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The classical genetic map of  Arabidopsis  includes more than 130 genes with an embryo-defective ( emb ) mutant phenotype. Many of these essential genes remain to be cloned. Hundreds of additional  EMB  genes have been cloned and catalogued ( www.seedgenes.org ) but not mapped. To facilitate  EMB  gene identification and assess the current level of saturation, we updated the classical map, compared the physical and genetic locations of mapped loci, and performed allelism tests between mapped (but not cloned) and cloned (but not mapped)  emb  mutants with similar chromosome locations. Two hundred pairwise combinations of genes located on chromosomes 1 and 5 were tested and more than 1100 total crosses were screened. Sixteen of 51 mapped  emb  mutants examined were found to be disrupted in a known  EMB  gene. Alleles of a wide range of published  EMB  genes ( YDA ,  GLA1, TIL1 ,  AtASP38 ,  AtDEK1, EMB506, DG1, OEP80 ) were discovered. Two EMS mutants isolated 30 years ago, T-DNA mutants with complex insertion sites, and a mutant with an atypical, embryo-specific phenotype were resolved. The frequency of allelism encountered was consistent with past estimates of 500 to 1000  EMB  loci. New  EMB  genes identified among mapped T-DNA insertion mutants included  CHC1 , which is required for chromatin remodeling, and  SHS1/AtBT1 , which encodes a plastidial nucleotide transporter similar to the maize Brittle1 protein required for normal endosperm development. Two classical genetic markers ( PY, ALB1 ) were identified based on similar map locations of known genes required for thiamine ( THIC ) and chlorophyll ( PDE166 ) biosynthesis. The alignment of genetic and physical maps presented here should facilitate the continued analysis of essential genes in  Arabidopsis  and further characterization of a broad spectrum of mutant phenotypes in a model plant.

Integrating the Genetic and Physical Maps of Arabidopsis thaliana: Identification of Mapped Alleles of Cloned Essential (EMB) Genes