Ethylene responsive factor (ERF) gene composition (haplotype) at the SUB1 locus of submergence tolerant and intolerant rice. Gene allele forms are indicated with a number following the gene name. Alleles are defined based on the nucleotide sequence encoding the ERF and not flanking or intervening sequences, which have additional polymorphisms (S. Heuer, personal communication). Japonica haplotypes lack SUB1A. Indica haplotypes are variable in allele composition and include accessions with or without a SUB1A gene. The deepwater rice variety Pin Gaew 56 lacks SUB1A and displays a more pronounced increase in accumulation of transcripts encoding SUB1B than SUB1C (Fukao and Bailey-Serres, unpublished). The two alleles of SUB1A have a single amino acid difference and are distinct in the level of transcript induction during submergence. Arrows above genes indicate transcript levels in leaves following submergence. Positions of introns are not shown. Oryza sativa data from Xu et al. (2006). Oryza nivara and Oryza rufipogon data from Fukao et al. (2009).