Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs.

Abstract

A population of Arabidopsis thaliana recombinant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random amplified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in coglunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed.The crucifer Arabidopsis thaliana is a useful system for basic studies in plant molecular genetics due to its relatively small genome size, small amounts of dispersed repetitive DNA, and rapid generation time (1). These attributes have made Arabidopsis an attractive model system for the analysis of genome organization and the development and use of technology to clone genes known only through their genetic map position.High-density genetic maps based upon DNA markers can provide starting points for chromosome walking experiments. Markers closely linked to a mutation of interest can reduce the amounts of DNA to be cloned and help establish the direction of the chromosome walk. Restriction fragment length polymorphisms (RFLPs) have been used as markers to construct genetic maps (2) and as starting points for chromosome walking (3). To date, two different RFLP maps have been reported in Arabidopsis (4, 5).Recently another class of genetic markers [random amplified polymorphic DNAs (RAPDs)] has been described (6, 7), which relies on the observation that a single oligonucleotide primer, of arbitrary nucleotide sequence, will direct the amplification of discrete loci (for a more detailed description of this method, see ref. 8). We report here the use of RAPD markers to construct a genetic map of A. thaliana. This map has been constructed with unprecedented speed by using RAPD markers and a recombinant inbred (RI) population. For many mapping purposes RI populations are superior to F2 or backcross populations because they constitute a permanent population in which segregation is fixed (9). Additional markers scored on the same RI population are automatically integrated with the existing map, making map information cumulative (9).Near-isogenic lines have been used to target RFLP (10) or RAPD (11) markers to specific segments of a genome. However, construction of near-isogenic lines is time consuming, and unlinked portions of the donor genome remain even after several crosses to the recurrent parent (12). Pooling DNA based on phenotype has been used as a means of either identifying additional RFLP loci (13) or mapping existing RFLP loci (14) ...

Uso de marcadores moleculares na análise da variabilidade genética em acerola (Malpighia emarginata D.C.)

“…Wesh e McClelland (1990) e Williams et al (1990) introduziram uma técnica que se baseia na detecção de polimorfismo de DNA amplificado ao acaso (RAPD), usando oligonucleotídios de dez bases. Esta técnica tem se mostrado eficiente na identificação da variabilidade genética em diversos grupos de plantas e pode ser usada como uma ferramenta auxiliar em programas de melhoramento, encontrando também aplicação na obtenção de mapas genéticos (Williams et al, 1990;Reiter et al, 1992;Philipp et al, 1994;Paillard et al, 1996) e identificação de marcadores moleculares úteis na seleção assistida (Michelmore et al, 1991;Ohmore et al, 1995;Tartarini, 1996) entre outras. Marcadores RAPD foram usados para acessar a variabilidade genética contida em coleções de milho (Welsh et al, 1991), rosa (Gallego & Martinez, 1996), centeio (Huff, 1997), sorgo (Menkir et al, 1997) e arroz (Fuentes et al, 1999).…”

Detection of genomic regions differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and Quercus robur L.

“…The low copy number of informative SCAR fragments that we obtained appears therefore to be an exception, when compared to other results obtained with RAPD fragments. Except for Arabidopsis, where low copy numbers were found for RAPD fragments (Reiter et a!., 1992), in all other cases RAPD fragments appear to be highly repeated in the genome: for example, 89 per cent of RAPD probes from Pinus pinaster (Plomion et a!., 1995) hybridized with highly repeated sequences whereas 50 per cent or less of RAPD probes from Eucalyptus (Grattapaglia & Sederoff, 1994), cocoa (N'Goran et a!., 1994), lettuce (Paran & Michelmore, 1993) and Petunia (Peltier et al, 1994) corresponded to low copy number sequences.…”

Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

“…Few additional mapped markers would be needed to fill the gap between these two groups. Local mapping based techniques (Reiter et al, 1992) should facilitate this objective. The number of major groups corresponded to the 12 expected based on the known karyotype of maritime pine (Saylor, 1964).…”