Figure 5.

Pup1 haplotype in diverse rice genotypes. Eighty-one diverse rice varieties and breeding lines were genotyped using the Pup1-specific markers indicated. Based on the Pup1 core marker set (highlighted with dashed lines; see text for details), an UPGMA cluster analysis was conducted using Powermarker version 3.25 (Sokal and Michener, 1958; Liu and Muse, 2005). Three main groups (I, II, III) with different allelic composition at the Pup1 locus were identified. The different allele calls (Kasalath, non-Kasalath, and heterozygous) are color coded as indicated at bottom left. The rice genotypes analyzed are adapted to different rice agroecosystems [upland (UL): aerobic, unfavorable, and drought prone; lowland/irrigated (LL): anaerobic, generally favorable conditions] as shown at right. For details on the genotypes analyzed, see text and Supplemental Table S1.