Shi Linyong, Zhang Heng, Chen Heyun, Liu Heqin, Liu Xiuhui, Zheng Xueqiang, Zou Guihua, Wang Junmei
College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
Institute of Crop and Nuclear Technology Utilization, Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
BMC Genomics. 2025 Jul 17;26(1):674. doi: 10.1186/s12864-025-11858-6.
Sorghum has a strong tolerance to multi-abiotic stresses such as drought, heat, poor soil fertility, and salinity, yet its growth and development are significantly affected by extreme abiotic stresses, ultimately reducing grain yield. Peroxidase (POD) proteins, which are members of the oxidoreductase enzyme family, play an important role in protecting plants against multi-abiotic stress. However, this gene family has rarely been studied in sorghum.
In this study, 114 POD gene members (SbPODs) were identified in sorghum and distributed unevenly throughout 10 chromosomes. Phylogenetic analysis clustered these genes into 12 subgroups. Gene structure and motif analyses showed the structural and functional diversity among the subgroups. These genes have undergone 16 segmental duplication and 32 tandem duplication events, indicating that both segmental and tandem duplications are major contributors to the expansion of the SbPOD gene family. Most duplicated SbPODs have undergone purifying selection with limited functional divergence during duplication events. Compared with maize, rice, and Arabidopsis, SbPOD gene family not only occurred the duplication on the whole-genome level, but also existed independent duplication events. The qRT-PCR results showed twenty SbPOD genes exhibited differential expression patterns in leaves under NaCl, HO and PEG stress treatments. Of twenty SbPOD genes, most SbPOD genes showed consistently significant downregulation under NaCl, HO, and 30% PEG6000 stress treatments, except for SbPOD81 and SbPOD26. Under NaCl stress, the expression level of SbPOD81 showed a down-up regulation trend. Under HO stress, the expression level of SbPOD81 showed a down regulation trend. Under 30% PEG6000 stress, SbPOD81 maintained down-up regulation trend but quite different under NaCl stress. In contrast, the expression level of SbPOD26 showed consistent down-up regulation trend under both NaCl and HO stress, while after 3 h of adaptation under 30% PEG6000 stress, the expression level of SbPOD26 continued to increase. The analysis of cis-elements and conserved domain showed that SbPOD81 contains one W-box, four MYB, and three MYC cis-elements, while SbPOD26 has two W-boxes, four MBS, four MYB, and eight MYC cis-elements. Additionally, SbPOD26 possesses one PAT1 domain, which is absent in SbPOD81 and other SbPOD genes. This structural distinction not only would explain the observed expression divergence but suggests SbPOD26 may perform specialized biological functions distinct from other SbPOD genes.
Totally, 114 POD gene members were identified in sorghum by a series of bioinformatics analysis. The expression patterns of some members of SbPOD gene family exhibited significantly difference under various stress conditions. These findings not only provide valuable insights into the evolutionary dynamics of the SbPOD gene family, but also lay a foundation for further studies on the functions of POD genes.
高粱对干旱、高温、土壤肥力差和盐度等多种非生物胁迫具有较强的耐受性，但其生长发育仍受到极端非生物胁迫的显著影响，最终导致籽粒产量降低。过氧化物酶（POD）蛋白属于氧化还原酶家族成员，在保护植物免受多种非生物胁迫方面发挥着重要作用。然而，该基因家族在高粱中鲜有研究。
本研究在高粱中鉴定出114个POD基因成员（SbPODs），它们不均匀地分布在10条染色体上。系统发育分析将这些基因聚类为12个亚组。基因结构和基序分析显示了亚组间的结构和功能多样性。这些基因经历了16次片段重复和32次串联重复事件，表明片段重复和串联重复都是SbPOD基因家族扩增的主要原因。大多数重复的SbPODs在重复事件中经历了纯化选择，功能分化有限。与玉米、水稻和拟南芥相比，SbPOD基因家族不仅在全基因组水平上发生了重复，还存在独立的重复事件。qRT-PCR结果表明，20个SbPOD基因在NaCl、HO和PEG胁迫处理下的叶片中呈现出差异表达模式。在20个SbPOD基因中，除SbPOD81和SbPOD26外，大多数SbPOD基因在NaCl、HO和30% PEG6000胁迫处理下均持续显著下调。在NaCl胁迫下，SbPOD81的表达水平呈现先下调后上调的趋势。在HO胁迫下，SbPOD81的表达水平呈现下调趋势。在30% PEG6000胁迫下，SbPOD81保持先下调后上调的趋势，但与NaCl胁迫下有很大不同。相比之下，SbPOD26的表达水平在NaCl和HO胁迫下均呈现一致的先下调后上调趋势，而在30% PEG6000胁迫下适应3小时后，SbPOD26的表达水平持续升高。顺式作用元件和保守结构域分析表明，SbPOD81含有1个W-box、4个MYB和3个MYC顺式作用元件，而SbPOD26有2个W-box、4个MBS、4个MYB和8个MYC顺式作用元件。此外，SbPOD26拥有1个PAT1结构域，这在SbPOD81和其他SbPOD基因中不存在。这种结构差异不仅可以解释观察到的表达差异，还表明SbPOD26可能执行与其他SbPOD基因不同的特殊生物学功能。
通过一系列生物信息学分析，在高粱中总共鉴定出114个POD基因成员。SbPOD基因家族的一些成员在各种胁迫条件下的表达模式表现出显著差异。这些发现不仅为SbPOD基因家族的进化动态提供了有价值的见解，也为进一步研究POD基因的功能奠定了基础。
