simple (CA)n repeat, but in some cases it is an apparent derivative of the linker sequence CACTTT. All but one of 33 database dimer elements have trinucleotide repeat tails (AGC)n, n = 1-9. Microsatellites, retroposons, and their truncated versions (C and/or A) often occur as clusters. We derived the consensus sequence (202bp) of the C-A element, and designed four primers for inter-SINE amplification with the aim of finding SINEmorph polymorphisms. The method is potentially powerful for rapidly producing polymorphic markers for artiodactyl genome mapping.

Animals↗