Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe)

Abstract

BackgroundSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating pathogen of soybean. Many gene expression profiling studies have been conducted to investigate the responses of soybean to the infection by this pathogen using primarily the first-generation soybean genome array that covered approximately 37,500 soybean transcripts. However, no study has been reported yet using the second-generation Affymetrix soybean whole-genome transcript array (Soybean WT array) that represents approximately 66,000 predicted soybean transcripts.ResultsIn the present work, the gene expression profiles of two soybean plant introductions (PIs) PI 437654 and PI 567516C (both resistant to multiple SCN HG Types) and cultivar Magellan (susceptible to SCN) were compared in the presence or absence of the SCN inoculum at 3 and 8 days post-inoculation using the Soybean WT array. Data analysis revealed that the two resistant soybean lines showed distinctive gene expression profiles from each other and from Magellan not only in response to the SCN inoculation, but also in the absence of SCN. Overall, 1,413 genes and many pathways were revealed to be differentially regulated. Among them, 297 genes were constitutively regulated in the two resistant lines (compared with Magellan) and 1,146 genes were responsive to the SCN inoculation in the three lines, with 30 genes regulated both constitutively and by SCN. In addition to the findings similar to those in the published work, many genes involved in ethylene, protein degradation, and phenylpropanoid pathways were also revealed differentially regulated in the present study. GC-rich elements (e.g., GCATGC) were found over-represented in the promoter regions of certain groups of genes. These have not been observed before, and could be new defense-responsive regulatory elements.ConclusionsDifferent soybean lines showed different gene expression profiles in the presence and absence of the SCN inoculum. Both inducible and constitutive gene expression may contribute to resistance to multiple SCN HG Types in the resistant soybean PI lines. Ethylene, protein degradation, and phenylpropanoid pathways, as well as many other pathways reported previously, may play important roles in mediating the soybean-SCN interactions. The revealed genes, pathways, and promoter elements can be further explored to regulate or engineer soybean for resistance to SCN.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1316-8) contains supplementary material, which is available to authorized users.

The plant‐parasitic cyst nematode effector GLAND4 is a DNA‐binding protein

“…The initial feeding cell is expanded through dissolution of the surrounding cell walls to form a multinucleated structure, referred to as a syncytium (Jones, 1981;Jones and Northcote, 1972). Gene expression profiling studies performed on whole roots and microdissected syncytia have revealed extensive alterations in host gene expression in response to cyst nematode infection (Hermsmeier et al, 1998;Hofmann et al, 2010;Ithal et al, 2007;Puthoff et al, 2003;Szakasits et al, 2009;Wan et al, 2015). The secretion of effector proteins, defined by their ability to modify host cell structure and function, is key to the breakdown of plant tissue for migration and the suppression of plant defences Hogenhout et al, 2009;Wang et al, 1999).…”

The Impact of Plant-Parasitic Nematodes on Agriculture and Methods of Control

“…Diferential genetic expression proiles of many speciic genes involved in plant immune responses has been shown in resistant and susceptible plants challenged by root-knot nematodes [48,95]. The identiication of novel defenserelated transcripts and the elucidation of pathways involved in plant immune responses to nematodes have been recorded for important economic crops including coton [96], rice [97], and soybean [98]. Transcriptome proiling of resistant and susceptible tobacco varieties infected with root-knot nematodes has shown diferential expression paterns among genes involved in cell wall modiication, auxin production and oxidative stress [99].…”

Plant elicitor peptides promote plant defences against nematodes in soybean

“…To investigate whether Pep seed treatments limit nematode infestation through transcriptional reprogramming of the roots, we examined the expression of several defence genes previously implicated in resistance to SCN or RKN. Genes encoding a putative respiratory burst oxidase protein (RBOHD) and a nucleotidebinding site leucine-rich repeat-type disease resistance protein (NBS-LRR) have been reported previously to be up-regulated by SCN infestation on resistant, but not susceptible, plants (Wan et al, 2015). In addition, a gene encoding a putative pectin methylesterase inhibitor (PMEI, Glyma10g02150) was identified as a candidate gene for RKN resistance through quantitative trait locus (QTL) mapping (Xu et al, 2013).…”

“…Previous studies have shown that PTI against RKNs in Arabidopsis is compromised in mutants with impairments in BAK1, BIK1 or NADPH oxidase genes (RBOHD/F) (Teixeira et al, 2016). Comparison of transcript profiles induced by SCN in resistant versus susceptible soybean cultivars also indicates that BIK1 and RBOHD induction correlate with cyst nematode resistance (Matsye et al, 2011;Wan et al, 2015). Given that Peps induce defence responses that are also associated with PTI or ETI against nematodes, Peps could potentially be utilized to induce nematode resistance in susceptible genotypes.…”