Category Archives: ORIGINAL ARTICLE

Characterization and pathogenicity of Fusarium species causing sugar beet root rot in Morocco

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Abstract

The sugar beet crop ranks second globally among the plant species grown mainly for sugar production. In Morocco, the area under sugar beet farming occupies approximately 57,000 ha yielding more than 3 million tons of roots. However, sugar beet root-tip rot (RTR) caused by Fusarium spp. dramatically reduces the anticipated yields, the purity of the resulting juice, and the sugar concentration. The current study aimed at identifying and characterizing the Fusarium species responsible for the root rot in sugar beet grown in the Khenifra-Beni Mellal region of Morocco. In this survey, 69 isolates of Fusarium were sampled from sugar beet roots showing typical symptoms of root rot from 2019 to 2021. After screening based on the pathogenicity test, 28 isolates were selected and identified based on morphological features and sequence analyses of the ribosomal internal transcribed spacer (ITS) region and translation elongation factor 1 α 34 (TEF-1 α). Fusarium oxysporum was the most frequently identified species, followed closely by F. solani, F. equiseti, F. nygmai, F. brachygibbosum, F. proliferatum, F. culmorum, and F. falciforme. Six weeks after inoculations under greenhouse conditions, the studied isolates caused internal vascular discoloration and tip rot of sugar beet roots, with disease incidences ranging from 37.5% to 100.0% and a disease index between 30.3% and 70.5%. Isolates belonging to F. solani were the most aggressive. Moreover, the majority of isolates significantly reduced plant growth. To our knowledge, this research article is the first report of Fusarium species inducing RTR in sugar beet in Morocco.

Aflatoxin levels and Aspergillus species in maize in the Province of Isabela, Philippines

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Abstract

The province of Isabela is the top maize producer in the Philippines. The intensive cultivation and the tropical climate in the region may favour fungal growth and aflatoxin contamination in maize grains. Thus, the study aimed to determine the occurrence of aflatoxin and mycotoxigenic Aspergillus species in maize varieties in this region. Samples were obtained in six municipalities from hybrid (Bt) maize (n = 101) and open-pollinated varieties (n = 6) during the dry season (March and April) of 2019. Aflatoxin levels were quantified through enzyme-linked immunosorbent assay, and Aspergillus species were identified through cultural and molecular methods. Aflatoxin was detected in 50.5% of maize samples; 49.5% of samples were less than the limit of detection (3 μg/kg), 16.8% with 3–20 μg/kg, 10.9% with 21–50 μg/kg and 22.8% above 50 μg/kg. Samples within the acceptable level were 66.3% for food (<20 μg/kg) and 77.2% for animal feed (<50 μg/kg), while 22.8% of samples were above the acceptable level of the Philippine National Standard for raw maize grains. More than 90% of Aspergillus species detected were A. flavus. Other species identified were A. tamarii and A. terreus. Despite the dry production season in the province with low relative humidity during harvesting, inadequate post-harvest practices and the presence of A. flavus elevated the level of aflatoxin in sample grains. Additional work involving multi-year surveys is needed to confirm the results and conclusions of this study.

Effect of environmental factors, fungicide sensitivity, and pathogenicity of Fusarium spp. associated with fruit rot of melon

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Abstract

Fusarium rot is one of the main postharvest diseases of melons, directly interfering with the quality and commercial use of the fruit. The purpose of this study was to assess the effect of environmental factors (temperature, pH and salinity) and the pathogenicity of four Fusarium species (F. falciforme, F. kalimantanense, F. pernambucanum and F. sulawesiense) belonging to three different species complexes on disease development on melon, as well as the in vitro and in vivo sensitivity of these species to the fungicides azoxystrobin + fludioxonil, imazalil and thiabendazole. The results showed optimum fungal growth temperatures from 24.5 to 27.2°C, and optimum pH from 6.10 to 8.37 for all Fusarium species. NaCl concentrations (250–1000 mM) significantly reduced in vitro mycelial growth for all isolates. All species were pathogenic to melon plants and fruit, with an isolate of F. falciforme being the most aggressive, causing the highest disease severity in plants and fruit (43.3% and 62.5%, respectively). The isolate of F. sulawesiense tested showed high in vitro sensitivity to two fungicides (azoxystrobin + fludioxonil and imazalil), with EC50 values below 1 mg/L of a.i. Fruit inoculated with the selected isolates of F. falciforme and F. pernambucanum showed a reduction in the disease severity on the peduncle when treated with the fungicide thiabendazole (9.0% and 4.0%, respectively). Azoxystrobin + fludioxonil was responsible for the lowest disease severity in the epicarp caused by the same isolates (0.0% and 2.5%, respectively). These results are relevant to improve management strategies for diseases of melon caused by Fusarium spp.

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

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Abstract

Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast-cooking and slow-cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant-seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast- and slow-cooking beans due to soaking. Candidate genes identified in the slow-cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall-strengthening enzymes in the slow-cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

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Abstract

Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome-wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

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Abstract

MicroRNAs (miRNAs) are 21–24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.

A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa

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Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free-living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A-genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence-match similarities with quinoa, along with its well-established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome-scale scaffolds and 93.9% Benchmarking Universal Single-Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A-subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single-nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H-genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A-genome sequences from the ATGC. We also present evidence for long-range dispersal of Chenopodium diploids between North and South America.

Antimicrobial peptides in Dendrobium officinale: Genomic parameters, peptide structures, and gene expression patterns

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Abstract

A weak codon usage bias was found in Dendrobium catenatum (D. officiale) antimicrobial peptides (AMPs), after the analysis of relative synonymous codon usage, GC contents, and the effective number of codons. The codon usage preference was mainly influenced by natural selection pressure. The self-optimized prediction method and SWISS-MODEL were applied for peptide structural and domain analyses, and some typical antimicrobial domains were found in D. officinale AMP amino sequences, such as knot1 domain, gibberellins-stimulated domain, cupin_1 domain, defensin_like domain, and SLR1-BP (S locus-related glycoprotein 1 binding pollen coat protein) domain. To investigate the AMPs gene expression pattern, abiotic stresses, such as salt stress, drought stress, salicylic acid (SA), and methyl jasmonate (JA), were applied and the gene expression levels were detected by the real-time fluorescent quantitative polymerase chain reaction. Results showed that, even though the basic AMPs gene expressions were low, some AMPs can still be induced by salt dress, while the drought dress did not show the same impact. The SA and JA signaling pathways might be involved in most of the AMPs expressions. The natural selection of the D. officinale AMPs and thus forming diverse types of AMPs enhanced the plant's innate immunity and disease resistance capability, which would lead to a better understanding of the molecular mechanism for D. officinale adapting to the environment. The finding that salt stress, SA, and JA signaling pathways can induce AMP expression lays a foundation for the further development and functional verification of D. officinale AMPs.

Meta‐analysis of the quantitative trait loci associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits in pigeonpea (Cajanus cajan L.)

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A meta-analysis of quantitative trait loci (QTLs), associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits was conducted for the first time in pigeonpea (Cajanus cajan L.). Data on 498 QTLs was collected from 9 linkage mapping studies (involving 21 biparental populations). Of these 498, 203 QTLs were projected onto “PigeonPea_ConsensusMap_2022,” saturated with 10,522 markers, which resulted in the prediction of 34 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs (2.54 cM) was 3.37 times lower than the CI of the initial QTLs (8.56 cM). Of the 34 MQTLs, 12 high-confidence MQTLs with CI (≤5 cM) and a greater number of initial QTLs (≥5) were utilized to extract 2255 gene models, of which 105 were believed to be associated with different traits under study. Furthermore, eight of these MQTLs were observed to overlap with several marker-trait associations or significant SNPs identified in previous genome-wide association studies. Furthermore, synteny and ortho-MQTL analyses among pigeonpea and four related legumes crops, such as chickpea, pea, cowpea, and French bean, led to the identification of 117 orthologous genes from 20 MQTL regions. Markers associated with MQTLs can be employed for MQTL-assisted breeding as well as to improve the prediction accuracy of genomic selection in pigeonpea. Additionally, MQTLs may be subjected to fine mapping, and some of the promising candidate genes may serve as potential targets for positional cloning and functional analysis to elucidate the molecular mechanisms underlying the target traits.

Transcriptome profiling reveals the expression and regulation of genes associated with Fusarium wilt resistance in chickpea (Cicer arietinum L.)

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Abstract

Fusarium wilt (FW) is one of the most significant biotic stresses limiting chickpea production worldwide. To dissect the molecular mechanism of FW resistance in chickpea, comparative transcriptome analyses of contrasting resistance sources of chickpea genotypes under control and Fusarium oxysporum f. sp. ciceris (Foc) inoculated conditions were performed. The high-throughput transcriptome sequencing generated about 1137 million sequencing reads from 24 samples representing two resistant genotypes, two susceptible genotypes, and two near-isogenic lines under control and stress conditions at two-time points (7th- and 12th-day post-inoculation). The analysis identified 5182 differentially expressed genes (DEGs) between different combinations of chickpea genotypes. Functional annotation of these genes indicated their involvement in various biological processes such as defense response, cell wall biogenesis, secondary metabolism, and disease resistance. A significant number (382) of transcription factor encoding genes exhibited differential expression patterns under stress. Further, a considerable number of the identified DEGs (287) co-localized with previously reported quantitative trait locus for FW resistance. Several resistance/susceptibility-related genes, such as SERINE/THREONINE PROTEIN KINASE, DIRIGENT, and MLO exhibiting contrasting expression patterns in resistant and susceptible genotypes upon Foc inoculation, were identified. The results presented in the study provide valuable insights into the transcriptional dynamics associated with FW stress response in chickpea and provide candidate genes for the development of disease-resistant chickpea cultivars.