QTL Mapping and Data Mining to Identify Genes Associated With the Sinorhizobium fredii HH103 T3SS Effector NopD in Soybean.

Jinhui Wang,Zhijun Sun,Hanxi Liu,Hongwei Jiang,Jieqi Wang,Junzan Zheng,Qinglin Kang,Decheng Yang,Qi Wang,Jianyi Li,Chunyan Liu,Xiaoxia Wu,Dawei Xin,Chao Ma,Lin Chen,Qingshan Chen,Zhaoming Qi,Ziqi Zhou,Huiwen Li,Zhou Hong-Yang ,Rong Zhu

doi:10.3389/fpls.2020.00453

Abstract

In some legume–rhizobium symbioses, host specificity is influenced by rhizobial type III effectors-nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. In this study, we aimed to identify candidate soybean genes associated with NopD, one of the type III effectors of Sinorhizobium fredii HH103. The results showed that the expression pattern of NopD was analyzed in rhizobia induced by genistein. We also found NopD can be induced by TtsI, and NopD as a toxic effector can induce tobacco leaf death. In 10 soybean germplasms, NopD played a positively effect on nodule number (NN) and nodule dry weight (NDW) in nine germplasms, but not in Kenjian28. Significant phenotype of NN and NDW were identified between Dongnong594 and Charleston, Suinong14 and ZYD00006, respectively. To map the quantitative trait locus (QTL) associated with NopD, a recombinant inbred line (RIL) population derived from the cross between Dongnong594 and Charleston, and chromosome segment substitution lines (CSSLs) derived from Suinong14 and ZYD00006 were used. Two overlapping conditional QTL associated with NopD on chromosome 19 were identified. Two candidate genes were identified in the confident region of QTL, we found that NopD could influence the expression of Glyma.19g068600 (FBD/LRR) and expression of Glyma.19g069200 (PP2C) after HH103 infection. Haplotype analysis showed that different types of Glyma.19g069200 haplotypes could cause significant nodule phenotypic differences, but Glyma.19g068600 (FBD/LRR) was not. These results suggest that NopD promotes S. fredii HH103 infection via directly or indirectly regulating Glyma.19g068600 and Glyma.19g069200 expression during the establishment of symbiosis between rhizobia and soybean plants.

Highlights

Soybean [Glycine max (L.) Merr.] is a widely grown commercial crop around the world and supplies a large amount of protein and oil for humans and animals (Xin et al, 2016)
Western blot results showed a band corresponding to NopD in samples from S. fredii HH103 induced with genistein, but not in NopD or TtsI mutants (Figure 1B)
The locus we identified in this study on soybean chromosome Gm08 overlaps with a previously identified quantitative trait locus (QTL) related to compatibility of soybean with Bradyrhizobium strains (Ramongolalaina et al, 2018)

Summary

Introduction

Soybean [Glycine max (L.) Merr.] is a widely grown commercial crop around the world and supplies a large amount of protein and oil for humans and animals (Xin et al, 2016). The genome of S. fredii HH103 has been uncovered, and extensive analyses of its genome and transcriptome have paved a good foundation for gene functional characterization (Margaret et al, 2011; Weidner et al, 2012; Vinardell et al, 2015; López-Baena et al, 2016; Pérez-Montaño et al, 2016). It is an ideal strain for studying the molecular mechanisms symbiosis between soybean and rhizobium

Objectives

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Results

Conclusion