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<p>Foxtail millet (<i>Setaria italica</i> L.), a vital climate-resilient crop, requires enhanced exploitation of its genetic resources for salinity tolerance. The <i>Exo70</i> gene family, crucial for vesicle trafficking and stress adaptation, remained uncharacterized in millet. We conducted the first genome-wide identification in foxtail millet, revealing 40 <i>SiExo70</i> genes unevenly distributed across nine chromosomes and expanded via tandem/segmental duplications. Phylogenetic analysis confirmed closer relationships with monocot OsExo70s and an independent Exo70F subgroup. Critically, we analyzed sequence variation across 1844 diverse accessions—a core genetic resource—identifying 36 haplotypes. <i>SiExo70A2a</i> emerged as the most polymorphic locus (10 haplotypes), with most polymorphic sites in coding regions suggesting functional impact, notably coinciding with its root-specific expression and salt-stress responsiveness. Tissue expression profiling indicated roles in development (e.g., <i>SiExo70C1</i>/<i>C2</i> in pollen; <i>SiExo70A2a</i> in roots), while salt stress triggered significant differential expression: 19 genes up-regulated, 7 down-regulated, 13 stables. This integrated analysis demonstrates the <i>SiExo70</i> family’s substantial intraspecific variation, particularly stress-linked coding polymorphisms like those in <i>SiExo70A2a</i>, provides foundational genomic resources. These enable developing functional molecular markers for efficient germplasm collection screening to identify accessions harboring favorable salt-tolerance alleles, directly facilitating genetic resource evaluation and utilization for breeding resilient cultivars.</p>

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Genome-wide identification of Exo70 genes in foxtail millet: implications for salt tolerance assessment and utilization of genetic resources

  • 期刊论文

  • 发表日期：

    2025年12月12日

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  • Zhuanzhuan Jiang,
  • Yutong Dai,
  • Qianping Jing,
  • Mohan Jiang

摘要

Foxtail millet (Setaria italica L.), a vital climate-resilient crop, requires enhanced exploitation of its genetic resources for salinity tolerance. The Exo70 gene family, crucial for vesicle trafficking and stress adaptation, remained uncharacterized in millet. We conducted the first genome-wide identification in foxtail millet, revealing 40 SiExo70 genes unevenly distributed across nine chromosomes and expanded via tandem/segmental duplications. Phylogenetic analysis confirmed closer relationships with monocot OsExo70s and an independent Exo70F subgroup. Critically, we analyzed sequence variation across 1844 diverse accessions—a core genetic resource—identifying 36 haplotypes. SiExo70A2a emerged as the most polymorphic locus (10 haplotypes), with most polymorphic sites in coding regions suggesting functional impact, notably coinciding with its root-specific expression and salt-stress responsiveness. Tissue expression profiling indicated roles in development (e.g., SiExo70C1/C2 in pollen; SiExo70A2a in roots), while salt stress triggered significant differential expression: 19 genes up-regulated, 7 down-regulated, 13 stables. This integrated analysis demonstrates the SiExo70 family’s substantial intraspecific variation, particularly stress-linked coding polymorphisms like those in SiExo70A2a, provides foundational genomic resources. These enable developing functional molecular markers for efficient germplasm collection screening to identify accessions harboring favorable salt-tolerance alleles, directly facilitating genetic resource evaluation and utilization for breeding resilient cultivars.