Mining sorghum pangenome enabled identification of new dw3 alleles for breeding stable-dwarfing hybrids

Abstract

Allele mining of crop pangenomes can enable the identification of novel variants for trait improvement, increase crop genetic diversity, and purge deleterious mutations around fixed genomic regions. Sorghum, a C4 cereal crop domesticated in the tropics, was selected for reduced plant height and maturity to develop combine-harvestable and photoperiod-insensitive US grain sorghums. To breed semi-dwarf US grain sorghum hybrids, public and private sector programs mostly used the dw3-ref allele, which produces undesirable height revertants (frequency of 0.1-0.3%) due to uneven crossing over at the 882 bp tandem duplication region. Although the dw3-ref allele produces revertants, US sorghum breeding programs continued using this allele in the absence of identified allelic variants that suppress revertants. In this study, we leveraged a sorghum pangenome resource (resequenced sorghum association panel and a global diversity panel of 1,661 lines) to identify 7 loss-of-function variants in the Dw3 gene using the SnpEff variant calling prediction. We validated the Segaolane dw3 loss-of-function variant, resulting from a 137 bp deletion in the third exon, to suppress revertant production. Segaolane nested association mapping family recombinant inbred line (RILs) with the dw3-ref allele produced revertants while no revertants were observed in RILs with the Segaolane dw3 allele. The availability of resequencing data enabled the designing of haplotype-based markers detecting the Segaolane stable dw3 allele for marker-assisted trait introgression into elite sorghum breeding lines. This research mining new stable-dwarfing dw3 alleles demonstrated the application of sorghum pangenome for trait improvement and developing marker-assisted breeding strategies.

Keywords: haplotype-based markers; sorghum NAM; sorghum allele mining; stable height; trait improvement.