Deleterious mutations predicted in the sorghum (Sorghum bicolor) Maturity (Ma) and Dwarf (Dw) genes from whole-genome resequencing

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.

Unveiling shared genetic regulators for plant architectural and biomass yield traits in sorghum

“…The genetic basis of DOF and plant height in sorghum has been extensively studied, regulated through many maturity genes (Ma1-Ma6) and four dwarfing loci (Dw1-Dw4) (Casto et al, 2019;Grant et al, 2023). Our GWAS analysis identified at least three known regulators (Ma1, Ma2, and Ma6), along with the identification of novel loci (S04_39191115; CRY) that regulate flowering (Sharma et al, 2022).…”

“…To date, four major genes controlling plant height have been described in sorghum (Dw1, Dw2, Dw3, and to a less detailed extent Dw4) across various environments (Quinby and Karper, 1954;Hilley et al, 2017;Chen et al, 2019). Similarly, six Maturity (Ma) loci (Ma1,Ma2,Ma3,Ma4,Ma5,and Ma6) have been shown to control sorghum flowering time (Quinby and Karper, 1945;Murphy et al, 2011;Casto et al, 2019;Grant et al, 2023). The sorghum ortholog of the maize domestication gene tb1, a C2H2 zinc finger protein, and Dormancy Associated Protein 1 (DRM1, a well-known marker of bud dormancy) are known to regulate sorghum tiller number (Kebrom et al, 2006;Govindarajulu et al, 2021).…”