biostudies-literatureWang Hxiaohu Lin859https://www.ebi.ac.uk/biostudies/studies/S-EPMC12190892biostudies-literatureUnknown15(6)Soil salinization and alkalization are becoming increasingly severe in recent decades, which poses serious threats to crop production and food security in the world. Foxtail millet (<i>Setaria italica</i> L.) is an important cereal crop in China, and it is important to elucidate its saline-alkali tolerance mechanisms for the breeding of new saline-alkali tolerant varieties. In this study, we used 75% seawater to treat two foxtail millet varieties with different saline-alkali tolerances (JK3, saline-alkali tolerant; B175, saline-alkali sensitive) during the seedling stage, and conducted morphological, cellular ultrastructure, physiological, and transcriptomic analyses on the two varieties. The morphological analysis of the saline-alkali response indicated that JK3 exhibited stronger saline-BiomoleculesPhysiological Mechanisms and Core Genes in Response to Saline-Alkali Stress in Foxtail Millet (&lt;i&gt;Setaria italica&lt;/i&gt; L.).PMC12190892HBCT2025070405Li YYang YFan XGuo ZLin XHan YWang HXu YfalsePhysiological Mechanisms and Core Genes in Response to Saline-Alkali Stress in Foxtail Millet (&lt;i&gt;Setaria italica&lt;/i&gt; L.).Soil salinization and alkalization are becoming increasingly severe in recent decades, which poses serious threats to crop production and food security in the world. Foxtail millet (<i>Setaria italica</i> L.) is an important cereal crop in China, and it is important to elucidate its saline-alkali tolerance mechanisms for the breeding of new saline-alkali tolerant varieties. In this study, we used 75% seawater to treat two foxtail millet varieties with different saline-alkali tolerances (JK3, saline-alkali tolerant; B175, saline-alkali sensitive) during the seedling stage, and conducted morphological, cellular ultrastructure, physiological, and transcriptomic analyses on the two varieties. The morphological analysis of the saline-alkali response indicated that JK3 exhibited stronger saline-2025-01-01T00:00:00Z2025 Jun2026-04-08T19:29:12.786Z2026-04-08T13:40:05.56ZS-EPMC121908924056349910.3390/biom15060859