Viruses and Phytoparasitic Nematodes of Cicer arietinum L.: Biotechnological Approaches in Interaction Studies and for Sustainable Control

Abstract

Cicer arietinum L. (chickpea) is the world's fourth most widely grown pulse. Chickpea seeds are a primary source of dietary protein for humans, and chickpea cultivation contributes to biological nitrogen fixation in the soil, given its symbiotic relationship with rhizobia. Therefore, chickpea cultivation plays a pivotal role in innovative sustainable models of agro-ecosystems inserted in crop rotation in arid and semi-arid environments for soil improvement and the reduction of chemical inputs. Indeed, the arid and semi-arid tropical zones of Africa and Asia have been primary areas of cultivation and diversification. Yet, nowadays, chickpea is gaining prominence in Canada, Australia, and South America where it constitutes a main ingredient in vegetarian and vegan diets. Viruses and plant parasitic nematodes (PPNs) have been considered to be of minor and local impact in primary areas of cultivation. However, the introduction of chickpea in new environments exposes the crop to these biotic stresses, compromising its yields. The adoption of high-throughput genomic technologies, including genome and transcriptome sequencing projects by the chickpea research community, has provided major insights into genome evolution as well as genomic architecture and domestication. This review summarizes the major viruses and PPNs that affect chickpea cultivation worldwide. We also present an overview of the current state of chickpea genomics. Accordingly, we explore the opportunities that genomics, post-genomics and novel editing biotechnologies are offering in order to understand chickpea diseases and stress tolerance and to design innovative control strategies.

Keywords: Cicer arietinum L.; RNA silencing; genome editing; plant parasitic nematodes; plant transformation; plant viruses; viral metagenomics.

Figure 1

Virus cycles in agro-ecosystems. (A) Schematic representation of replication cycles of Turnip crinkle virus (TCV) family Tombusviridae, genus Carmovirus), a virus that has been found associated to chickpea in open field. TCV has a positive (+) sense RNA genome that replicates (blue line). The viral RNA-dependent RNA polymerase (RdRp) amplifies the viral genome in the cytoplasm via negative (−) sense RNA template synthesis (red line). (+) RNA enters into the cellular translation machinery and codes for the RdRp. Moreover, movement proteins (MPs) and coat protein (CP) are the products of translation on viral sub-genomic RNAs. TCV genomic RNA can be encapsidated by the CP to form an icosahedral virion that can be then acquired by insects such as coleoptera. (B) Schematic representation of replication cycles of single stranded (ss) DNA viruses of the family Geminiviridae. Circular viral genomic ssDNA (1) functions as template for the synthesis of antisense ssDNA (orange line) due to the activity of host DNA-dependent DNA polymerase (yellow element) (2) to form a viral double stranded (ds)DNA intermediate (3). Viral dsDNA can be transcribed in the nucleus by the host DNA-dependent RNA polymerase PolII. Viral RNA transcripts are transferred to the cytoplasm, and enter into the translational machinery to release viral replicase (rep, blue element), MP and CP. One strand of the viral dsDNA can undergo cleavage by viral rep (4), thus allowing the access to the host DNA polymerase that extends the viral ssDNA and generates several copies of the circular genome (5). The ssDNA can be encapsidated and acquired by leafhopper vectors. (C) Chickpea is a permissive, non-symptomatic host for several viruses and it is often used in rotation with and/or in proximity to other crops for a sustainable agriculture. It therefore functions as a reservoir of virus inoculum that can be spread through insect vectors to other permissive crops that can show viral symptoms such as leaf yellowing, curling deformation and a general impact on the crop production. Metagenomics of nucleic acids of viral origin can be applied on either symptomatic or non-symptomatic plant tissues, as well as to other environmental samples (soil, insects) in order to explore viral entities associated to agro-ecosystems.

Figure 2

Selected photos showing symptoms induced by viruses on chickpea plants. (A) Tip wilting induced by mechanical inoculation with TuMV (from Schwinghamer et al., 2007). (B) Symptoms of chlorotic stunt disease caused by CpCDV on chickpea (from Kanakala et al., 2013).

Figure 3

Symptoms of nematode infection on chickpea plants in field and greenhouse. (A) Symptoms of infection visible in the field on C. arietinum: plant reduced in crop yield with chlorotic, pale, and yellow leaves. (B) Greenhouse pot test: control plant (left) and M. incognita infected plant (right). (C) Root system of control (c) and M. incognita infected plants (+n). (D) Egg masses (em) generated by M. incognita mature female, in root galling tissue. (E) Newly formed cysts (cy) of H. goettingiana.

Figure 4

Three important PPNs associated to chickpea roots. Meloidogyne artiellia: (A) Longitudinal root section showing anatomical alterations; (B) Scanning electron microscopy (SEM) photo of a female on the root. Heterodera ciceri: (C) The tissues disruption caused by the cyst nematode is shown in longitudinal root section; (D) SEM image of a mature female. Pratylenchus thornei: (E) Longitudinal section of the root showing lesions caused by the nematode; (F) Fuchsin-stained root cortex section, showing the migratory endoparasite. n, nematode; e, eggs; gc, giant cell; ne, necrotic tissues; s, syncytium. Scale bars: (A,C,E) = 500 μm; (B,D,F) = 200 μm (Source: Nicola Vovlas, CNR).

Figure 5

Simplified life cycles of cyst nematodes (CNs) and root-knot (RKNs) nematodes. Larvae hatch from cysts or from egg masses; the first-stage juvenile molts inside the eggshell become an invasive second-stage juvenile (J2) adapted to penetrate the root using an intra, inter-cellular migration and to the establishment of the feeding site (Syncytium and Giant cell). The nematode has to change molts (J3, J4) to become a fully mature (male or female) adult. Parthenogenetic and amphimictic reproduction modalities are different between CNs and RKNs.

Figure 6

Phylogenetic tree of seven legume species with Vitis vinifera as the out-group. The phylogenetic tree was constructed with a genome-wide single-copy orthologous genes of legume species i.e., Glycine max, (cultivated soybean), Glycine soja (wild soybean), Medicago truncatula (barrel clover), Lotus japonicus (bird's-foot trefoil), Cajanus cajan (Pigeonpea) Cicer arietinum (chickpea), Phaseolus vulgaris (common bean). Modified from Zheng et al. (2016).

Figure 7

NBS-LRR silencing cascade mechanism. Schematic representation of NBS-LRR silencing cascade mechanism triggered by miR2118 (a legume specific miRNAs discovered in soybean), highly conserved in C. arietinum. In red circles, viral silencing suppressors (Csorba et al., 2015) that can impair the cascade mechanism.

Figure 8

Serine hydroxymethyltransferase gene model. Shmt model and polymorphism in resistant (Forrest) and susceptible (Essex) soybean cultivars and alignment of predicted chickpea shmt 1-like mRNA sequences (NCBI reference XM_004504310.1 and XM_004502186.1) showing the two functional SNPs positions.