Marla Sandeep R, Olatoye Marcus, Davis Matthew, Otchere Vincent, Sexton-Bowser Sarah, Morris Geoffrey P, Felderhoff Terry
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.
Center for Sorghum Improvement, Kansas State University, Manhattan, KS 66506, USA.
G3 (Bethesda). 2025 May 8;15(5). doi: 10.1093/g3journal/jkaf054.
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.
作物泛基因组的等位基因挖掘能够识别用于性状改良的新变异，增加作物遗传多样性，并清除固定基因组区域周围的有害突变。高粱是一种在热带地区驯化的C4谷类作物，为降低株高和成熟度，培育可联合收获且对光周期不敏感的美国谷物高粱。为培育半矮秆美国谷物高粱杂交种，公共和私营部门项目大多使用dw3-ref等位基因，由于在882 bp串联重复区域交叉不均匀，该等位基因会产生不良的高度回复株（频率为0.1 - 0.3%）。尽管dw3-ref等位基因会产生回复株，但在美国高粱育种项目中，由于未发现抑制回复株的等位基因变体，仍继续使用该等位基因。在本研究中，我们利用高粱泛基因组资源（重测序的高粱关联群体和由1661个品系组成的全球多样性群体），通过SnpEff变异位点预测，在Dw3基因中鉴定出7个功能丧失变体。我们验证了Segaolane dw3功能丧失变体（由第三个外显子中的137 bp缺失导致）可抑制回复株的产生。携带dw3-ref等位基因的Segaolane巢式关联作图群体重组自交系（RILs）产生了回复株，而携带Segaolane dw3等位基因的RILs未观察到回复株。重测序数据的可用性使得能够设计基于单倍型的标记，用于检测Segaolane稳定的dw3等位基因，以便将性状通过标记辅助导入优良高粱育种系。这项挖掘新的稳定矮化dw³等位基因的研究证明了高粱泛基因组在性状改良和开发标记辅助育种策略方面的应用。
