The physical and genomic organization of microsatellites in sugar beet.

Abstract

Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites ofmicrosatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis.Runs of repetitions of short sequence motifs 2-5 bp long, described as microsatellites or simple sequence repeats, are probably ubiquitous elements of eukaryotic genomes (1-3). They provide highly informative and polymorphic markers for genetics (4-6) or plant, fungal, and animal fingerprinting (7,8). Genetic mapping using microsatellites as markers involves amplification of repeat arrays using PCR with primers flanking the arrays. Primers are often chosen based on database searches or sequence data from cloned arrays (9-12), whichgive selective data about genomic distribution. However, little is known about the real chromosomal organization and physical localization of microsatellite motifs within plant genomes. The only microsatellite repeat mapped physically in plants, the polypurine motif (GAA)7, has been correlated with the positions of C-bands in barley (13). Some physical mapping in fish and primates (8, 14) using in situ hybridization shows clustering of microsatellites on some chromosomes. Recent data in mouse show that mapped microsatellites, mostly (CA)n repeats mapped by PCR polymorphisms, are distributed among autosomes in proportion to chromosome length, while the X chromosome shows a clear deficit of the microsatellites (15). Within chromosomes, the frequency of both large and small clusters with respect to meiotic crossovers slightly exceeded expectation.Sugar beet (Beta vulgaris L.; 2n = 2x = 18) is a valuable model species for investigating the large scale organization of the nuclear genome because (i) the genome is relatively small with 758 Mbp (16), (ii) fluorescent in situ hybridization can accurately locate sequences along the metaphase chromosomes and within interphase nuclei (17), (iii) major classes of the repetitive DNA have been characterized including both satellite and retrotransposon sequences (18)(19)(20)(21)(22), and (iv) microsatellites are known to be highly abundant (23).Here, we aimed to characterize the genomic distribution of microsatellite sequences in sugar beet. We used seven simple sequences representing a range of nucleotide motifs, many used for g...

Isolation and chromosomal localization of new MITE-like sequences from Secale

“…Based on SSR analysis, the genetic polymorphism among species has been extensively investigated, and the cytological markers, including the chromosome-, genomic-or species specific markers, were also effectively developed in plants (Cuadrado & Schwarzacher 1998;Fuchs et al 1998;Schmidt & Heslop-Harrison, 1996), while chromosome identification and genome organization are also observed by SSR analysis such as Aegilops tauschii (Pestsova 2000), Lophopyrum elongatum (Mullan et al 2005) and Dasypyrum ). In our previous study, 102 SSR primer pairs distributing in all chromosomes of T. aestivum, were investigated on Secale, wheat -Secale amphiploid and its derivatives using Chinese Spring wheat as control.…”

Identification of microsatellite loci according to BAC sequencing data and their physical mapping to the bread wheat 5B chromosome

“…Первые оценки распределения по хромосомам микросателлитных локусов были сделаны по результатам картирования генома растений и на основании прямой in situ гибридизации. При изучении распределения мик-росателлитов для ряда объектов, например, у сахарной свеклы, методом in situ гибридизации было показано, что они группируются в определенных районах хромо-сом (Schmidt, Heslop-Harrison, 1996). При картировании микросателлитов томатов показано, что они локализуются в прицентромерной области хромосом (Areshchenkova, Ganal, 1999).…”

Cassava Genetic Improvement

“…This type of polymorphism is highly reproducible. These primers are very useful for rapid and accurate detection of polymorphic loci and the information could be used for developing a high-density genetic map based on these sequence tags (Schmidt and Heslop-Harrison, 1996;Roder et al, 1998). For most plant and animal species where no sequence data are available, a large effort using hybridization and sequencing is needed to identify microsatellites suitable for use as genetic markers (Liu, 1998).…”