Zuo Huifang, Gao Huanhuan, Huo Mengying, He Mengshi, Xu Mengjun, Zhang Lina, Huang Qiqi, Lü Haiyan, Chu Shanshan, Xiong Erhui, Li Jinying, Hu Dandan, Zhang Dan
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China.
Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, China.
Plant Genome. 2025 Sep;18(3):e70094. doi: 10.1002/tpg2.70094.
Phosphorus (P) deficiency severely limits soybean productivity, yet the genetic basis of P efficiency remains underexplored. Here, we systematically identified 27 GmGDPD genes in soybean (Glycine max), revealing that family expansion was driven by segmental/tandem duplication events, accompanied by functional diversification through acquisition of protein kinases, catalytic domain-like kinase and GUB_WAK_bind domains. Transcriptome and reverse transcription quantitative PCR analyses demonstrated that genes, including GmGDPD2/9/12/14, were significantly induced under low Pi stress, correlating with enhanced root apical meristem activity. Haplotype association analysis across 559 soybean accessions identified elite haplotypes (GmGDPD4-Hap4, GmGDPD9-Hap3, GmGDPD14-Hap4, and GmGDPD12-Hap4) associated with enhanced Pi efficiency traits. Notably, these superior haplotypes were enriched in wild soybeans (Glycine soja) but drastically reduced in cultivated varieties due to domestication bottlenecks. A high-accuracy kompetitive allele-specific PCR marker targeting GmGDPD2-Hap5 enabled rapid screening of Pi-efficient germplasm. Hydroponic validation confirmed that Hap5 materials significantly enhanced root traits under low Pi conditions, with 41% longer roots, 36% larger root surface area, 31% the relative root volume, and 100% relative root tip number compared to non-Hap5 genotypes. Evolutionary analyses highlighted soybean-specific domain innovation in the GmGDPD members, suggesting adaptive roles in coordinating phospholipid metabolism and kinase signaling under Pi stress. Our findings propose an allele-replenishment strategy to reintroduce wild-derived Pi-efficient alleles into modern cultivars, bridging the gap between domestication-driven allele loss and sustainable breeding. The functional markers and mechanistic insights established here advance precision breeding for reducing fertilizer dependency while stabilizing yields in Pi-deficient soils, offering a genomic toolkit for soybean improvement.
磷（P）缺乏严重限制了大豆产量，然而磷效率的遗传基础仍未得到充分研究。在此，我们系统地鉴定了大豆（Glycine max）中的27个GmGDPD基因，发现该家族的扩张是由片段/串联重复事件驱动的，同时通过获得蛋白激酶、催化结构域样激酶和GUB_WAK_bind结构域实现了功能多样化。转录组和逆转录定量PCR分析表明，包括GmGDPD2/9/12/14在内的基因在低磷胁迫下显著上调，这与根尖分生组织活性增强相关。对559份大豆种质进行单倍型关联分析，确定了与磷效率性状增强相关的优良单倍型（GmGDPD4-Hap4、GmGDPD9-Hap3、GmGDPD14-Hap4和GmGDPD12-Hap4）。值得注意的是，这些优良单倍型在野生大豆（Glycine soja）中富集，但由于驯化瓶颈，在栽培品种中大幅减少。针对GmGDPD2-Hap5的高精度竞争性等位基因特异性PCR标记能够快速筛选磷高效种质。水培验证证实，与非Hap5基因型相比，Hap5材料在低磷条件下显著增强了根系性状，根长增加41%，根表面积增加36%，相对根体积增加31%，相对根尖数增加100%。进化分析突出了GmGDPD成员中大豆特有的结构域创新，表明其在磷胁迫下协调磷脂代谢和激酶信号传导中具有适应性作用。我们的研究结果提出了一种等位基因补充策略，将野生来源的磷高效等位基因重新引入现代品种，弥合驯化导致的等位基因丢失与可持续育种之间的差距。本文建立的功能标记和机制见解推动了精准育种，以减少肥料依赖，同时在缺磷土壤中稳定产量，为大豆改良提供了一个基因组工具包。
