Progressive fine mapping in experimental populations: an improved strategy toward positional cloning

A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions

The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg erecta (Col-0×Ler-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and Ler-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/Ler-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used Arabidopsis accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.

Fine mapping of the epistatic suppressor gene (esp) of a recessive genic male sterility in rapeseed (Brassica napus L.)

9012AB, a recessive genic male sterility (RGMS) line derived from spontaneous mutation in Brassica napus, has been playing an important role in rapeseed hybrid production in China. The male sterility of 9012AB is controlled by two recessive genes (ms3 and ms4) interacting with one recessive epistatic suppressor gene (esp). The objective of this study was to develop PCR-based markers tightly linked to the esp gene and construct a high-resolution map surrounding the esp gene. From the survey of 512 AFLP primer combinations, 3 tightly linked AFLP markers were obtained and successfully converted to codominant or dominant SCAR markers. Furthermore, a codominant SSR marker (Ra2G08) associated with the esp gene was identified through genetic map integration. For fine mapping of the esp gene, these PCR-based markers were analyzed in a large BC1 population of 2545 plants. The esp gene was then genetically restricted to a region of 1.03 cM, 0.35 cM from SSR marker Ra2G08 and 0.68 cM from SCAR marker WSC6. The SCAR marker WSC5 co-segregated with the target gene. These results lay a solid foundation for map-based cloning of esp and will facilitate the selection of RGMS lines and their temporary maintainers.