Yang Sheng, Yu Xiaomei, Gao Xinke, Fatima Kinza, Tahir Ul Qamar Muhammad
Pomology Institute, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, China.
College of Horticulture, Shanxi Agricultural University, Jinzhong, Shanxi, China.
Front Genet. 2024 May 10;15:1393487. doi: 10.3389/fgene.2024.1393487. eCollection 2024.
In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight genomes: Cuiguan (), Shanxi Duli (), Zhongai 1 [() × spp.], Nijisseiki (. ), Yunhong No.1 (. ), d'Anjou (), Bartlett v2.0 (), and Dangshansuli v.1.1 (). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of TIR1/AFBs. The expansion of this gene family in is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The GO and PPI analysis showed that genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of genes were enriched in hormone-, light-, development-, and stress-related elements. Furthermore, publicly available RNA-seq data analysis showed that have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in , elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.
在植物基因组学和植物生态系统中，梨属植物是营养最为丰富的水果之一，其含有的纤维对人体健康大有裨益。梨主要种植于温带地区，是全球种植最为广泛的梨果之一。梨树极易遭受生物和非生物胁迫，从而影响其产量。TIR1/AFB蛋白在核生长素信号传导过程中作为生长素共受体，在与发育相关的调控过程以及对生物和非生物胁迫的反应中发挥着主要作用。然而，该基因家族及其成员在梨基因组中尚未得到研究，了解这些基因将有助于深入了解梨树的胁迫耐受性，并最终有助于维持梨树的高产。本研究报告了对来自八个梨基因组（翠冠、山西杜梨、中矮1号、丰水、云红1号、安久、巴梨v2.0和砀山酥梨v1.1）的TIR1/AFB基因进行的泛基因组范围研究。这些基因在每个基因组的17条染色体上随机分布。基于系统发育学，鉴定出的TIR1/AFB基因被分为六组。它们的基因结构和基序模式显示出种内结构保守性以及TIR1/AFB基因的进化模式。该基因家族在梨中的扩增主要由片段重复引起；然而，少数基因显示出串联重复。此外，正选择和负选择压力同样影响着基因的重复过程。基因本体（GO）和蛋白质-蛋白质相互作用（PPI）分析表明，梨基因与非生物胁迫和发育相关的信号通路有关。梨基因的启动子区域富含与激素、光、发育和胁迫相关的元件。此外，对公开可用的RNA测序数据分析表明，梨基因在各种组织、发育阶段、果实硬化病条件和干旱胁迫条件下具有不同水平的表达。这表明梨基因可能在应对生物和非生物胁迫中发挥关键作用。梨的TIR1/AFB蛋白具有相似的结构，这表明它们参与相同的功能。因此，本研究将拓宽我们对梨中TIR1/AFB基因家族的认识，阐明它们在赋予梨树抵御各种环境胁迫能力方面的作用，也将为未来的研究人员提供有价值的见解。
