Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

中文翻译：

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面包小麦盐胁迫响应在渗透和离子阶段的转录组分析揭示了特异的候选基因。

面包小麦是人类饮食中最重要的作物之一，但是土壤盐碱化的加剧正在导致全球单产下降。改善小麦的盐胁迫耐受性需要阐明植物对这种非生物胁迫因素的响应的机械基础。尽管已经进行了数项研究来分析小麦对盐胁迫的适应性，但仍然存在一些空白，无法完全理解从初始信号感知到响应性耐受途径的出现的分子机制。这项研究的主要目的是利用基本QTL区域中的动态盐胁迫转录组，以发现控制面包小麦耐盐胁迫的候选基因。3'-末端测序方案的大规模分析被用于分析渗透和离子相的叶子样品。之后，鉴定了两个作图种群中与盐胁迫相关性状的QTL重叠的胁迫响应基因。在过度代表的盐响应基因类别中，在耐受基因型中发现的钙结合和细胞壁合成基因的早期上调可能是应对盐相关渗透胁迫的策略。另一方面，光合作用和钙结合基因的下调，以及易感基因型中氧化应激反应的增加与渗透期光合作用的抑制作用有关。在离子阶段，某些ABC转运蛋白和Na + / Ca2 +交换子在耐受基因型中的特定上调表明它们参与了钠排泄和体内稳态的机制。此外，在两个应激阶段都鉴定了与蛋白质合成和分解相关的基因。基于连锁不平衡块，在QTL间隔内的盐响应基因被鉴定为在导致盐胁迫耐受性的途径中起作用的潜在成分。此外，这项研究为面包小麦中转录的新区域提供了证据。动态转录组分析可以比较盐胁迫反应的渗透相和离子相，并提供了对对比小麦基因型盐胁迫适应过程中涉及的关键分子机制的见解。高度连续的染色体水平参考基因组序列装配的利用，通过靶向新的耐盐候选基因，促进了QTL解剖。在QTL间隔内的盐敏感基因被鉴定为在导致盐胁迫耐受性的途径中起作用的潜在成分。此外，这项研究为面包小麦中转录的新区域提供了证据。动态转录组分析可以比较盐胁迫反应的渗透相和离子相，并提供了对对比小麦基因型盐胁迫适应过程中涉及的关键分子机制的见解。高度连续的染色体水平参考基因组序列装配的利用，通过靶向新的耐盐候选基因，促进了QTL解剖。在QTL间隔内的盐敏感基因被鉴定为在导致盐胁迫耐受性的途径中起作用的潜在成分。此外，这项研究为面包小麦中转录的新区域提供了证据。动态转录组分析可以比较盐胁迫反应的渗透相和离子相，并提供了对对比小麦基因型盐胁迫适应过程中涉及的关键分子机制的见解。高度连续的染色体水平参考基因组序列装配的利用，通过靶向新的耐盐候选基因，促进了QTL解剖。这项研究为面包小麦的转录提供了新的区域。动态转录组分析可以比较盐胁迫反应的渗透相和离子相，并提供了对对比小麦基因型盐胁迫适应过程中涉及的关键分子机制的见解。高度连续的染色体水平参考基因组序列装配的利用，通过靶向新的耐盐候选基因，促进了QTL解剖。这项研究为面包小麦的转录提供了新的区域。动态转录组分析可以比较盐胁迫响应的渗透相和离子相，并提供了对与对比小麦基因型盐胁迫适应有关的关键分子机制的见解。高度连续的染色体水平参考基因组序列装配的利用，通过靶向新的耐盐候选基因，促进了QTL解剖。