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

Abstract

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.

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

“…The PIC value is commonly used in genetics as a measure of polymorphism for a marker locus used in linkage analysis (Matin et al 2012). Table 3 showed that PIC values varied greatly for all the SSR loci tested with an average of 0.61 indicating that the primers could develop high polymorphism which is useful for assessing genetic variation of genotypes studied in this research (Vaiman et al 1994). The PIC values revealed are comparable to those reported for faba bean cultivars in other countries such as Korea.…”

Fine Mapping and Physical Characterization of Two Linked Quantitative Trait Loci Affecting Milk Fat Yield in Dairy Cattle on BTA26

“…Microsatellite sequence isolation from these 39 bovine BAC clones was performed according to standard procedures (Vaiman et al 1994). The protocol was slightly improved to increase the yield.…”

Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis

“…The structure of the loci are shown in Supplementary Figure S2. They were typed using 20-30 ng of DNA in PCR protocols on an MJ Research PTC 200 Peltier Thermal Cycler (MJ Research Inc., MA, USA) with a hot lid: INRA124 (Vaiman et al, 1994), INRA126 (Vaiman et al, 1994), INRA189 (Kappes et al, 1997) and BM861 (Bishop et al, 1994) were according to Edwards et al (2000), and BYM-1 (Matthews and Reed, 1991) according to Ward et al (2001). The size characterization of PCR products was carried out on a Pharmacia ALF-express Automated Sequencer for loci INRA124, INRA126, INRA189 and BM861, and on an Amersham MegaBACE 500 DNA Sequencer for locus BYM-1.…”