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<p>YABBY transcription factors are plant-specific regulators of organ polarity, lamina outgrowth and reproductive development. In wheat (<i>Triticum aestivum</i> L.), previous genome-wide studies identified core TaYABBY loci and described their expression across tissues and selected stresses. Here, we re-examined YABBY-associated protein models and integrated phylogenetic, structural, promoter, public transcriptomic and qRT-PCR analyses, with emphasis on cold and PEG-induced osmotic stress. We recovered 60 TaYABBY protein-model entries, which correspond to 25 unique wheat gene IDs, including multiple transcript/protein models for 14 loci, thereby reconciling our entry number with earlier reports of approximately 20 wheat YABBY genes. Nineteen entries shorter than 100 amino acids and one HMG-box-only entry lacking explicit YABBY annotation were flagged as partial or low-confidence and excluded from strong functional inference. Phylogenetic analysis grouped TaYABBY candidates with barley, rice, maize, sorghum and <i>Arabidopsis</i> homologs into the canonical FIL/YAB3, YAB2, INO and CRC/DL subfamilies, supporting broad family conservation. Promoter analysis of 1-kb upstream regions identified light-, hormone- and stress-related motifs, including ABRE, MBS and MeJA/SA-responsive elements, which are reported as motif-composition observations rather than enriched regulatory modules. Public expVIP RNA-seq data suggested stress-responsive expression for subsets of <i>TaYABBY</i> entries. qRT-PCR of six prioritized candidates, <i>TaYABBY4, TaYABBY24, TaYABBY27, TaYABBY38, TaYABBY44,</i> and <i>TaYABBY50</i>, revealed time-dependent regulation under PEG-6000, cold and combined PEG + cold treatments, with several genes showing stronger induction under combined stress. These patterns indicate transcriptional responsiveness, but not direct evidence of stress-tolerance function. Overall, this revised study provides a curated <i>TaYABBY</i> resource and prioritizes candidates for future functional validation under controlled osmotic and cold stress conditions.</p>

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Integrated genome-wide and expression analysis of YABBY genes in Triticum aestivum under PEG-induced osmotic, cold and combined stress

  • 期刊论文

  • 发表日期：

    2026年7月6日

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  • Khairiah Mubarak Alwutayd,
  • Ashwag Shami,
  • Ahmad M. Alqudah,
  • Samar G. Thabet

摘要

YABBY transcription factors are plant-specific regulators of organ polarity, lamina outgrowth and reproductive development. In wheat (Triticum aestivum L.), previous genome-wide studies identified core TaYABBY loci and described their expression across tissues and selected stresses. Here, we re-examined YABBY-associated protein models and integrated phylogenetic, structural, promoter, public transcriptomic and qRT-PCR analyses, with emphasis on cold and PEG-induced osmotic stress. We recovered 60 TaYABBY protein-model entries, which correspond to 25 unique wheat gene IDs, including multiple transcript/protein models for 14 loci, thereby reconciling our entry number with earlier reports of approximately 20 wheat YABBY genes. Nineteen entries shorter than 100 amino acids and one HMG-box-only entry lacking explicit YABBY annotation were flagged as partial or low-confidence and excluded from strong functional inference. Phylogenetic analysis grouped TaYABBY candidates with barley, rice, maize, sorghum and Arabidopsis homologs into the canonical FIL/YAB3, YAB2, INO and CRC/DL subfamilies, supporting broad family conservation. Promoter analysis of 1-kb upstream regions identified light-, hormone- and stress-related motifs, including ABRE, MBS and MeJA/SA-responsive elements, which are reported as motif-composition observations rather than enriched regulatory modules. Public expVIP RNA-seq data suggested stress-responsive expression for subsets of TaYABBY entries. qRT-PCR of six prioritized candidates, TaYABBY4, TaYABBY24, TaYABBY27, TaYABBY38, TaYABBY44, and TaYABBY50, revealed time-dependent regulation under PEG-6000, cold and combined PEG + cold treatments, with several genes showing stronger induction under combined stress. These patterns indicate transcriptional responsiveness, but not direct evidence of stress-tolerance function. Overall, this revised study provides a curated TaYABBY resource and prioritizes candidates for future functional validation under controlled osmotic and cold stress conditions.