Fig 1.
Stem internode length QTL identified in a population from Hegari x 80M.
F2 plants from a cross of Hegari and 80M (n = 218) were grown in the greenhouse and the length of each internode was measured. The average internode length was used to map QTL. (A) The resulting graph shows four QTL, including Dw1 and Dw2. The x-axis is the genetic map and the y-axis is the LOD score. The boxes above each trait identify the Dw loci, if any, the percentage of the variation explained by the QTL, and the location of the peak LOD value. (B) Photograph of Hegari (left) and 80M. (C) Photograph of F5 plants that are Dw1Dw1 (left), Dw1dw1 (center), and dw1dw1 (right) in otherwise uniform genetic backgrounds at the other loci that affect internode length.
Table 1.
QTL for Average Internode Length Identified in the Entire Population of Hegari x 80M F2.
Fig 2.
A schematic of the region of SBI-09 encoding Dw1.
The top bar shows the Dw1 locus delimited by QTL mapping in the F2. The region was refined in the F3 population (n = 75 for each of six families) using the DG markers labeled in the diagram. The numbers below the bar are the number of recombinants (both bars). Note that all members of one of the families (237) had a breakpoint in between Fse5 and the end of the region shown. The lower bar represents the delimited Dw1 locus defined by mapping in the F3 generation with SNP markers labeled. Dark purple shows the location of Dw1 based on fine mapping. SNP markers are named with the last six digits of the gene name of the gene the SNP is in or near. Fse4 is included for perspective though it was not scored in the F4.
Table 2.
Genes in the Delimited Dw1 Locus.
Fig 3.
Gene annotation models of Dw1 (Sobic.009G229800).
(A) Gene model from Sorghum bicolor Genome v2.1 (Phytozome). (B) Gene model based on cDNA sequence analysis. Boxes (blue) represent exons and lines are introns. Regions colored green represent the 5’ UTR and those colored red the 3’ UTR. Exons are numbered within boxes and introns are numbered in black. The asterisk/vertical line marks the location of the Lys199 > stop codon mutation that distinguishes Dw1 from dw1.
Table 3.
Polymorphisms Distinguishing 80M and Hegari in Genes in the Delimited Dw1 Locus.
Table 4.
Sequence Variants in Exons of Sobic.009G229800 in Diverse Sorghum Genotypes.
Table 5.
Distribution of Dw1 Coding Sequence Variants in Sorghum Genotypes.
The polymorphism number corresponds to the number in Table 4.
Fig 4.
Relative expression of Dw1 in stem internodes.
RNA was extracted from a full length internode (Mature), the lower half of an elongating internode, and the upper half of an elongating internode for each parental genotype (n = 3 each). Relative expression was determined by qRT-PCR using the ΔΔCt method with 18S rRNA as the normalizer and the sample from 80M mature tissue as the calibrator.
Fig 5.
Protein alignment of Dw1 and select homologs.
Alignment of Dw1 with the two maize homologs, the two rice homologs, and the Arabidopsis homolog compiled in Jalview using the T-Coffee function (dark blue color indicates higher percent identity). The red rectangle marks the functional polymorphism that distinguishes Hegari (Dw1) and 80M (dw1). The orange rectangle marks a polymorphism present in Rio and Early White Milo not found in the other sequenced lines. The black box is the possible transmembrane domain predicted by PSIPRED-MEMSAT-SVM.