Category Archives: ORIGINAL ARTICLE

Identification of potential sources of mungbean yellow mosaic India virus resistance in black gram (Vigna mungo) and expression of antioxidants and R‐genes modulating resistance response in cultivated and its two wild relatives

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Abstract

Black gram is one of the most important short duration grain legume, which contributes significantly towards nutritional security and environmental sustainability. The virus specific primers confirms the presence of mungbean yellow mosaic India virus (MYMIV) in representative samples. A total of 27 cultivated and two wild species were found as highly resistant (HR) to MYMIV and validated through molecular markers. The start codon target (SCoT) markers analysis revealed that the SCoT loci, namely, SCoT-4 (2200 bp), SCot-9 (1150/ 1200 bp), SCoT-15 (1150/1100 bp), SCoT-16 (700 bp), SCoT-24 (2500 bp), SCoT-25 (700 bp), SCoT-33 (900/1000 bp), and SCoT-34 (600 bp), were found unique, able to distinguish HR and highly susceptible (HS) genotypes. Biochemical characterization and gene expression profiling revealed the higher expression of antioxidants and R-genes just after pathogen inoculation indicated the activation of defence mechanism in both cultivated and its wild relatives, which modulates the resistant responses in cultivated and wild accessions. These information will be really helpful in accelerating resistance breeding in black gram.

Genetic analysis and identification of SSR marker linked to Phomopsis blight resistance in eggplant (Solanum melongena L.)

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Abstract

The present investigation was carried out to decipher inheritance of resistance and to identify linked SSR markers for Phomopsis blight resistance in eggplant. An F2 population comprising 161 plants was developed from the cross of Pusa Kranti and BR-40-7. Genetic analysis was carried out using Chi square test. Artificial inoculation of fruits was carried out using pin prick method, and scoring was done as per the standard scoring scale. The F2 plants segregated into 92 susceptible (77—highly susceptible, 15—susceptible): 69 resistant (17—highly resistant, 27—resistant, 25—moderately resistant) suggesting complimentary epistasis with ratio of 9:7. To identify the putatively linked markers to resistance gene, parental polymorphic markers were subjected to bulk segregant analysis (BSA), and two markers (emk03O04 and emf11A03) could differentiate resistant and susceptible bulk and co-segregated with resistance gene. The genetic distance between the identified markers was found to be 18.12 cM using QTL IciMapping V3.2 software depicting two new QTLs on chromosome number 6. The identified QTLs have great significant importance in marker assisted breeding programme.

Characterization of resistance to angular leaf spot of common bean (Phaseolus vulgaris L.) breeding line SPS50HB

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Abstract

The common bean (Phaseolus vulgaris L.) makes an important contribution to the human diet, particularly in Africa and Latin America. Because angular leaf spot (ALS), caused by the fungal pathogen Pseudocercospora griseola, is one of the most severe foliar diseases of the bean plant, an important priority is to identify genes encoding resistance. The present study focused on the resistance shown by the Mesoamerican common bean breeding line SPS50HB. From the pattern of segregation for resistance displayed in an F2 population bred from a cross between SPS50HB and the ALS-susceptible Ethiopian variety Red Wolaita, it was concluded that the resistance of SPS50HB is controlled by two unlinked dominant genes. An allelism test indicated that one of these genes was either identical with, allelic to, or closely linked to the major gene Phg-2 carried by variety Mexico 54. The sequence-characterized amplified region assays OPEO4 and PF13, which are diagnostic for an ALS resistance gene carried by the germplasm accession G10909, both tracked a possible second gene present in SPS50HB.

Morphological and molecular characterization of Fusarium incarnatum as a causal disease agent of pepper (Capsicum annuum) fruit rot

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Abstract

Chilli pepper (Capsicum annuum L.) is one of the most important commercially cultivated and consumed vegetables in Turkey. During a disease survey, typical symptoms of fruit rot were observed on mature chilli pepper fruits in several surveyed fields and on dried pepper fruits obtained from local retailers/bazaars in Hatay Province, Turkey. Disease incidence varied from 15 to 45% of the plants in the inspected fields. Following standard isolation procedures, 40 fungal isolates were isolated, purified and single-spore cultures were obtained from surface-disinfected, rotted dried pepper tissue. Of these isolates, six fungal isolates with dense, cottony white aerial mycelia that became beige with age, were isolated on a potato sucrose agar. All isolates were found to be pathogenic on artificially inoculated chilli pepper fruit. Based on morphological characteristics, the isolates were initially identified as Fusarium incarnatum (Desm.) Sacc. 1886. Morphological identification of F. incarnatum isolates was further confirmed by MALDI-TOF and molecular analyses using the sequences of the i nternal t ranscribed s pacer (ITS), partial t ranslation e longation f actor-1α (TEF-1α) and second largest subunit of RNA polymerase II (RPB2) loci. Phylogenetic analysis based on ITS, TEF-1α, RPB2 and concatenation of TEF-1α, RPB2 loci sequences performed with several isolates of Fusarium spp. confirmed that representative fungal isolates (MKUZF1 and MKUZF4) belong to F. incarnatum. To our knowledge, this is the first report of F. incarnatum causing fruit rot in chilli peppers grown in Turkey.

Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits

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Abstract

Pumpkins are important vegetable crops widely grown worldwide, and seeds are considered a popular nutraceutical food and an excellent source of protein, oil, and vitamins. Seed size is one of the most important targets for commercial breeding in Cucurbita species; studies have shown that pumpkin seed size variation has a similar trend with fruit size, shape, and seed yield. However, few studies have been conducted to identify genetic loci controlling seed-related traits in cultivated pumpkins. This study analyzed the genomic characteristics of pumpkin breeding materials of 321 Cucurbita accessions collected worldwide, including Cucurbita moschata, Cucurbita maxima, and Cucurbita pepo, using extensive single nucleotide polymorphisms obtained from the genotyping-by-sequencing method, significant genetic variations were identified within and between Cucurbita species. Four major cultivar fruit types were further revealed in C. moschata species, and significant differentiation patterns were detected in several chromosomal regions. A total of 15 significant loci associated with pumpkin seed traits were mapped through a genome-wide association approach; 32 genes previously reported to be associated with seed size regulation in Arabidopsis and Oryza sativa were located in the intervals defined by linkage disequilibrium. Through this study, we gained a deep understanding of the genomic variation distribution across Cucurbita species. The available genetic resources and the associated genetic contents could be used in commercial pumpkin breeding and will facilitate molecular marker-assisted selection in pumpkin seed trait improvement.

Genetic diversity and resistance assessment among maize genotypes against banded leaf and sheath blight (caused by Rhizoctonia solani f. sp. sasakii) utilizing SSR markers

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Abstract

A field investigation was carried out during the consecutive kharif seasons of 2021 and 2022 to assess the resistance response of 38 maize genotypes against banded leaf and sheath bight (BLSB). The trials were conducted at CCS Haryana Agricultural University, Regional Research Station, Karnal (India) under artificial epiphytotic conditions. Throughout both seasons, six genotypes (HKI 163, HKI 193-2, HKI 488, IQPMH-18-2, HKI 194-7 and HKI 1128) exhibited resistant reactions, one genotype (HM 8) showed susceptible reaction, whereas 19 genotypes showed moderately resistant response to BLSB. To analyse molecular aspects of BLSB resistance, genomic DNA was extracted and PCR amplification was performed using 22 SSR markers. Ten SSR markers (bnlg238, bnlg161, bnlg127, bnlg339, bnlg615, bnlg1272, phi077, phi080, phi035 and umc1275) revealed distinct banding patterns in resistant and susceptible genotypes. Among these, marker bnlg339 exhibited a band size of 120 bp across 14 genotypes, with six (HKI 163, HKI 193-2, HQPM 5, IQPMH-18-2, HKI 194-7 and HKI 1128) classified as resistant and eight (HKI 193-1, HKI 1657, HKI 1378, HPQM 1, HKI 1659, HPQM 2, T Bio 259 ER and HKI 191-2-5) as moderately resistant, resembling the amplified profile of the resistant check genotype (HKI 163). Similarly, the markers phi080 and bnlg1272 exhibited differential amplified profile of approximately 150 bp and 240 bp, respectively, in 10 (five resistant and five moderately resistant) and 12 (four resistant and eight moderately resistant) maize genotypes throughout the study. The percentage of polymorphism for the SSR markers varied from 0 to 100%, with an average value of 95.45% per primer among all genotypes. The identification of resistant and moderately resistant genotypes and characterization of specific SSR markers associated with resistance offer practical tools for breeders to develop BLSB-resistant maize varieties, ultimately enhancing crop resilience and food security.

Identification and characterization of Entyloma eschscholziae, a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.

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Identification and characterization of Entyloma eschscholziae, a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.

The morphology, phylogeny and species boundaries of Entyloma eschscholziae are revisited, and a new species Entyloma dendromeconis is described.


Abstract

Entyloma includes pathogenic and saprobic species that infect or colonize dicotyledonous host plants. Although most Entyloma species are known only from native areas of occurrence, some species were introduced with their host plants and spread outside their natural areas. The identification of introduced species is important for detection and management of invasive species. In this study, the morphology, phylogeny and species boundaries of Entyloma eschscholziae, recently introduced from North America to Europe, are revisited. Morphology was similar among the type and other specimens of E. eschscholziae analysed on Eschscholzia californica. Both asexual and sexual morphs were observed. The rDNA ITS1-5.8S-ITS2 sequences of the E. eschscholziae specimens from Europe and New Zealand and the environmental sequence obtained from grassland soil in California, United States, were identical. Morphological and molecular analyses confirm that the causative agents of white smut on E. californica in native (North America) and introduced (Europe, New Zealand) areas belong to the same species. DNA barcodes obtained in this study (especially ITS sequence from the designated epitype specimen) could be used to facilitate its molecular identification. Specimens on Dendromecon rigida, previously assigned to E. eschscholziae, are morphologically distinct. An attempt to obtain DNA barcode data from degraded holotype material was not successful and no more recent material is available. However, based on the morphological differences and high host specificity found in Entyloma spp., it is appropriate to describe a new species, Entyloma dendromeconis, for this smut pathogen.

Cucurbit chlorotic yellows virus, a crinivirus infecting Cannabis sativa plants

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Cucurbit chlorotic yellows virus, a crinivirus infecting Cannabis sativa plants

Cucurbit chlorotic yellows virus (CCYV-Can), a crinivirus, was transmitted by the whitefly Bemisia tabaci to Cannabis sativa plants causing interveinal chlorosis and leaf yellowing in high-CBD plants.


Abstract

High cannabidiol-containing plants of Cannabis sativa (high-CBD) growing in farms in Israel displayed foliar symptoms of interveinal chlorosis and yellowing, brittleness and occasionally necrosis. These symptoms, which were more apparent in older leaves, resembled those caused by the crinivirus lettuce chlorosis virus (LCV). However, this virus was not detected by reverse transcription (RT)-PCR using specific primer sets. High-throughput sequencing of viral RNA extracted from symptomatic leaves revealed the presence of cucurbit chlorotic yellows virus (CCYV), a crinivirus in the Closteroviridae family. The complete viral genome sequence was obtained using RT-PCR followed by Sanger sequencing. The two CCYV RNA genomic segments shared 99.5%–99.85% nucleotide sequence identity with CCYV isolates from the GenBank. The virus was transmitted from symptomatic cannabis leaves to healthy plants of cannabis and Cucumis sativus ‘King Star’ (cucumber) by the whitefly Bemisia tabaci Middle Eastern Asia Minor 1 (MEAM1) species, causing disease symptoms identical to those of the donor plants. Cannabis-CCYV was also transmitted between infected cucumber plants and cannabis seedlings of unknown genotype. Severe disease symptoms of yellowing and leaf-edge necrosis were observed on high-CBD and high Δ9-tetrahydrocannabinol-containing (high-THC) flowering cannabis plants and were associated with mixed infections of LCV and CCYV. To the best of our knowledge, this is the first report of CCYV infecting C. sativa plants.

QTL mapping and candidate gene analysis of low‐temperature tolerance at the germination stage of soybean

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Abstract

When soybean seeds encounter low temperature during germination, the vigour and germination of soybean seeds are affected, which leads to a lack of seedlings and weak seedlings, resulting in yield reduction. In-depth analysis of the genetic mechanism of soybean seed germination tolerance to low-temperature stress and the cultivation of soybean-tolerant varieties is the key to resisting low-temperature stress at the germination stage. In the present study, a chromosome segment substitution line (CSSL) population constructed by wild soybean ZYD00006 and cultivated soybean SN14 was used to map three quantitative trait loci (QTLs). Five candidate genes were obtained by gene annotation, GO enrichment analysis and protein function prediction. The candidate genes were subjected to bioinformatics analysis, qRT-PCR analysis, trypsin activity analysis and soluble protein content analysis. The results showed that the secondary and tertiary structures of the Glyma.09G162700 proteins were mutated. Within 0–72 h, the expression of Glyma.09G162700 in the two materials with different tolerances was consistent, and the change in trypsin activity was consistent with the change in protein expression. Through haplotype analysis, Glyma.09G162700 produced two haplotypes at −2420 bp. The germination rate (GR) and relative germination rate (RGR) of the two haplotypes were significantly different, indicating that the two haplotypes have wide applicability in soybean resources. In summary, Glyma.09G162700 may be a candidate gene for low-temperature tolerance at the germination stage of soybean. These results provide an important theoretical basis and marker information for analysing the mechanism of low-temperature tolerance in soybean germination stage and cultivating low-temperature-tolerant varieties.

Cucumber mosaic virus subgroup IA isolates infect four varieties of Nandina domestica in China

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Abstract

Cucumber mosaic virus (CMV) subgroup IA isolates were first identified from Nandina domestica plants in Zhejiang province of China by small RNA deep sequencing followed by bioinformatics analysis and was confirmed by RT-PCR amplification, 5′ and 3′ RACE and DNA sequencing. The complete nucleotide sequences of this virus shared the highest sequence similarities (97–98%) with CMV subgroup IA isolate CTL RNA1 and RNA3 (GenBank accession no: EF213023, EF213025) and RP48 RNA2 (KC527727), respectively; and converged with CMV subgroup IA isolates into a branch in phylogenetic tree using full length nucleotide sequences. Pathogenicity test confirmed that this virus can be mechanically transmitted to N. domestica, Nicotiana tabacum and N. benthamiana. All thirty randomly collected samples of four major N. domestica varieties (N. domestica cv. Hong Baoshi, Nana, Fire Power and Xiu Dada) in Lin'an Zhejiang province were positive for CMV subgroup IA. This is the first report of CMV subgroup IA isolate on varieties of N. domestica in China.