Identification of Sources of Multiple Disease Resistance in Mini-core Collection of Chickpea

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance

Pratylenchus thornei is an economically important species of root-lesion nematode adversely affecting chickpea (Cicer arietinum) yields globally. Integration of resistant crops in farming systems is recognised as the most effective and sustainable management strategy for plant-parasitic nematodes. However, breeding for P. thornei resistance in chickpea is limited by the lack of genetic diversity. We deployed a genome-wide association approach to identify genomic regions and candidate genes associated with P. thornei resistance in 285 genetically diverse chickpea accessions. Chickpea accessions were phenotyped for P. thornei resistance in replicated glasshouse experiments performed for two years (2018 and 2020). Whole genome sequencing data comprising 492,849 SNPs were used to implement six multi-locus GWAS models. Fourteen chickpea genotypes were found to be resistant to P. thornei. Of the six multi-locus GWAS methods deployed, FASTmrMLM was found to be the best performing model. In all, 24 significant quantitative trait nucleotides (QTNs) were identified, of which 13 QTNs were associated with lower nematode population density and 11 QTNs with higher nematode population density. These QTNs were distributed across all of the chickpea chromosomes, except chromosome 8. We identified, receptor-linked kinases (RLKs) on chromosomes 1, 4 and 6, GDSL-like Lipase/Acylhydrolase on chromosome 3, Aspartic proteinase-like and Thaumatin-like protein on chromosome 4, AT-hook DNA-binding and HSPRO2 on chromosome 6 as candidate genes for P. thornei resistance in the chickpea reference set. New sources of P. thornei resistant genotypes were identified that can be harnessed into breeding programs and putative candidate P. thornei resistant genes were identified that can be explored further to develop molecular markers and accelerate the incorporation of improved P. thornei resistance into elite chickpea cultivars.

Ascochyta rabiei: A threat to global chickpea production

The necrotrophic fungus Ascochyta rabiei causes Ascochyta blight (AB) disease in chickpea. A. rabiei infects all aerial parts of the plant, which results in severe yield loss. At present, AB disease occurs in most chickpea-growing countries. Globally increased incidences of A. rabiei infection and the emergence of new aggressive isolates directed the interest of researchers toward understanding the evolution of pathogenic determinants in this fungus. In this review, we summarize the molecular and genetic studies of the pathogen along with approaches that are helping in combating the disease. Possible areas of future research are also suggested.

TAXONOMY

kingdom Mycota, phylum Ascomycota, class Dothideomycetes, subclass Coelomycetes, order Pleosporales, family Didymellaceae, genus Ascochyta, species rabiei.

PRIMARY HOST

A. rabiei survives primarily on Cicer species.

DISEASE SYMPTOMS

A. rabiei infects aboveground parts of the plant including leaves, petioles, stems, pods, and seeds. The disease symptoms first appear as watersoaked lesions on the leaves and stems, which turn brown or dark brown. Early symptoms include small circular necrotic lesions visible on the leaves and oval brown lesions on the stem. At later stages of infection, the lesions may girdle the stem and the region above the girdle falls off. The disease severity increases at the reproductive stage and rounded lesions with concentric rings, due to asexual structures called pycnidia, appear on leaves, stems, and pods. The infected pod becomes blighted and often results in shrivelled and infected seeds.

DISEASE MANAGEMENT STRATEGIES

Crop failures may be avoided by judicious practices of integrated disease management based on the use of resistant or tolerant cultivars and growing chickpea in areas where conditions are least favourable for AB disease development. Use of healthy seeds free of A. rabiei, seed treatments with fungicides, and proper destruction of diseased stubbles can also reduce the fungal inoculum load. Crop rotation with nonhost crops is critical for controlling the disease. Planting moderately resistant cultivars and prudent application of fungicides is also a way to combat AB disease. However, the scarcity of AB-resistant accessions and the continuous evolution of the pathogen challenges the disease management process.

USEFUL WEBSITES

https://www.ndsu.edu/pubweb/pulse-info/resourcespdf/Ascochyta%20blight%20of%20chickpea.pdf https://saskpulse.com/files/newsletters/180531_ascochyta_in_chickpeas-compressed.pdf http://www.pulseaus.com.au/growing-pulses/bmp/chickpea/ascochyta-blight http://agriculture.vic.gov.au/agriculture/pests-diseases-and-weeds/plant-diseases/grains-pulses-and-cereals/ascochyta-blight-of-chickpea http://www.croppro.com.au/crop_disease_manual/ch05s02.php https://www.northernpulse.com/uploads/resources/722/handout-chickpeaascochyta-nov13-2011.pdf http://oar.icrisat.org/184/1/24_2010_IB_no_82_Host_Plant https://www.crop.bayer.com.au/find-crop-solutions/by-pest/diseases/ascochyta-blight.

An Evaluation of Aluminum Tolerant Pseudomonas aeruginosa A7 for In Vivo Suppression of Fusarium Wilt of Chickpea Caused by Fusarium oxysporum f. sp. ciceris and Growth Promotion of Chickpea

Chickpea wilt, caused by Fusarium oxysporum f. sp. ciceris, is a disease that decreases chickpea productivity and quality and can reduce its yield by as much as 15%. A newly isolated, moss rhizoid-associated Pseudomonas aeruginosa strain A7, demonstrated strong inhibition of Fusarium oxysporum f. sp. ciceris growth. An in vitro antimicrobial assay revealed A7 to suppress the growth of several fungal and bacterial plant pathogens by secreting secondary metabolites and by producing volatile compounds. In an in vivo pot experiment with Fusarium wilt infection in chickpea, the antagonist A7 exhibited a disease reduction by 77 ± 1.5%, and significantly reduced the disease incidence and severity indexes. Furthermore, A7 promoted chickpea growth in terms of root and shoot length and dry biomass during pot assay. The strain exhibited several traits associated with plant growth promotion, extracellular enzymatic production, and stress tolerance. Under aluminum stress conditions, in vitro growth of chickpea plants by A7 resulted in a significant increase in root length and plant biomass production. Additionally, hallmark genes for antibiotics production were identified in A7. The methanol extract of strain A7 demonstrated antimicrobial activity, leading to the identification of various antimicrobial compounds based on retention time and molecular weight. These findings strongly suggest that the strain’s significant biocontrol potential and plant growth enhancement could be a potential environmentally friendly process in agricultural crop production.

Core Collections: Is There Any Value for Cotton Breeding?

Global plant breeding activities are reliant on the available genetic variation held in extant varieties and germplasm collections. Throughout the mid- to late 1900s, germplasm collecting efforts were prioritized for breeding programs to archive precious material before it disappeared and led to the development of the numerous large germplasm resources now available in different countries. In recent decades, however, the maintenance and particularly the expansion of these germplasm resources have come under threat, and there has been a significant decline in investment in further collecting expeditions, an increase in global biosecurity restrictions, and restrictions placed on the open exchange of some commercial germplasm between breeders. The large size of most genebank collections, as well as constraints surrounding the availability and reliability of accurate germplasm passport data and physical or genetic characterization of the accessions in collections, limits germplasm utilization by plant breeders. To overcome these constraints, core collections, defined as a representative subset of the total germplasm collection, have gained popularity. Core collections aim to increase germplasm utilization by containing highly characterized germplasm that attempts to capture the majority of the variation in a whole collection. With the recent availability of many new genetic tools, the potential to unlock the value of these resources can now be realized. The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program supplies 100% of the cotton cultivars grown in Australia. The program is reliant on the use of plant genetic resources for the development of improved cotton varieties to address emerging challenges in pest and disease resistance as well as the global changes occurring in the climate. Currently, the CSIRO germplasm collection is actively maintained but underutilized by plant breeders. This review presents an overview of the Australian cotton germplasm resources and discusses the appropriateness of a core collection for cotton breeding programs.

A sick plot-based protocol for dry root rot disease assessment in field-grown chickpea plants

PREMISE

A comprehensive field-based screening protocol is lacking for dry root rot (DRR) disease in chickpea, which is caused by Macrophomina phaseolina (formerly referred to as Rhizoctonia bataticola). Here, we describe a protocol for establishing a sick plot for DRR to enable disease assessment of a large number of chickpea plants during the natural growing season.

METHODS AND RESULTS

We used a chickpea plot with >30% DRR incidence, and enriched the inoculum by cultivating highly susceptible chickpea plant genotypes and incorporating infected plant material into the soil. The chickpea plants were then subjected to infection in developed sick plots with various levels of soil moisture under natural field conditions.

CONCLUSIONS

Our protocol provides a robust way to impose M. phaseolina infection on chickpea plants under natural field conditions and to investigate plant responses to the infection at morphological, physiological, and molecular levels. This method can also be used to screen for other soil-borne diseases in a variety of plants.

Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories

BACKGROUND

The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. Further, using transcriptomic profiling, we sought to identify gene expression patterns that characterize highly nodulated genotypes.

RESULTS

A study involving six chickpea varieties demonstrated large genotype by soil nitrogen interaction effects on nodulation and further identified agronomic traits of genotypes (such as shoot weight) associated with high nodulation. We broadened our scope to consider 29 varieties and breeding lines to examine the relationship between soilborne disease resistance and the number of nodules developed and real-time nitrogen fixation. Results of this larger study supported the earlier genotype specific findings, however, disease resistance did not explain differences in nodulation across genotypes. Transcriptional profiling of six chickpea genotypes indicates that genes associated with signalling, N transport and cellular localization, as opposed to genes associated with the classical nodulation pathway, are more likely to predict whether a given genotype will exhibit high levels of nodule formation.

CONCLUSIONS

This research identified a number of key abiotic and genetic factors affecting chickpea nodule development and nitrogen fixation. These findings indicate that an improved understanding of genotype-specific factors affecting chickpea nodule induction and function are key research areas necessary to improving the benefits of rhizobial symbiosis in chickpea.

Field-Relevant New Sources of Resistance to Anthracnose Caused by Colletotrichum truncatum in a Mungbean Mini-Core Collection

Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives

Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, and M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri, and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars.

Biochemical diversity evaluation in chickpea accessions employing mini-core collection

The seeds of chickpea provide an exceptional source of dietary proteins and is one of the important legumes in both developed and developing countries over the world. The available germplasm of cultivated chickpea is deficient in desired biochemical signatures. To identify new sources of variations for breeding, reduced subsets of germplasm such as mini-core collection can be explored as an effective resource. In the present investigation, mini-core collections consisting of 215 accessions of chickpea were extensively evaluated for tapping biochemical diversity. Analysis included ten biochemical parameters comprising total protein, total free amino acids, phytic acid, tannin, total phenolics, total flavonoids, lectin, DPPH radical scavenging activity, in vitro digestibility of protein and starch. The spectrum of diversity was documented for total protein (4.60-33.90%), total free amino acids (0.092-9.33 mg/g), phytic acid (0.009-4.06 mg/g), tannin (0.232-189.63 mg/g), total phenolics (0.15-0.81 mg/g), total flavonoids (0.04-1.57 mg/g), lectin (0.07-330.32 HU/mg), DPPH radical scavenging activity (26.74-49.11%), in vitro protein digestibility (59.45-76.22%) and in vitro starch digestibility (45.63-298.39 mg of maltose/g). The principal component analysis revealed association of chickpea higher protein content to the lower level of total phenolics and flavonoid contents. The dendrogram obtained by unweighted pair group method using arithmetic average cluster analysis grouped the chickpea accessions into two major clusters. This is the first comprehensive report on biochemical diversity analysed in the mini-core chickpea accessions. The ultimate purpose of conducting such studies was to deliver information on nutritional characteristics for effective breeding programmes. Depending on the objectives of the breeding aforesaid accessions could be employed as a parent.

A Case of Need: Linking Traits to Genebank Accessions

Genebanks are responsible for collecting, maintaining, characterizing, documenting, and distributing plant genetic resources for research, education, and breeding purposes. The rationale for requests of plant materials varies highly from areas of anthropology, social science, small-holder farmers, the commercial sector, rehabilitation of degraded systems, all the way to crop improvement and basic research. Matching "the right" accessions to a particular request is not always a straightforward process especially when genetic resource collections are large and the user does not already know which accession or even which species they want to study. Some requestors have limited knowledge of the crop; therefore, they do not know where to begin and thus, initiate the search by consultation with crop curators to help direct their request to the most suitable germplasm. One way to enhance the use of genebank material and aid in the selection of genetic resources is to have thoroughly cataloged agronomic, biochemical, genomic, and other traits linked to genebank accessions. In general, traits of importance to most users include genotypes that thrive under various biotic and abiotic stresses, morphological traits (color, shape, size of fruits), plant architecture, disease resistance, nutrient content, yield, and crop specific quality traits. In this review, we discuss methods for linking traits to genebank accessions, examples of linked traits, and some of the complexities involved, while reinforcing why it is critical to have well characterized accessions with clear trait data publicly available.

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 4.568-4.618 Mb 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.

Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes

The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs.

Quantitative and microscopic assessment of compatible and incompatible interactions between chickpea cultivars and Fusarium oxysporum f. sp. ciceris races

BACKGROUND

Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris, a main threat to global chickpea production, is managed mainly by resistant cultivars whose efficiency is curtailed by Fusarium oxysporum f. sp. ciceris races.

METHODOLOGY

We characterized compatible and incompatible interactions by assessing the spatial-temporal pattern of infection and colonization of chickpea cvs. P-2245, JG-62 and WR-315 by Fusarium oxysporum f. sp. ciceris races 0 and 5 labeled with ZsGreen fluorescent protein using confocal laser scanning microscopy.

FINDINGS

The two races colonized the host root surface in both interactions with preferential colonization of the root apex and subapical root zone. In compatible interactions, the pathogen grew intercellularly in the root cortex, reached the xylem, and progressed upwards in the stem xylem, being the rate and intensity of stem colonization directly related with the degree of compatibility among Fusarium oxysporum f. sp. ciceris races and chickpea cultivars. In incompatible interactions, race 0 invaded and colonized 'JG-62' xylem vessels of root and stem but in 'WR-315', it remained in the intercellular spaces of the root cortex failing to reach the xylem, whereas race 5 progressed up to the hypocotyl. However, all incompatible interactions were asymptomatic.

CONCLUSIONS

The differential patterns of colonization of chickpea cultivars by Fusarium oxysporum f. sp. ciceris races may be related to the operation of multiple resistance mechanisms.

Resistance to Foliar Diseases in a Mini-Core Collection of Sorghum Germplasm

Anthracnose, leaf blight, and rust are important biotic constraints to grain and forage sorghum production worldwide and are best managed through host plant resistance. A sorghum mini-core collection, consisting of 242 germplasm accessions developed from a core collection of 2,246 landrace accessions originating from 58 countries, was evaluated to identify sources of resistance to foliar diseases. The mini-core accessions were evaluated in anthracnose- and leaf-blight-screening nurseries under artificial inoculation in the rainy and late rainy seasons, respectively, during 2009 and 2010. For rust resistance, screening was done under artificial inoculation in the greenhouse as well as in the field under natural infection. In all, 13 accessions were found resistant (score ≤3.0 on a 1-to-9 scale) to anthracnose and 27 to leaf blight in both 2009 and 2010. Six accessions exhibited resistance to rust in both the greenhouse and the field. In the resistant accessions, a wide range of diversity was observed for agronomic traits such as days to 50% flowering, plant height, and grain yield/plant, and morphological characteristics such as grain or glume color, glume coverage, endosperm texture, and panicle type (ear head compactness). Three mini-core accessions (IS 473, IS 23684, and IS 23521) exhibited resistance to all three diseases. These accessions with multiple disease resistance will be useful in sorghum disease resistance breeding programs.

Mapping QTLs for improving grain yield using the USDA rice mini-core collection

Yield is the most important and complex trait for genetic improvement in crops, and marker-assisted selection enhances the improvement efficiency. The USDA rice mini-core collection derived from over 18,000 accessions of global origins is an ideal panel for association mapping. We phenotyped 203 O. sativa accessions for 14 agronomic traits and identified 5 that were highly and significantly correlated with grain yield per plant: plant height, plant weight, tillers, panicle length, and kernels/branch. Genotyping with 155 genome-wide molecular markers demonstrated 5 main cluster groups. Linkage disequilibrium (LD) decayed at least 20 cM and marker pairs with significant LD ranged from 4.64 to 6.06% in four main groups. Model comparisons revealed that different dimensions of principal component analysis affected yield and its correlated traits for mapping accuracy, and kinship did not improve the mapping in this collection. Thirty marker-trait associations were highly significant, 4 for yield, 3 for plant height, 6 for plant weight, 9 for tillers, 5 for panicle length and 3 for kernels/branch. Twenty-one markers contributed to the 30 associations, because 8 markers were co-associated with 2 or more traits. Allelic analysis of OSR13, RM471 and RM7003 for their co-associations with yield traits demonstrated that allele 126 bp of RM471 and 108 bp of RM7003 should receive greater attention, because they had the greatest positive effect on yield traits. Tagging the QTLs responsible for multiple yield traits may simultaneously help dissect the complex yield traits and elevate the efficiency to improve grain yield using marker-assisted selection in rice.

In planta and soil quantification of Fusarium oxysporum f. sp. ciceris and evaluation of Fusarium wilt resistance in chickpea with a newly developed quantitative polymerase chain reaction assay

Fusarium wilt of chickpea caused by Fusarium oxysporum f. sp. ciceris can be managed by risk assessment and use of resistant cultivars. A reliable method for the detection and quantification of F. oxysporum f. sp. ciceris in soil and chickpea tissues would contribute much to implementation of those disease management strategies. In this study, we developed a real-time quantitative polymerase chain reaction (q-PCR) protocol that allows quantifying F. oxysporum f. sp. ciceris DNA down to 1 pg in soil, as well as in the plant root and stem. Use of the q-PCR protocol allowed quantifying as low as 45 colony forming units of F. oxysporum f. sp. ciceris per gram of dry soil from a field plot infested with several races of the pathogen. Moreover, the q-PCR protocol clearly differentiated susceptible from resistant chickpea reactions to the pathogen at 15 days after sowing in artificially infested soil, as well as the degree of virulence between two F. oxysporum f. sp. ciceris races. Also, the protocol detected early asymptomatic root infections and distinguished significant differences in the level of resistance of 12 chickpea cultivars that grew in that same field plot infested with several races of the pathogen. Use of this protocol for fast, reliable, and cost-effective quantification of F. oxysporum f. sp. ciceris in asymptomatic chickpea tissues at early stages of the infection process can be of great value for chickpea breeders and for epidemiological studies in growth chambers, greenhouses and field-scale plots.

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.

Resistance to Grain Mold and Downy Mildew in a Mini-Core Collection of Sorghum Germplasm

Grain mold and downy mildew are important biotic constraints to grain sorghum (Sorghum bicolor) production worldwide and are best managed through host plant resistance. A sorghum mini-core collection composed of 242 germplasm accessions developed from a core collection of 2,246 landrace accessions from 58 countries was evaluated to identify sources of grain mold and downy mildew resistance. Of the 242 accessions, 140 that flowered during the rainy season (the other 102 accessions were photoperiod sensitive) were screened for grain mold resistance in a grain mold nursery under field epiphytotic conditions during 2007 and 2008. All 242 accessions were screened for downy mildew in the greenhouse using a sandwich inoculation technique. Fifty accessions were resistant to grain mold (≤10% mean severity). These resistant accessions represented four basic and six intermediate races of sorghum that originated from 21 countries and exhibited considerable diversity for agronomic and morphological traits. Downy mildew resistance (mean incidence ≤10%) was observed only in six (IS 28747, IS 31714, IS 23992, IS 27697, IS 28449, and IS 30400) of the 242 accessions. One accession, IS 23992, exhibited resistance to both the diseases. The morphologically and agronomically diverse accessions that are resistant to grain mold or downy mildew should be useful to sorghum disease resistance breeding programs.

Infection by Meloidogyne artiellia does not break down resistance to races 0, 1a, and 2 of Fusarium oxysporum f. sp. ciceris in chickpea genotypes

Fusarium oxysporum f. sp. ciceris, and the root-knot nematode Meloidogyne artiellia, coinfect chickpea crops in several countries of the Mediterranean Basin. The influence of root infection by M. artiellia on the reactions of chickpea genotypes with different reaction to infection with F. oxysporum f. sp. ciceris races 0, 1A, and 2 was investigated under controlled environmental conditions. Results demonstrated that co-infection of chickpea genotypes resistant to specific fungal races by M. artiellia did not influence the Fusarium wilt reaction of the plant, irrespective of the F. oxysporum f. sp. ciceris race assayed. However, in some of the assayed combinations, coinfection by both pathogens significantly affected the level of colonization by the fungus or reproduction of the nematode in the root system. Thus, coinfection of chickpea plants with Foc-0 and M. artiellia significantly decreased the level of colonization of the root system by F. oxysporum f. sp. ciceris in genotypes 'CA 336.14.3.0' and 'PV 61', but not in 'ICC 14216 K' and 'UC 27'. Similarly, the nematode reproduction index was also significantly reduced by coinfection with Foc-0 in the four chickpea genotypes tested and inoculated with this race. Conversely, coinfection of chickpea plants with Foc-1A and M. artiellia significantly increased colonization of the root system by the fungus in all genotypes inoculated with this race, except for line BG 212. Altogether, we confirmed the complete resistance phenotype of 'UC 27' and 'ICC 14216 K' to Foc-0, and of 'ICC 14216 K' to Foc-1A and Foc-2, and demonstrated that this resistance was not modified by coinfection of the resistant plant with M. artiellia.