Efficacy of Metarhizium anisopliae in controlling the two‐spotted spider mite Tetranychus urticae on common bean in screenhouse and field experiments

The efficacy of aqueous and emulsifiable formulations of the fungus Metarhizium anisopliae isolate ICIPE78 was evaluated on the population density of Tetranychus urticae infesting common bean plants under screenhouse and field conditions. Synthetic acaricide abamectin was included as a check. Bean plants were artificially infested with T. urticae and allowed to multiply. Three treatments were applied in the screenhouse and 1 treatment in field trials. Mite density was recorded 2 d before spraying and weekly postspraying. The number of pods per plant, number of seeds per pod, and the dry weight of seeds per plant were recorded only in the screenhouse trials. In both screenhouse and field trials, fungal formulations applied at the concentration of 10⁸ conidia/mL and the acaricide reduced the population density of mites as compared to the controls. There were significant differences in T. urticae population densities between the treatments at the various post‐spraying sampling dates. In the screenhouse, the mite densities were near zero from 3‐week postspraying in the treated leaves. At 4‐week postspraying, there were no more leaves in the untreated control (T1) and in the control water + Silwet‐L77 (T2). Fungal formulations were as effective as abamectin in reducing mite densities in both screenhouse and field experiments. There were significant differences in the production parameters during the 2 screenhouse trials, with fungal and abamectin treatments generally having the highest yield. Results of this study underline the potential of the M. anisopliae isolate ICIPE78 as an alternative to acaricides for T. urticae management.     

Serological and molecular characterisations of the Egyptian isolate of Bean common mosaic virus

Bean common mosaic virus (BCMV) was isolated from the naturally infected bean plants collected from the Kafr El-Sheikh and El-Gharbia Governorates. BCMV induced sever mosaic, vein banding, malformation, leaf curling and stunting on bean plants cv. Giza 6. The isolated virus was propagated in bean plants cv. Giza 6. The identification of BCMV was carried out serologically by an indirect enzyme-linked immunosorbent assay using BCMV antiserum. Positive reaction indicated that the virus under study was related serologically to Potyvirus. The molecular biology techniques were used to identify and characterise the coat protein gene of BCMV. Oligonucleotide primers were designed for BCMV according to the published nucleotide sequences of BCMV and were successfully amplified with a DNA fragment (300 bp) from BCMV CP gene by RT-PCR. The total RNA was extracted from bean leaves and was reverse-transcribed and amplified using the oligonucleotide primer. The amplified product was analysed by gel electrophoresis. Also, Southern and dot blot hybridisations were used to establish the authenticity and specificity to the RT-PCR-amplified products of BCMV. The nucleotide sequences of the Egyptian isolate of BCMV/CP showed similarity with an isolate (BCMV-NY 15) which belongs to Puerto Rico.     

Identification of Genes for Resistance to Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus in Snap Bean (Phaseolus vulgaris L.) Breeding Lines Using Conventional and Molecular Methods

Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are among the biggest threats for snap bean production in Bulgaria due to their seed, aphid and mechanical transmission. Old valuable Bulgarian snap bean varieties are being neglected, because of the high percentage of virus‐infected seeds. Breeding resistant cultivars is the best way to solve the problem. The genetic control towards both viruses is assured by one dominant I gene and a number of recessive (bc‐u, bc‐1, bc‐1², bc‐2, bc‐2² and bc‐3) genes. Our aim was to identify resistance gene combinations in advanced F8 breeding lines, derived from two crosses (A‐8‐40‐7‐2‐1 × IVT 7214) and (Zaria × RH 26D), by the application of conventional and molecular approaches. Four methods were applied for the characterization of their resistance gene makeup: (i) leaf‐abscission infection test designed to identify I gene by direct inoculation with NL3 strain of BCMNV; (ii) intact‐plant infection test with strain NY15 of BCMV to separate immune genotypes, possessing bc‐ubc‐1², bc‐ubc‐2^2,bc‐ubc‐2bc‐3, I, Ibc‐1², Ibc‐2² or Ibc‐3; (iii) PCR analysis with the following markers: SCAR – SW13 (for I gene), SBD5 (for bc‐1²), ROC11 (for bc‐3) and CAPS – eIFE4 (for bc‐3); and 4) high‐temperature (more than 30°C) infection test with NL3 of BCMNV to provoke systemic necrosis in I, Ibc‐1, Ibc‐1², Ibc‐1²bc‐2² or Ibc‐3. The four methods applied worked properly and complemented each other. Valuable gene combination (Ibc‐3) was established in seven breeding lines with immune reaction to BCMNV. They will be included in the snap bean breeding programme for virus resistance.     

Immunocapture RT-PCR detection of Bean common mosaic virus and strain blackeye cowpea mosaic in common bean and black gram in India

The strains of Bean common mosaic virus (BCMV) and blackeye cowpea mosaic (BICM), genus Potyvirus, were detected from 25 common bean and 14 black gram seeds among 142 seed samples collected from different legume-growing regions of India. The samples were subjected to a growing-on test, an indicator plant test, an electron microscopic observations, an enzyme linked immunosorbent assay and an immunocapture RT-PCR. The incidence of the two tested viruses in common bean and black gram seed samples was 1–6% and 0.5–3.5%, respectively in growing-on test evaluations. Electron microscopic observations revealed filamentous virion particles from the leaves of plants showing characteristic virus disease symptoms in growing-on and host inoculation tests. The identity of the strains was confirmed by immunocapture RT-PCR, with a final amplification product of approximately 700 bp for BCMV and BCMV–BICM. The complete identity of the two viruses was further confirmed by nucleotide sequencing of the partial coat protein and 3′-UTR regions. The sequences of the four BCMV and BCMV–BICM isolates each consisted of 583–622 and 550–577 nucleotides. The present report confirms the widespread nature of these two serious potyviruses in the two most important legume crops in India.     

Far‐eastern strains of bean common mosaic virus and methods of their immunodiagnostics

The paper presents data of investigation on the physico‐chemical and antigenic properties of capsid proteins of the Bean common mosaic virus isolated from Phaseolus plants in the Russian Far East (BCMV‐R) and from China (BCMV‐C). A method for isolation of the virus preparation was selected. The purified preparations of two isolates BCMV have been obtained. The presence of one polypeptide in structural proteins of virions was established and their molecular masses determined (BCMV‐R ‐ 31,6 kD; BCMV‐C ‐ 32,1 kD). Polyclonal antiserum was obtained with titre 1:12800 and the indirect and “sandwich"‐variants of ELISA were developed to detect this virus. The allied relationships were established with the bean yellow mosaic virus and with the type representative of the genus Potyvirus ‐ PVY. Based on the data of physico‐chemical and antigenic properties it was concluded that isolates BCMV‐R and BCMV‐C are two independent strains of this virus. The presence of strain‐, virus‐ and genusspecific epitopes of capsid proteine was revealed as a result of comparison of antigenic characteristics of the Russian Far Eastern and Chinese strains of BCMV. A high antigenic activity of capsid protein of the Russian Far Eastern strain was observed.     

Effect of azoxystrobin and kresoxim‐methyl on rice blast and rice grain yield in China

Sensitivity to azoxystrobin and kresoxim‐methyl of 80 single‐spore isolates of Magnaporthe oryzae was determined. The EC₅₀ values for azoxystrobin and kresoxim‐methyl in inhibiting mycelial growth of the 80 M. oryzae isolates were 0.006–0.056 and 0.024–0.287 µg mL^?1, respectively. The EC₅₀ values for azoxystrobin and kresoxim‐methyl in inhibiting conidial germination of the M. oryzae populations were 0.004–0.051 and 0.012–0.105 µg mL^?1, respectively. There was significant difference in sensitivity to azoxystrobin or kresoxim‐methyl between the tested isolates representing differential sensitivity to carbendazim (MBC) and kitazin P (IBP); however, there was no correlation between this difference in sensitivity to azoxystrobin or kresoxim‐methyl and sensitivity to MBC or IBP, indicating that there was no cross‐resistance between azoxystrobin or kresoxim‐methyl and MBC or IBP. In the protective and curative experiments, kresoxim‐methyl exhibited higher protective and curative activity than azoxystrobin when applied at 150 and 250 µg mL^?1 accordingly, while azoxystrobin exhibited stronger inhibitory activity against M. oryzae isolates than that of kresoxim‐methyl in the in vitro test. The results of field experiments also suggested that both azoxystrobin and kresoxim‐methyl at 187.5 g.a.i. ha^?1 gave over 73% control efficacy in both sites, exhibiting excellent activity against rice blast. Taken together, azoxystrobin and kresoxim‐methyl could be a good substitute for MBC or IBP for controlling rice blast in China, but should be carefully used as they were both at‐risk.     

The I gene of bean: a dosage-dependent allele conferring extreme resistance, hypersensitive resistance, or spreading vascular necrosis in response to the potyvirus Bean common mosaic virus

The resistance to the potyvirus Bean common mosaic virus (BCMV) conferred by the I allele in cultivars of Phaseolus vulgaris has been characterized as dominant, and it has been associated with both immunity and a systemic vascular necrosis in infected bean plants under field, as well as controlled, conditions. In our attempts to understand more fully the nature of the interaction between bean with the I resistance allele and the pathogen BCMV, we carefully varied both I allele dosage and temperature and observed the resulting, varying resistance responses. We report here that the I allele in the bean cultivars we studied is not dominant, but rather incompletely dominant, and that the system can be manipulated to show in plants a continuum of response to BCMV that ranges from immunity or extreme resistance, to hypersensitive resistance, to systemic phloem necrosis (and subsequent plant death). We propose that the particular phenotypic outcome in bean results from a quantitative interaction between viral pathogen and plant host that can be altered to favor one or the other by manipulating I allele dosage, temperature, viral pathogen, or plant cultivar.     

Potassium phosphites in the protection of common bean plants against anthracnose and biochemical defence responses

The aim of this study was to investigate the effectiveness of potassium phosphites for the control of anthracnose and the mode of action of these products on common bean plants against Colletotrichum lindemuthianum, comparing it with the standard resistance inducer acibenzolar‐S‐methyl. The protection of plants against anthracnose was evaluated in greenhouse after treatment with potassium phosphites (Phosphite A and B, 5.0 ml/L), acibenzolar‐S‐methyl (0.25 g/L), or no treatment (control). Two sprayings of the treatments were performed, respectively, at V4 stage (three trifoliate leaves) and at the R5 stage (flower buds present). The inoculation with C. lindemuthianum was performed 5 days after the first spraying. Phosphite formulations A and B reduced the severity of anthracnose by 68.7% and 55.6%, respectively, and the presence of phosphites in the leaf tissues were detected at concentrations between 1 and 3 mm by 7 days after spraying. These same concentrations of phosphites reduced the mycelial growth of C. lindemuthianum in vitro by 15.0% to 25.7%. In addition, the activities of defence enzymes and the levels of phenolic compounds and lignin were assessed. Phosphite treatments enhanced the activity of various enzymes, including superoxide dismutase, peroxidase, chitinase, and β‐1,3‐glucanase, and increased the lignin and a small increase in the levels of soluble phenolics. This study provides evidence that phosphite treatments control anthracnose by acting directly on C. lindemuthianum and by inducing the production of defence responses.     

Biological control of common blight of bean (Phaseolus vulgaris) causedby Xanthomonas axonopodis pv. phaseoli by using the bacteriumRahnella aquatilis

The aim of this study was to evaluate the bacterium Rahnella aquatilis (Ra) for protection of bean plants against common blight disease caused by Xanthomonas axonopodis pv. phaseoli (Xap). Xap isolates were isolated from a naturally blighted leaves of bean plants grown in Assiut governorate. The blight symptoms were produced by all three isolates, but the isolates differed in their degree of the pathogenicity. Xap1 was the most virulence one against bean plants. The effect of Ra against common blight of bean plant was tested. In vitro studies, Ra exhibited inhibitor effect against the pathogen. Under greenhouse and field conditions, beanvariety “Giza 6” treated by Ra resulted in marked disease suppression. Ahigh decrease of the disease was correlated with a reduction of the bacterial multiplication. In physiological studies, bean plants treated by Ra exhibited higher phenolic compounds contents and higher activity of peroxidase (PO) enzyme than untreated plants. In conclusion, application of Ra was effective and could be recommended for controlling the bean common blight disease.     

Occurrence of a New Orange Variant of Curtobacterium flaccumfaciens pv. flaccumfaciens,Causing Common Bean Wilt in Iran

A new orange variant of Curtobacterium flaccumfaciens pv. flaccumfaciens was isolated from seeds of common bean cv. Daneshkadeh and Dehghan stored in the seed banks in Khomein Bean Research Station, and field plants (cv. Local Khomein) in Arak, Iran. The pathogenicity of the isolates was confirmed on 5‐ to 7‐day‐old seedlings of cv. Daneshkadeh. Marginal necrosis and interveinal chlorosis on first trifoliate leaves were observed 10–15 days after inoculation. Amplification of 306 bp fragment of orange‐pigmented strains using CffFOR2‐ and CffREV4‐specific prime pair characterized them as C. flaccumfaciens pv. flaccumfaciens. Although the yellow‐pigmented variant of the causal agent was previously reported on cowpea, this is the first report of orange variant of C. flaccumfaciens pv. flaccumfaciens causing bacterial wilt on common bean in Iran.     

BCMV-ukr: isolate of bean common mosaic virus revealed in Ukraine

SUMMARY

Bean common mosaic virus (BCMV) is distributed worldwide and causes a serious disease in bean reducing growth and crops yield. The aim of this study was to investigate the occurrence of BCMV and Bean common mosaic necrotic virus (BCMNV) in Ukraine, to characterise host range and reactions of indicator plants to mechanical inoculation with the isolate and to differentiate it by using Drijfhout’s differentials. Leaf samples were positive for BCMV infection in RT-PCR assay employing specific primers with amplification of a 340-bp product. Based on a biological test on bean differentials, the isolate was assigned to pathogroup VII despite the fact that strain differed markedly from the standard strains in symptoms producing on differential groups IV and V. Partial sequence data of the coat protein region show 100% identity with BCMV 125 sequences tested. To our knowledge, this is the first attempt to characterise the BCMV circulating in Ukraine.     

Bean common mosaic virus and cucumber mosaic virus naturally infecting Aristolochia spp. plants in Brazil

In April 2022, Aristolochia plants with symptoms of mosaic were observed in a garden at Jardim Botânico Plantarum, Nova Odessa, São Paulo State, Brazil. Potyviridae-like particles were observed by transmission electron microscopy in leaf extracts. Total RNA extracted from symptomatic plants used in RT-PCR with universal and BCMV-specific primers detected the potyvirus bean common mosaic virus (BCMV). The cucumovirus cucumber mosaic virus (CMV) was identified only in Aristolochia littoralis plants that tested negative by RT-PCR for BCMV. Phylogenetic analysis grouped samples of Aristolochia in a different clade among samples of Phaseolus vulgaris. Phylogenetic analysis indicated that the CMV isolate from Aristolochia belongs to the CMV group IA. BCMV was mechanically transmitted to healthy plants of A. fimbriata, Chenopodium quinoa, P. vulgaris cv. Jalo and Macroptilium lathyroides. CMV was mechanically transmitted to plants of A. fimbriata and C. quinoa. The BCMV and CMV were aphid transmitted only by Aphis gossypii to Aristolochia plants. This is the first report of BCMV and CMV infecting Aristolochia plants in Brazil.     

Immunological detection of bean common mosaic virus in French bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) leaves

Bean common mosaic potyvirus (BCMV) is an important seed borne pathogen of French bean. Differential inoculation with bean common mosaic virus at cotylodonary trifoliate leaf stage and pre-flowering stage of crop growth revealed that cotyledonary leaf infection favored maximum disease expression. Under immunosorbent electron microscopy (ISEM) the virus particles of filamentous structure having a diameter of 750 nm (l) and 15 nm (w) were observed. These particles gave positive precipitin tests with polyclonal antiserum of Potato virus Y.     

Patterns of accumulation of Bean common mosaic virus in Phaseolus vulgaris genotypes nearly isogenic for the I locus

The I locus of Phaseolus vulgaris is genetically and phenotypically well described, conferring incompletely dominant, temperature‐dependent resistance against viruses currently assigned to at least four Potyvirus species. Despite the fact that the resistance allele at this locus, the I gene, has been incorporated into nearly all bean germplasm worldwide, little is known regarding its resistance mechanism. In the present study, P. vulgaris lines nearly isogenic for I were challenged with Bean common mosaic virus (BCMV; genus Potyvirus) in order to investigate at the cellular level the temperature‐dependent resistance reaction. Immunolocalisation and confocal laser scanning microscopy were employed to visualise the virus and to identify patterns of BCMV accumulation in resistant, susceptible and heterozygous genotypes. Virus was detected in all three genotypes regardless of temperature, supporting previous findings that BCMV accumulates in protoplasts containing the I allele. Genotype‐specific and temperature‐specific patterns of virus accumulation suggested a resistance mechanism that depends on host recognition of viral replication and/or local movement.     

The Intensity of a Bean Fusarium Root Rot Epidemic is Dependent on Planting Strategies

Restricting Fusarium root rot (FRR) epidemics and improving productivity using fewer chemicals is a major concern in bean‐growing regions. The main purpose of this research was to identify the planting strategies associated with FRR development and seed production in bean crops. A 2‐year study of 122 commercial bean farms in four major producing regions in Zanjan, Iran, was performed to characterize the associations of farming indicators with FRR and productivity. Linear mixed‐effect models, contingency tables and correspondence analyses were used to describe the variables relationships. Low disease and high productivity were linked to herbicide and manure applications, fungicidal treatment of seeds, manual sowing and sprinkler irrigation. Furrow irrigation, mechanical sowing, planting on raised seedbeds, the lack of fertilizer and herbicide use accounted for high disease and low seed production. The results of the study provide further evidence of factors contributions to the wider FRR spread over bean‐cropping systems. Overall, this suggests that the selected composition of planting strategies can improve bean production and reduce FRR intensity.     

Activity of fungicide mixtures against Botrytis cinerea isolates resistant to benzimidazoles,strobilurins and dicarboximides

Botrytis cinerea, the causal agent of grey mould in a broad range of crops, is considered a high‐risk plant pathogen for fungicide resistance development. The use of fungicide mixtures, particularly combinations with synergistic activity, can be a useful tactic to counteract resistance build‐up in pathogen populations. The present study aimed to investigate the effects of different ratios of two‐way mixtures of carbendazim, iprodione, kresoxim‐methyl, tebuconazole and penconazole on four B. cinerea isolates that were sensitive or resistant to benzimidazoles, dicarboximides and strobilurins. The isolates that were resistant to benzimidazoles and strobilurins had E198A and G143A mutations in β‐tubulin and cytochrome b genes, respectively. The mixtures had different effects on each of the isolates in vitro but, in 13 combinations, the synergistic effect was observed against all or three isolates. In greenhouse experiments, 11 fungicide combinations used in decreased (EC₇₅) concentrations showed the maximum control efficiency. The two follow‐up greenhouse experiments using six selected combinations revealed they were highly effective against additional isolates with various fungicide resistance profiles. The identified mixtures‐ratios have potential for use in grey mould management programs in the greenhouse.     

中国普通菜豆种质资源朊蛋白变异及多样性分析

朊蛋白是研究普通菜豆遗传多样性的一种重要且有效的生化标记。本试验通过SDS-PAEG凝胶电泳检测中国普通菜豆种质资源的朊蛋白变异类型,分析中国普通菜豆种质资源的遗传多样性及组成特点。来自中国13个省(自治区)的445份供试材料共检测到S、Sb、Sd、B、C、CA、T、PA、To、H、H1、CH 12种朊蛋白类型,表明中国普通菜豆种质朊蛋白变异类型丰富,遗传多样性水平较高。其中,Sb型朊蛋白种质最多,占比29.0%;T型其次,占比28.1%。依据朊蛋白类型在不同基因库的特异性,将研究材料明显地区分为中美基因库和安第斯基因库两大类。研究还发现中国普通菜豆种质资源中地方种质朊蛋白类型变异丰富,多样性明显高于现代育成品种或品系。最后,对种质朊蛋白类型与百粒重、子粒颜色、粒型进行相关性分析,结果表明朊蛋白类型与百粒重呈极显著正相关,而朊蛋白类型与子粒颜色、粒型2个性状之间无明显相关性。本研究结果将为普通菜豆种质资源的保护及有效地挖掘优质种质资源提供理论依据。     

Mixed Infection and Natural Spread of ‘Candidatus Phytoplasma asteris’ and Mungbean Yellow Mosaic India Virus Affecting Soya Bean Crop in India

Suspected phytoplasma and virus‐like symptoms of little leaf, yellow mosaic and witches’ broom were recorded on soya bean and two weed species (Digitaria sanguinalis and Parthenium hysterophorus), at experimental fields of Indian Agricultural Research Institute, New Delhi, India, in August–September 2013. The phytoplasma aetiology was confirmed in symptomatic soya bean and both the weed species by direct and nested PCR assays with phytoplasma‐specific universal primer pairs (P1/P6 and R16F2n/R16R2n). One major leafhopper species viz. Empoasca motti Pruthi feeding on symptomatic soya bean plants was also found phytoplasma positive in nested PCR assays. Sequencing BLASTn search analysis and phylogenetic analysis revealed that 16Sr DNA sequences of phytoplasma isolates of soya bean, weeds and leafhoppers had 99% sequence identity among themselves and were related to strains of ‘Candidatus Phytoplasma asteris’. PCR assays with Mungbean yellow mosaic India virus (MYMIV) coat‐protein‐specific primers yielded an amplicon of approximately 770 bp both from symptomatic soya bean and from whiteflies (Bemisia tabaci) feeding on soya bean, confirmed the presence of MYMIV in soya bean and whitefly. Hence, this study suggested the mixed infection of MYMIV and ‘Ca. P. asteris’ with soya bean yellow leaf and witches’ broom syndrome. The two weed species (D. sanguinalis and P. hysterophorus) were recorded as putative alternative hosts for ‘Ca. P. asteris’ soya bean Indian strain. However, the leafhopper E. motti was recorded as putative vector for the identified soya bean phytoplasma isolate, and the whitefly (B. tabaci) was identified as vector of MYMIV which belonged to Asia‐II‐1 genotype.     

Increased multiple virus resistance in transgenic soybean overexpressing the double-strand RNA-specific ribonuclease gene PAC1

Viruses constitute a major constraint to soybean production worldwide and are responsible for significant yield losses every year. Although varying degrees of resistance to specific viral strains has been identified in some soybean genetic sources, the high rate of mutation in viral genomes and mixed infections of different viruses or strains under field conditions usually hinder the effective control of viral diseases. In the present study, we generated transgenic soybean lines constitutively expressing the double-strand RNA specific ribonuclease gene PAC1 from Schizosaccharomyces pombe to evaluate their resistance responses to multiple soybean-infecting virus strains and isolates. Resistance evaluation over three consecutive years showed that the transgenic lines displayed significantly lower levels of disease severity in field conditions when challenged with soybean mosaic virus (SMV) SC3, a prevalent SMV strain in soybean-growing regions of China, compared to the non-transformed (NT) plants. After inoculation with four additional SMV strains (SC7, SC15, SC18, and SMV-R), and three isolates of bean common mosaic virus (BCMV), watermelon mosaic virus (WMV), and bean pod mottle virus (BPMV), the transgenic plants exhibited less severe symptoms and enhanced resistance to virus infections relative to NT plants. Consistent with these results, the accumulation of each virus isolate was significantly inhibited in transgenic plants as confirmed by quantitative real-time PCR and double antibody sandwich enzyme-linked immunosorbent assays. Collectively, our results showed that overexpression of PAC1 can increase multiple virus resistance in transgenic soybean, and thus provide an efficient control strategy against RNA viruses such as SMV, BCMV, WMV, and BPMV.

     

Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean

Background

Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV).

Results

We physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study.

Conclusions

We demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-903) contains supplementary material, which is available to authorized users.