Revealing Nature’s Edits: Unmasking Deleterious Variants in Maturity and Dwarf Loci for Precision Control of Sorghum Flowering Time and Plant Height

Circadian clock, light quality, phytohormones, developmental stage and temperature each play a role in regulating inflorescence meristem development in sorghum. Different varieties of sorghum have different flowering profiles. For instance, in grain sorghum early flowering (42–90 days after planting) allows for a reduction in the risk of exposure to abiotic stress during the reproductive and maturity phases, while in sweet sorghum later flowering (70–100 days after planting) gives the plant more time for later sugar accumulation. Another significant agronomic trait is plant height; smaller plants have a reduced risk of lodging and can more easily be machine harvested. Three of the four Dwarf loci (Dw1, Dw2, Dw3) have been correlated with short stature and five of the six Maturity loci (Ma1, Ma2, Ma3, Ma5, Ma6) control flowering time in sorghum. Researchers from the University of Nebraska-Lincoln and the USDA-ARS analyzed genomic variation in the Maturity and Dwarf  loci in an effort to identify novel loss of function alleles in the sorghum. Using publicly available genotypes of 860 accessions in the sorghum association mapping population (SAP), the study identified 1445 potentially deleterious variants within the Ma and Dw loci. This study analyzed the loci for insertion, deletion, missense (nonsynonymous variants), nonsense (stop gain), and splice site mutations, all of which can impair the encoded protein’s function. Compared to the other maturity loci, Ma1 had the most deleterious, highly impactful genomic variants. The previously characterized mutant alleles Sbprr37-1, Sbprr37-2, and Sbprr37-3 were predicted most frequently in the accessions analyzed. SbPRR37 is a central component of the flowering regulatory pathway and is influenced by Ma2, and possibly Ma4, downstream of SbPHYB and SbPHYC. Significant altering of this protein would have a great impact on flowering time. On the Dwarf  Dw1 and Dw2 loci only one new deleterious genomic variant was identified; however, known mutations dw1 and dw2, were found in many accessions. The Maturity and Dwarf alleles represent valuable information that can be used to genetically manipulate germplasm to create cultivars with flowering time and height optimized for the desired end use.

The work employs genomic analyses of publicly available re-sequencing data from 860 sorghum accessions to examine the critical loci controlling flowering time and plant height in sorghum. Loss of function mutations at these loci have transformed sorghum into the ideotypes used for grain, forage and sweet sorghums. The identification and characterization of predicted alleles at these loci are paramount to new sorghum improvement strategies. – Grant

SorghumBase examples: 

Figure 1: SorghumBase view of the ma1 locus. Protein alignments in the gene tree show the gene model is truncated in six loci, including BTx623. The BTx623 v5 annotation include a second gene model for the other open reading frame.


Figure 2: Variant image views of BTx623 and Tx2783 ma1 gene models that reveal the stop codon allele which causes the truncated protein in some lines. According to the SAP genotypes called by Lozano et al., 2021 the early stop codon occurs in ~10% of the panel.


Grant NP, Toy JJ, Funnell-Harris DL, Sattler SE. Deleterious mutations predicted in the sorghum (Sorghum bicolor) Maturity (Ma) and Dwarf (Dw) genes from whole-genome resequencing. Sci Rep. 2023 Oct 3;13(1):16638. PMID: 37789045. doi: 10.1038/s41598-023-42306-8. Erratum in: Sci Rep. 2023 Oct 18;13(1):17737. Read more

Related Project Websites:

Scott Sattler’s page at the University of Nebraska-Lincoln: 

Deanna Funnell-Harris ‘s page at the University of Nebraska-Lincoln: 

Image 1: USDA sorghum experimental field(s) in Lincoln, Nebraska. Photo credit Scott Sattler.


Image 2: USDA sorghum experimental field(s) in Lincoln, Nebraska. Photo credit Scott Sattler.