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J Integr Plant Biol
Function identification of MdTIR1 in apple root growth benefited from the predicted MdPPI network
Lin Liu1†, Zipeng Yu1†, Yang Xu2, Cheng Guo1, Lei Zhang1, Changai Wu1, Guodong Yang1, Jinguang Huang1, Kang Yan1, Huairui Shu1, Chengchao Zheng1* and Shizhong Zhang1*
1 State Key Laboratory of Crop Biology, Shandong Agricultural University, Taiʼan 271018, China
2 Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China

These authors contributed equally to this work.
*Correspondences:
Email: Chengchao Zheng(cczheng@sdau.edu.cn); Shizhong Zhang (shizhong@sdau.edu.cn, Dr. Zhang is fully responsible for the distribution of all materials associated with this article)
doi: 10.1111/jipb.12996
Abstract

Protein–protein interaction (PPI) network analysis is an effective method to identify key proteins during plant development, especially in species for which basic molecular research is lacking, such as apple (Malus domestica ). Here, an MdPPI network containing 30,806 PPIs was inferred in apple and its quality and reliability were rigorously verified. Subsequently, a root‐growth sub‐network was extracted to screen for critical proteins in root growth. Because hormone‐related proteins occupied the largest proportion of critical proteins, a hormone‐related sub‐sub‐network was further extracted from the root‐growth sub‐network. Among these proteins, auxin‐related M. domestica TRANSPORT INHIBITOR RESISTANT 1 (MdTIR1) served as the central, high‐degree node, implying that this protein exerts essential roles in root growth. Furthermore, transgenic apple roots overexpressing an MdTIR1 transgene displayed increased primary root elongation. Expression analysis showed that MdTIR1 significantly upregulated auxin‐responsive genes in apple roots, indicating that it mediates root growth in an auxin‐dependent manner. Further experimental validation revealed that MdTIR1 interacted with and accelerated the degradation of MdIAA28, MdIAA43, and MdIAA46. Thus, MdTIR1‐mediated degradation of MdIAAs is critical in auxin signal transduction and root growth regulation in apple. Moreover, our network analysis and high‐degree node screening provide a novel research technique for characterizing molecular mechanisms more generally.

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Received: 25 April 2020      Accepted:    Online on:23 July 2020
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