Efficient mapping of plant height quantitative trait loci in a sorghum association population with introgressed dwarfing genes

Abstract

Of the four major dwarfing genes described in sorghum, only Dw3 has been cloned. We used association mapping to characterize the phenotypic effects of the dw3 mutation and to fine map a second, epistatic dwarfing QTL on sorghum chromosome 9 (Sb-HT9.1). Our panel of 378 sorghum inbreds includes 230 sorghum conversion (SC) lines, which are exotic lines that have been introgressed with dwarfing quantitative trait loci (QTL) from a common parent. The causal mutation in dw3 associates with reduced lower internode length and an elongation of the apex, consistent with its role as an auxin efflux carrier. Lines carrying the dw3 mutation display high haplotype homozygosity over several megabases in the Dw3 region, but most markers linked to Dw3 do not associate significantly with plant height due to allele sharing between Dw3 and dw3 individuals. Using markers with a high mutation rate and the dw3 mutation as an interaction term, significant trait associations were detected across a 7-Mb region around Sb-HT9.1, largely due to higher detection power in the SC lines. Conversely, the likely QTL interval for Sb-HT9.1 was reduced to approximately 100 kb, demonstrating that the unique structure of this association panel provides both power and resolution for a genomewide scan.

Figure 1.—

Height component phenotypes and their associations with the Dw3 locus. A typical dw3 plant is portrayed at left and a typical Dw3 plant at right. dw3 plants carry a tandem duplication of 882 bp in the fifth exon. The three height components that make up total plant height are shown at left. Apical internodes are longer and basal internodes are shorter in a dw3 background. Rachis length and branch length were also measured, but did not associate with Dw3.

Figure 2.—

Trait associations and patterns of linkage disequilibrium in the Dw3 region. Eight markers in the Dw3 region were tested, including three within the Dw3 locus. (A) Comparison of trait associations and extended haplotype homozygosity (EHH), which provides a means of comparing LD decay between groups carrying different core haplotypes. In this case, the core haplotype is defined as the presence/absence of the tandem duplication in exon 5, which is the causal mutation. (B) Comparison of r² and D′ decay as a result of recombination and shared ancestry for markers linked to the dw3 mutation. The recombinant fraction is defined as the proportion of lines carrying the causal mutation that do not carry the BTx406 allele at the marker being tested. The shared ancestral fraction is defined as the proportion of lines not carrying the causal mutation that do carry the BTx406 allele at the marker being tested. D′ is affected only by recombination, whereas r² is affected by both recombination and shared ancestry.

Figure 3.—

Association mapping of Sb-HT9.1. Thirteen dinucleotide repeat SSRs over 7 Mb on sorghum chromosome 9 were genotyped and are indicated with thick black lines along the x-axis. (Top) Association results are shown: markers were tested first using the basic Q + K model (Yu et al. 2006), then with dw3 added as a covariate, and finally with an interaction term between dw3 and Sb-HT9.1. The nominal significance threshold of P = 0.001 is shown as a dashed horizontal line. (Bottom) The number of alleles (shaded boxes) and the frequency of the converted allele (solid line) for each marker are shown. Markers that show evidence of conversion in IS3620C are marked with an asterisk above the solid line: this information was used to select markers to span the QTL. Results shown are for the preflag leaf-height trait; results for total plant height are very similar but slightly less significant.

Figure 4.—

Linkage disequilibrium and trait associations for the Sb-HT9.1 QTL region in the sorghum converted (SC) lines (n = 230) vs. the rest of the panel (n = 148). The panels at left show trait associations: axes are the same as in Figure 3. Only the terms from the Dw3 interaction model are shown. The shaded area in each panel indicates the region of contiguous significant P-values around the putative Sb-HT9.1 QTL: this region extends 2.75 Mb in the converted lines vs. only 220 kb in the rest of the panel. The LD plots at right show both r² (top right) and D′ (bottom left) between the dw3 duplication and the 13 Sb-HT9.1 markers.