Deleterious mutations predicted in the sorghum (sorghum bicolor) maturity (Ma) and dwarf (Dw) genes from whole genome resequencing

Authors: Grant, Nathan; Toy, John; Funnell-Harris, Deanna; Sattler, Scott

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/7/2023
Publication Date: 10/3/2023
Citation: Grant, N.P., Toy, J.J., Funnell-Harris, D.L., Sattler, S.E. 2023. Deleterious mutations predicted in the sorghum (sorghum bicolor) maturity (Ma) and dwarf (Dw) genes from whole genome resequencing. Scientific Reports. 13. Article 16638. https://doi.org/10.1038/s41598-023-42306-8.
DOI: https://doi.org/10.1038/s41598-023-42306-8

Interpretive Summary: Sorghum is a climate resilient crop grown across the U.S. for several uses based on its three main types: grain, sweet and forage/bioenergy. Mutations in six Maturity genes allow sorghum to flower under long summer days found in U.S. from its African origins where it only flowers during the short days of winter. These genes encode components that sense the day length and repress the signal to flower under long days. Flowering time is critical to crop development, so early flowering sorghum may avoid the extreme heat of summer or mature before a killing frost in the fall. Likewise, mutations in four Dwarf genes were used to convert sorghum from its natural state 7-10 feet tall to shorter plants 3-4 feet tall that can be mechanically harvested. Different combinations of these mutations have been used to control timing of flowering and plant height in sorghum. Next-generation DNA sequencing has become an essential tool for obtaining large amounts of information about every gene. In this study, DNA sequences of these 10 important genes were examine from 860 different sorghum lines to find new mutations and confirm previously characterized ones. These new mutations are valuable tools for manipulating flowering time and plant height in sorghum. Combining different mutations should improve hybrid performance across all the sorghum types and lead to increased productivity.

Technical Abstract: In sorghum [Sorghum bicolor (L.) Moench] the Maturity (Ma1, Ma2, Ma3, Ma4, Ma5, Ma6) and Dwarf (Dw1, Dw2, Dw3, Dw4) loci, encode genes controlling flowering time and plant height, respectively, which are critical for designing sorghum ideotypes for a maturity timeframe and a harvest method. Publicly available whole-genome resequencing data from 860 sorghum accessions was analyzed in silico to identify genomic variants at 8 of these loci (Ma1, Ma2, Ma3, Ma5, Ma6, Dw1, Dw2, Dw3) to identify novel loss of function alleles and previously characterized ones in sorghum germplasm. From ~ 33 million SNPs and ~ 4.4 million InDels, 1445 gene variants were identified within these 8 genes then evaluated for predicted effect on the corresponding encoded proteins, which included newly identified mutations (4 nonsense, 15 frameshift, 28 missense). Likewise, most accessions analyzed contained predicted loss of function alleles (425 ma1, 22 ma2, 40 ma3, 74 ma5, 414 ma6, 289 dw1, 268 dw2 and 45 dw3) at multiple loci, but 146 and 463 accessions had no predicted ma or dw mutant alleles, respectively. The ma and dw alleles within these sorghum accessions represent a valuable source for manipulating flowering time and plant height to develop the full range of sorghum types: grain, sweet and forage/biomass.