An in silico strategy towards the development of legume genome anchor markers using comparative sequence analysis

Abstract

Development of molecular markers and the transfer of marker information from one species to another are limiting steps in the assembly of genetic maps and the use of map information in breeding programs. To identify potential marker sequences more efficiently, we have established procedures combining multi-species EST and genome sequence data for a genome-wide, in silico identification of molecular markers. Taking advantage of information from a few related species, comparative EST sequence analysis identifies evolutionarily conserved sequences (ECSs) that with high probability are conserved in less characterised species in the same family. The chance of observing variation between any two mapping parents is increased by selecting ECS that are interrupted by introns in corresponding genomic regions. Our procedure simultaneously optimizes (1) primer selection for stable performance of PCR across species by choosing ECS as the target sequences for priming, (2) the likelihood of polymorphism discovery by selecting intron-containing ECSs, (3) marker transfer between species, and (4) information content by counting copy numbers of homologous sequences in Arabidopsis. We illustrate our procedure in legumes, where model plant genome and EST sequence data have great potential re influencing crop legume breeding programs.