Compositdb: Databases

The databases above currently use AceDB, and the AceBrowser interface. Support for the older WebAce display has been discontinued as it is incompatible with newer versions of the AceDB software.

We plan to migrate these databases away from AceDB at some point in the near future.

A Brief Overview of Genetic Mapping in Lettuce

Over the past two decades several research groups have collaborated to develop a detailed genetic map of lettuce using a wide variety of molecular and phenotypic markers. These efforts built on earlier studies with limited numbers of morphological markers (reviewed in Robinson et al., 1983; Michelmore et al., 1994).

The first cross to be analyzed using molecular markers was an intraspecific cross between L. sativa cv. Calmar (crisphead) x cv. Kordaat (butterhead) (Landry et al., 1987 a & b; Kesseli et al., 1994; unpublished data). This map now comprises over 800 markers, including RFLP, RAPD, AFLP, and SSR loci as well as isozyme, disease resistance and morphological markers. RFLP, RAPD and AFLP markers have similar distributions through the genome and identified similar levels of polymorphism (Hill et al., 1995). Despite this large number of markers, the map did not coalesce into the nine chromosomal linkage groups.

Therefore a population from a wide inter-specific cross, L. saligna UC82US1 x L. sativa cv. Vanguard 75 was analyzed (R. Kesseli et al., unpublished). This cross now has over 750 RFLP, RAPD and AFLP markers. The majority of markers fall into 10 linkage groups. However, there was extreme segregation distortion, cytological differences between the parents, and varying levels of sterility in the progeny. Therefore, although this population was useful in coalescing some linkage groups, it was not useful as a permanent core mapping population.

Another inter-specific population, L. serriola 92G489 x L. sativa cv. Salinas has now been established as the core mapping population. L. serriola is probably the progenitor of L. sativa and there are no obvious cytological differences and fertility in the progeny is high. In collaboration with Keygene and CPRO, Wageningen, NL, as well as Seminis Seeds, Woodland, CA, this population has so far been analyzed for 750 AFLP markers (mostly scored co-dominantly) and 80 SSR loci as well as markers for the disease resistance clusters. These fall into 10 linkage groups. 128 recombinant inbred lines (RILs) have been developed from this population; this is being expanded to 300 RILs.

Analysis of an experimental intraspecific population ("the Ryder cross") using predominantly RAPD markers allowed the mapping of over 10 morphological markers (Waycott et al., 1999). SSR markers have recently been added to align this map with the others.

Integration of the four maps has resulted in a consensus map of over 1400 markers and 9 linkage groups (R. van Wijk, et al., unpublished).

Several horticultural and morphological traits have been mapped. We have conducted a quantitative trait locus (QTL) analysis of several traits including bolting, root architecture and the ability to extract water from different levels of the soil profile using the L. serriola x Salinas reference mapping population (Johnson et al., 2000). Many genes for resistance to several diseases have been mapped. The majority but not all of these resistance genes have mapped to three major clusters (Kesseli et al., 1993, 1994; Bonnier et al., 1994; Maisonneuve et al., 1994; Robbins et al., 1994; Witsenboer et al., 1995; Irwin et al., 2000).

PCR with degenerate oligonucleotide primers designed from resistance genes cloned from other species is being used to identify resistance gene candidates (RGCs) from lettuce (Shen et al., 1998 & unpublished). Seven families of sequences have so far been identified. Genetic analysis demonstrated that five of the six RGCs were present as clustered multigene families. Two of the six families mapped to known clusters of resistance genes; RGC1 cosegregated with Dm13 and RGC2 cosegregated with Dm3 in the major cluster.

The majority of the lettuce RFLP probes have been sequenced. Most of the 158 RFLP probes were derived from random cDNA clones made from leaf mRNA (Landry et al., 1987a; Kesseli et al., 1994). Of these, 77% had significant sequence similarity to genes from other higher plants (D. Lavelle et al., unpublished) and 47% could be placed on either orthologous or paralogous positions on the portion of the Arabidopsis genome so far sequenced and annotated (92% complete, ~60% fully annotated; May 2000, TAIR). Many of the clones that did not have significant sequence similarity were short and contained mostly 3'UTR sequence reflecting the manner in which the cDNA clones were originally generated (Landry et al., 1987a). The majority of the cDNAs that had open reading frames produced significant similarities to other plant species and to Arabidopsis.

A comparative genomics project involving lettuce, sunflower and Arabidopsis is being initiated (subject to funding not being cancelled). This will involve sequencing of over 40,000 cDNA clones from both lettuce and sunflower, identification of single nucleotide polymorphisms, and mapping of up to 1,000 new sequences as well as QTL analyses of horticultural traits. Results will be made available through Compositdb.

Bonnier, F.J.M., Reinink, K., Groenwald, R. (1994).
Genetic analysis of Lactuca accessions with new major gene resistance to lettuce downy mildew. Phytopathology 84:462-468.

Hill, M., Witsenboer, H., Zabeau, M., Vos, P., Kesseli, R., Michelmore, R.W. (1996).
AFLP fingerprinting as a tool for studying genetic relationships in Lactuca spp. Theor. Appl. Genet. 93:1202-1210.

Irwin, S.V., Kesseli, R.V., Waycott, W., Ryder, E.J., Cho, J.J., Michelmore, R.W. (1999).
Identification of PCR-based markers flanking the recessive LMV resistance gene mo1 in an intraspecific cross of lettuce. Genome 42: 982-986.

Johnson, W.C., Jackson, L.E., Ochoa, O., van Wijk, R., Peleman, J., St Clair, D.A., Michelmore, R.W. (2000).
A shallow-rooted crop and its wild progenitor differ at loci determining root architecture and deep soil water extraction. Theor. Appl. Genet. in press.

Kesseli, R.V., Paran, I., Michelmore, R.W. (1994).
Analysis of a detailed genetic linkage map of Lactuca sativa (lettuce) constructed from RFLP and RAPD markers. Genetics 136:1435-1446.

Kesseli, R.V., Witsenboer, H., Vandemark, G.J., Stangellini, M.E., Michelmore, R.W. (1993).
Recessive resistance to Plasmopara lactucae-radicis maps by bulked segregant analysis to a cluster of dominant resistance genes in lettuce. Mol. Pl. Microbe Interact. 6:722-728.

Landry, B.S., Kesseli, R.V. Leung, H. and Michelmore, R.W. (1987a).
Comparison of restriction endonucleases and sources of probes for their efficiency in detecting restriction fragment length polymorphisms in lettuce (Lactuca sativa). Theor. Appl. Genet. 74:646-653.

Landry, B.S., Kesseli, R.V., Farrara, B., Michelmore, R.W. (1987b).
A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphism, isozyme, disease resistance, and morphological markers. Genetics 116:331-337.

Maisoneuve, B., Anderson, P., Michelmore, R.W. (1994).
Rapid mapping of two genes for resistance to downy mildew derived from Lactuca serriola to existing clusters of resistance genes. Theor. Appl. Genet. 89:96-104.

Michelmore, R.W., Kesseli, R.V., Ryder, E.J. (1994).
Genetic mapping in lettuce. In: DNA Markers in Plants, eds, R.L. Phillips and I.K. Vasil. Kluwer Acad. Pub. pp 223-239.

Robbins, M.A., Witsenboer, H., Michelmore, R.W. Laliberte, J.-F., Fortin M.G. (1994).
Genetic mapping of turnip mosaic virus resistance in Lactuca sativa. Theor. Appl. Genet. 89:583-589.

Robinson, R.W., McCreight, J.D., Ryder, E.J. (1983).
The genes of lettuce and closely related species. Pl. Breed. Rev. 1:267-294.

Shen, K.A., Meyers, B.C., Islam-Faridi, M.N. Chin, D.B., Stelly, D.M., Michelmore, R.W. (1998).
Resistance gene candidates identified using PCR with degenerate primers map to resistance genes clusters in lettuce. Molecular Plant-Microbe Interac. 11:815-823.

Waycott, W., Fort, S., Ryder, E.J., Michelmore, R.W. (1999).
Mapping of twelve morphological genes relative to molecular markers in lettuce (Lactuca sativa L.). Heredity 82:245-251.

Witsenboer, H., Kesseli, R.V., Fortin, M., Stangellini, M., Michelmore, R.W. (1995).
Sources and genetic structure of a cluster of genes for resistance to three pathogens in lettuce. Theor. Appl. Genet. 91:178-188.