Genetic and physical map of the SUB1 locus on the long arm of chromosome 9. High-resolution maps represent FR13A derivative IR40931-26, Teqing (indica) and Nipponbare (japonica). The vertical lines indicate markers between maps. (a) The chromosomal segment defined by recombinant mapping as the SUB1 region, and its orientation relative to the centromere is indicated. Amplified fragment length polymorphism markers and their derivatives are prefixed with the letter “A.” Genetic distances between adjacent markers are measured using the number of recombinant plants (one recombinant plant = 0.0012 cM). (b) Physical map spanning the SUB1 locus constructed by establishment and analysis of a BAC contig of six clones, including one from IRBB21 and five from Teqing, both intolerant indica. A contig of binary clones from IR40931-26, a submergence tolerant FR13A derivative, was also assembled across this region. The SUB1 locus was delimited to 42 kb between SSR1A and 14A11-481 and 112 kb between 14A11-f15 and AFLP209rf. Three group VII ERF genes are encoded in this region in IR04931-26 and Teqing, SUB1A, SUB1B, and SUB1C. IR40931-26 has the SUB1A-1 allele and Teqing the SUB1A-2 allele. (c) Physical map of the SUB1 region in the Nipponbare genome. Based on DNA sequence data from GenBank, colinearity with the two physical maps (b, c) holds for most markers, SUB1B and SUB1C. However, there is an inversion and deletion of the region with the landmark marker 101O9L and SUB1A. The sequenced SUB1 region in Nipponbare is 142 kb. Adapted from Supplementary Fig. 1 of Xu et al. (2006). Photo by Pamela Ronald.