Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea

Danamma Kalavikatte,Mahendar Thudi,Sonal Channale,John P Thompson,Prasad Bajaj,Rebecca S Zwart,Himabindu Kudapa,Rajeev K Varshney

doi:10.1038/s41598-021-96906-3

Abstract

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (resistant advanced breeding line), PBA HatTrick (moderately resistant cultivar), and Kyabra (susceptible cultivar) were studied at 20 and 50 days post inoculation using the RNA-seq approach. On analyzing the 633.3 million reads generated, 962 differentially expressed genes (DEGs) were identified. Comparative analysis revealed that the majority of DEGs upregulated in the resistant genotype were downregulated in the moderately resistant and susceptible genotypes. Transcription factor families WRKY and bZIP were uniquely expressed in the resistant genotype. The genes Cysteine-rich receptor-like protein kinase 10, Protein lifeguard-like, Protein detoxification, Bidirectional sugar transporter Sugars Will Eventually be Exported Transporters1 (SWEET1), and Subtilisin-like protease were found to play cross-functional roles in the resistant chickpea genotype against P. thornei. The identified candidate genes for resistance to P. thornei in chickpea can be explored further to develop markers and accelerate the introgression of P. thornei resistance into elite chickpea cultivars.

Highlights

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum)
P. thornei adults and juveniles were observed in the roots of PBA HatTrick and Kyabra at 5 dpi, whereas for D05253 they were first observed at 10 dpi (Fig. 1e)
Understanding the molecular mechanisms and candidate genes involved in P. thornei resistance will be useful for designing stategies to overcome crop production losses

Summary

Introduction

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). Among plant-parasitic nematodes, Pratylenchus thornei is one of the most economically important root-lesion nematodes (RLN), widely distributed in chickpea growing areas throughout the world[2]. The reduced functionality of the host plant roots due to the damage caused by RLN feeding and reproducing inside the root cells results in similar symptoms to nutrient deficiencies, water stress, and soil-borne fungal pathogens viz., stunting, wilting, chlorotic leaves, reduced number of flower and pods, reduced yield and patchiness in the field[2]. In the case of cereals like wheat (Triticum aestivum), candidate genes responsible for resistance to P. thornei have been reported to encode key enzymes involved in the phenylpropanoid biosynthetic pathway, nucleotidebinding site-leucine-rich repeat (NBS-LRR) proteins and protein k inases[8]. In the case of legumes like alfalfa (Medicago sativa), induction of the phenylpropanoid pathway and accumulation of secondary metabolites play critical roles in resistance to P. penetrans[10]

Methods

Results

Conclusion