Resistance In Chickpea Research Articles

Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea.

Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea.

SummaryAscochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were mainly related to pathogenesis‐related proteins, disease resistance genes like NBS‐LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome datasets identified 12 miRNA‐mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be post‐transcriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.

Physical interaction between nuclear accumulated CC-NB-ARC-LRR protein and WRKY64 promotes EDS1 dependent Fusarium wilt resistance in chickpea

Fusarium wilt is one of the most serious diseases affecting chickpea (Cicer arietinum L.). Here, we identified a putative Resistance Gene Analog (CaRGA) from chickpea, encoding a coiled-coil (CC) nucleotide-binding oligomerization domain (NB-ARC) containing leucine-rich repeat (LRR) protein (CC-NLR protein) that confers resistance against Fusarium oxysporum f. sp. ciceri race1 (Foc1). Over-expression and silencing of CaRGA in chickpea resulted in enhanced resistance and hyper-susceptibility, respectively against Foc1. Furthermore, defense response to Foc1 depends on CC-NLR interaction with WRKY64 transcription factor. CaRGA mediated wilt resistance largely compromised when WRKY64 was silenced. We also determined in planta intramolecular interactions and self-association of chickpea CC-NLR protein. The study shows CC domain suppressing auto-activation of the full-length CC-NLR protein in the absence of pathogen through self-inhibitory intramolecular interaction with NB-ARC domain, which is attenuated by self-interactions to LRR domain. Chickpea CC-NLR protein forms homocomplexes and then interacts with WRKY64. CC-NLR protein further phosphorylates WRKY64 thereby, ubiquitination and proteasome mediated degradation are protected. Phosphorylated WRKY64 with increased stability binds to EDS1 promoter and stimulates its transcription that induces in planta ectopic cell-death. The detailed analysis of CC-NLR and WRKY interactions provide a better understanding of the immune regulation by NLR proteins under biotic stresses.

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea.

SummaryWhole‐genome sequencing‐based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next‐generation sequencing (NGS)‐based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR‐01 and CPR‐02. Eleven QTLs in CPR‐01 and six QTLs in CPR‐02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR‐01 using conventional biparental mapping approach were used to compare the efficiency of NGS‐based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR‐01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS‐based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR‐02 population. This study demonstrated the efficiency of NGS‐based BSA as a rapid and cost‐effective method to identify QTLs associated with ascochyta blight in chickpea.

Bukhuldaria vietnamensis mediated induced wilt resistance in chickpea

The efficacy of root dipping with Bukhuldaria vietnamensis isolate KM2 (Bv-KM2) an antagonist of Fusarium oxysporum was evaluated to improve the tolerance mechanism of chickpea against wilt. The increase in activity of key ROS enzymes of root tissues viz., peroxidase, catalase and superoxide dismutase was reported with the increase in time course of infection in resistance and susceptible varieties at 1 and 5 DAI. The pre-treatment with Bv-KM2 helps to maintain the higher level of ROS enzymes in susceptible variety JG-62, hence imparts resistance against Foc stress. In resistant variety WR-315 it further improves resistance towards Foc stress through enhanced production of ROS enzymes. The role of phenolic compounds and polyamines was studied from root tissues using HPTLC at 5 DAI. Among the polyphenols, ferulic acid was found to be constitutively expressing in both varieties over the treatment condition, the salicylic acid was found in resistant variety WR-315 over the treatment whereas it was found to be induced in susceptible variety JG-62. Four polyamines were detected through HPTLC of which two were unidentified where as two were identified as cadvarine and spermine. One of unidentified polyamiens (P2) was reported only in resistant variety WR-315 under different treatment conditions. Overall the Bv-KM2 treatment leads to alteration in ROS enzymes, polyphenols and polyamines which result in improved tolerance to Foc in both resistant and susceptible varieties.

Evaluation of chickpea (Cicer arietinum L.) irradiation-induced mutants for resistance to ascochyta blight in controlled environment

Induced mutation is one of the best alternatives for the improvement in chickpea resistance to ascochyta blight. This study was conducted to determine the lethal dose of 50% for the irradiation of chickpea seeds (LD50) and select chickpea mutant lines resistant to Ascochyta rabiei Pass. Irradiation of chickpea seeds with a range of gamma ray doses led to define the LD50 as 150 Gy. In addition, a genetic variability among plants derived by mutagenesis (M2 generation) was demonstrated by the ISSR technique. Among 36 studied mutant lines we selected three mutant lines resistant to A. rabiei in M2 and M3 generations.

MQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family gene in Ascochyta blight resistance of chickpea.

Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a serious foliar disease of chickpea (Cicer arietinum L.). Despite many genetic studies on chickpea-Ascochyta interaction, genome-wide scan of chickpea for the identification of AB-associated quantitative trait loci (QTLs) and their gene(s) has not been accomplished. To elucidate narrow QTLs for AB resistance, here, we report the use of multiple QTL-sequencing approach on 2 sets of extreme AB phenotype bulks derived from Cicer intraspecific and interspecific crosses. Two major QTLs, qABR4.1 and qABR4.2, and a minor QTL, qABR4.3, were identified on assembled chickpea pseudomolecule 4. We narrowed qABR4.1 to a "robust region" at 4.568-4.618Mb through mapping on a larger intraspecific cross-derived population and comparative analysis. Among 4 genes, the CaAHL18 gene showed higher expression under Ascochyta stress in AB resistant parent suggesting that it is the candidate gene under "robust qABR4.1." Dual-luciferase assay with CaAHL18 polymorphic cis-regulatory sequences showed that allelic variation is associated with higher expression. Thus, our findings on chickpea-Ascochyta interaction have narrowed down AB resistance associated QTLs on chickpea physical map. The narrowed QTLs and gene-associated markers will help in biotechnological and breeding programs for chickpea improvement.

Analysis of differential transcript expression in chickpea during compatible and incompatible interactions with Fusarium oxysporum f. sp. ciceris Race 4.

The present study reports the transcriptome analysis of resistance (WR315) and susceptible (JG62) genotypes of chickpea in response to Fusarium oxysporum f. sp. ciceris (Foc)race 4 using the method of suppression subtractive hybridization. Altogether, 162 chickpea-expressed sequence tags (ESTs) were identified from two libraries and analyzed to catalog eight functional categories. These ESTs could be assembled into 18 contigs and 144 singletons with 10 contigs and 68 singletons from compatible and 8 contigs and 70 singletons from incompatible interaction. The largest category consisted of ESTs which encode for proteins related to hypothetical proteins (22.8%), followed by energy and metabolism (20.3%)-related genes, defense and cell rescue-related genes (17.9%) and signal transduction-related genes (16%). Among them, 17.1 and 18.7% were defense-related genes in compatible and incompatible interaction, respectively. These ESTs mainly includes various putative genes related to oxidative burst, pathogenesis and secondary metabolism. Induction of putative superoxide dismutase, metallothionein, 4-coumarate-CoA ligase, heat shock proteins and cysteine proteases indicated oxidative burst after infection. The ESTs belonged to various functional categories which were directly and indirectly associated with defense signaling pathways. Quantitative and semi-quantitative polymerase chain reaction exhibited differential expression of candidate genes and detected higher levels in incompatible interaction compared to compatible interaction. The present study revealed partial molecular mechanism associated with the resistance in chickpea against Foc, which is the key to design a strategy for incorporation of resistance via either biotechnological means or introgression of resistance genes.

Induction of systemic resistance in chickpea against Fusarium wilt by Bacillus strains

Plant growth promoting rhizobacteria (PGPR) strains Rb29 (B. amyloliquefaciens MF352007), Bs1 (B. subtilis MF352017) and Bt1 (B. tequilensis MF352019) were tested for growth promotion and for their ability to induce systemic resistance against Fusarium wilt, a vascular disease of chickpea, using two methods that include whole plant and a split-root system. Bacillus strains and Fusarium oxysporum f. sp. ciceris (FOC) were inoculated on separate halves of roots of chickpea seedlings at the same time and then planted in separate pots either in superposition or one side of the other. All Bacillus strains systemically induced resistance against FOC, and significantly (p < 0.05) reduced the wilt disease by 98–100%. Application of Bacillus strains effectively enhanced plant growth, leading to increased plant height, root length, a fresh and dry weight of shoots and roots. These results help to explain the role of strains of Bacillus in growth promotion and biological control of Fusarium wilt in chickpea. This is the first report of systemic-induced resistance against Fusarium wilt in chickpea obtained by application of Bacillus strains to a root system spatially separated from the FOC-inoculated root.

Role of trichomes on leaves and pods for imparting resistance in chickpea [Cicer arientinum (L.)] genotypes against Helicoverpa armigera (Hübner)

In chickpea, trichomes provide a potential resistance mechanism against Helicoverpa armigera (Hübner). The present study was conducted to evaluate the trichome density and trichome length on leaves and pods on nine genotypes of chickpea. Two types of trichomes were observed, i.e. non-glandular (on leaves) and glandular (pods). Few glandular trichomes were observed on leaves and a very few non-glandular trichomes were observed on pods. Highest number of non-glandular trichomes on leaves (33.66 trichomes/mm2) were observed in chickpea genotype 5282. Minimum number of glandular trichomes were observed on pods of genotype GL 25016 (12.66 glandular trichomes per mm2). In case of leaves, genotypes ICCL 86111 and GL 25016 recorded maximum non-glandular trichome length of 347.23 and 301.53 ?m, respectively. However, genotypes GL 25016, RSG 963 and 5282 rec-orded maximum glandular trichome length of 538.33, 564.97 and 432.61 ?m, respectively in pods. Density of non glandular trichomes on leaves showed significant and negative correlation with number of eggs, larval population, larval survival and per cent pod damage. However, density of glandular trichomes on pods showed significant and positive correlation with number of eggs , larval population of H. armigera, larval survival and pod damage. Length of non-glandular trichomes on leaves and glandular trichomes on pods showed non-significant and negative correlation with number of eggs, larval population of H. armigera, larval survival and pod damage. Hence, genotypes with more pubescent leaves, lesser pubescent pods and longer trichomes (both on leaves and pods) should be preferred for developing H. armigera tolerant chickpea genotypes.

Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

Fusarium wilt is one of the major biotic stresses reducing chickpea productivity. The use of wilt-resistant cultivars is the most appropriate means to combat the disease and secure productivity. As a step towards understanding the molecular basis of wilt resistance in chickpea, we investigated the transcriptomes of wilt-susceptible and wilt-resistant cultivars under both Fusarium oxysporum f.sp. ciceri (Foc) challenged and unchallenged conditions. Transcriptome profiling using LongSAGE provided a valuable insight into the molecular interactions between chickpea and Foc, which revealed several known as well as novel genes with differential or unique expression patterns in chickpea contributing to lignification, hormonal homeostasis, plant defense signaling, ROS homeostasis, R-gene mediated defense, etc. Similarly, several Foc genes characteristically required for survival and growth of the pathogen were expressed only in the susceptible cultivar with null expression of most of these genes in the resistant cultivar. This study provides a rich resource for functional characterization of the genes involved in resistance mechanism and their use in breeding for sustainable wilt-resistance. Additionally, it provides pathogen targets facilitating the development of novel control strategies.

Association analysis of biotic and abiotic stresses resistance in chickpea (Cicer spp.) using AFLP markers

ABSTRACTChickpea suffers from different biotic and abiotic stresses, which has led to considerable decreases in seed yield. Since the economic value of a cultivar is determined by its phenotypic characteristics, good knowledge of the genetic structure and identification of genomic loci associated with desired traits will facilitate crop breeding. Amplified fragment length polymorphism (AFLP) markers associated with different agro-morphological characteristics, cold and drought tolerance as well as Ascochyta blight resistance were identified in chickpea by using 44 genotypes comprising cultigens, landraces, internationally developed improved lines and wild relatives, evaluated in a randomized complete block design with three replications at the Urmia rainfed research station. Using six AFLP primer combinations, 64 clear and reproducible markers were developed. The polymorphism information content values calculated for each primer pair ranged from 0.155 (EcoR1-ACC/Mse1-CAG) to 0.270 (EcoR1-ACC/ Mse1-CTG) with an average of 0.237. Analysis of molecular variance (AMOVA) revealed that 90% of the total variance was due to differences within populations and 10% due to differences among populations. Using a general linear model and applying multiple testing corrections, 24 AFLP markers associated with genes controlling the studied traits were identified. Some identified markers were associated with more than one trait. The identified markers could be of interest in marker-assisted selection in chickpea breeding programmes.

Identification of resistant sources and DNA markers linked to genomic region conferring dry root rot resistance in chickpea (Cicer arietinum L.)

AbstractA set of 520 chickpea germplasm lines was screened under laboratory conditions using blotter paper technique for reaction to dry root rot caused by Rhizoctonia bataticola (Taub.) Butler. The lines PG06102, BG2094 and IC552137 were identified as resistant for dry root rot. Phenotyping the mapping population consisting of 129 F2:3 progeny derived from the cross L550 × PG06102 during 2013 winter indicated monogenic inheritance of dry root rot resistance. Fifty‐two of 381 simple sequence repeat (SSR) primers polymorphic between the two parents were used to genotype F2 resistant and susceptible bulks prepared on the basis of reaction of F2:3 progeny. Four markers differentiated the resistant and susceptible bulks. All the four polymorphic markers were then assayed on the entire F2 population. Linkage analysis using 129 F2 plants revealed that two markers ICCM0299 and ICCM0120b were co‐segregating with resistance to dry root rot. These two markers appeared to have additive effects on resistance and could be potentially utilized in dry root resistance breeding programme.

Dry Root Rot Resistance in Chickpea: Studies on Genetic and Molecular Variations

Dry Root Rot Resistance in Chickpea: Studies on Genetic and Molecular Variations

Antioxidant systems, germination in chickpea under drought.

The role of antioxidant systems in resistance of chickpea and performance on germination and on number nodule. The strong correlation was found between different variable. The experiment uncovered a resistant varieties and understand the effect of antioxidant systems under drought.

Dynamics of Colonization and Expression of Pathogenicity Related Genes in Fusarium oxysporum f.sp. ciceri during Chickpea Vascular Wilt Disease Progression.

Fusarium wilt caused by Fusarium oxysporum f.sp. ciceri (Foc) is a constant threat to chickpea productivity in several parts of the world. Understanding the molecular basis of chickpea-Foc interaction is necessary to improve chickpea resistance to Foc and thereby the productivity of chickpea. We transformed Foc race 2 using green fluorescent protein (GFP) gene and used it to characterize pathogen progression and colonization in wilt-susceptible (JG62) and wilt-resistant (Digvijay) chickpea cultivars using confocal microscopy. We also employed quantitative PCR (qPCR) to estimate the pathogen load and progression across various tissues of both the chickpea cultivars during the course of the disease. Additionally, the expression of several candidate pathogen virulence genes was analyzed using quantitative reverse transcriptase PCR (qRT-PCR), which showed their characteristic expression in wilt-susceptible and resistant chickpea cultivars. Our results suggest that the pathogen colonizes the susceptible cultivar defeating its defense; however, albeit its entry in the resistant plant, further proliferation is severely restricted providing an evidence of efficient defense mechanism in the resistant chickpea cultivar.

Biochemical analysis of induced resistance in chickpea against broomrape (Orobanche foetida) by rhizobia inoculation.

This study examined the capacity of Rhizobium sp. strain PchAZM to reduce parasitism of chickpea by Orobanche foetida under greenhouse conditions, and assessed the relative impact of rhizobia on the expression of chickpea defense response against broomrape. Growth chamber experiments using Petri dishes revealed that rhizobia infection on chickpea roots reduced broomrape seed germination, and restricted the broomrape attachment to host roots while retarding tubercle formation and development by the parasite. In pot experiments, chickpea roots inoculated with rhizobia reduced the total number of broomrape by up to 90%. Broomrape necrosis was observed both before and after parasite attachment to inoculated chickpea roots in Petri dishes and pot experiments. Reduction in infection was accompanied by enhanced levels of the defence-related enzymes phenylalanine ammonia lyase (PAL) and peroxidase (POX). Increased levels of phenolics were recorded in the roots of rhizobia-inoculated plants grown in the presence of broomrape. The results suggest that rhizobia could be used for protection of chickpea against O. foetida .

Defence gene expression profiling to Ascochyta rabiei aggressiveness in chickpea.

Significant differences in defence pathway-related gene expression were observed among chickpea cultivars following A. rabiei infection. Differential gene expression is indicative of diverse resistances, a theoretical tool for selective breeding. A high number of Ascochyta rabiei pathotypes infecting chickpea in Australia has severely hampered efforts towards breeding for sustained quantitative resistance in chickpea. Breeding for sustained resistance will be aided by detailed knowledge of defence responses to isolates with different aggressiveness. As an initial step, the conserved and differential expressions of a suit of previously characterised genes known to be involved in fungal defence mechanisms were assessed among resistant and susceptible host genotypes following inoculation with high or low aggressive A. rabiei isolates. Using quantitative Real-Time PCR (qRT-PCR), 15 defence-related genes, normalised with two reference genes, were temporally differentially expressed (P<0.005) as early as 2h post inoculation of Genesis090 (resistant) or Kaniva (susceptible). The highly aggressive isolate, 09KAL09, induced vastly different expression profiles of eight key defence-related genes among resistant and susceptible genotypes. Six of these same genes were differentially expressed among ten host genotypes, inclusive of the best resistance sources within the Australian chickpea breeding program, indicating potential use for discrimination and selection of resistance "type" in future breeding pursuits.

An Update on Genetic Resistance of Chickpea to Ascochyta Blight

Ascochyta blight (AB) caused by Ascochyta rabiei (Pass.) Labr. is an important and widespread disease of chickpea (Cicer arietinum L.) worldwide. The disease is particularly severe under cool and humid weather conditions. Breeding for host resistance is an efficient means to combat this disease. In this paper, attempts have been made to summarize the progress made in identifying resistance sources, genetics and breeding for resistance, and genetic variation among the pathogen population. The search for resistance to AB in chickpea germplasm, breeding lines and land races using various screening methods has been updated. Importance of the genotype × environment (GE) interaction in elucidating the aggressiveness among isolates from different locations and the identification of pathotypes and stable sources of resistance have also been discussed. Current and modern breeding programs for AB resistance based on crossing resistant/multiple resistant and high-yielding cultivars, stability of the breeding lines through multi-location testing and molecular marker-assisted selection method have been discussed. Gene pyramiding and the use of resistant genes present in wild relatives can be useful methods in the future. Identification of additional sources of resistance genes, good characterization of the host–pathogen system, and identification of molecular markers linked to resistance genes are suggested as the key areas for future study.

Development of molecular map and identification of QTLs linked to Fusarium wilt resistance in chickpea.

A number of genetic maps for Fusarium wilt resistance in chickpea have been reported in earlier studies, however QTLs identified for Fusarium wilt resistance were unstable. Hence, the present study aims to map novel molecular markers and to identify QTLs for Fusarium wilt resistance in chickpea. An intraspecific linkage map of chickpea (Cicer arietinum L.) was constructed using F10-F11 recombinant inbred lines (RILs) derived from a cross between K850 and WR315 segregating for H2 locus. A set of 31 polymorphic simple sequence repeat (SSR) markers obtained by screening 300 SSRs and were used for genotyping. The linkage map had four linkage groups and coverage of 690 cM with a marker density of 5.72 cM. The RILs were screened for their wilt reaction across two seasons in wilt sick plot at International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, India. Five major quantitative trait loci (QTLs) were detected in both seasons for late wilting (60 days after sowing). A stable QTL (GSSR 18-TC14801) for wilt resistance was identified in both the seasons, and the QTL explained a variance of 69.80 and 60.80% in 2007 and 2008 rabi respectively.