Category Archives: ORIGINAL ARTICLE

Salinity stress tolerance prediction for biomass‐related traits in maize (Zea mays L.) using genome‐wide markers

Posted on by

Abstract

Maize (Zea mays L.) is the third most important cereal crop after rice (Oryza sativa) and wheat (Triticum aestivum). Salinity stress significantly affects vegetative biomass and grain yield and, therefore, reduces the food and silage productivity of maize. Selecting salt-tolerant genotypes is a cumbersome and time-consuming process that requires meticulous phenotyping. To predict salt tolerance in maize, we estimated breeding values for four biomass-related traits, including shoot length, shoot weight, root length, and root weight under salt-stressed and controlled conditions. A five-fold cross-validation method was used to select the best model among genomic best linear unbiased prediction (GBLUP), ridge-regression BLUP (rrBLUP), extended GBLUP, Bayesian Lasso, Bayesian ridge regression, BayesA, BayesB, and BayesC. Examination of the effect of different marker densities on prediction accuracy revealed that a set of low-density single nucleotide polymorphisms obtained through filtering based on a combination of analysis of variance and linkage disequilibrium provided the best prediction accuracy for all the traits. The average prediction accuracy in cross-validations ranged from 0.46 to 0.77 across the four derived traits. The GBLUP, rrBLUP, and all Bayesian models except BayesB demonstrated comparable levels of prediction accuracy that were superior to the other modeling approaches. These findings provide a roadmap for the deployment and optimization of genomic selection in breeding for salt tolerance in maize.

Whole‐genome versus per‐chromosome targeted recombination: Simulations and predicted gains in maize with an integer programming model

Posted on by

Abstract

Per-chromosome targeted recombination, with one to two recombinations at specific marker intervals on each chromosome, doubles the predicted genetic gains in biparental populations. We developed an integer programing model to identify where a fixed number of targeted recombinations should occur across the whole genome, without restrictions on the number of targeted recombinations on each chromosome. We compared whole-genome and per-chromosome targeted recombination in 392 biparental maize (Zea mays L.) populations and in simulation experiments. For yield, moisture, test weight, and a simulated trait controlled by 2000 quantitative trait loci (QTL), predicted gains were 8%–9% larger with 10 targeted recombinations across the entire genome than with one targeted recombination on each of the 10 chromosomes. With whole-genome targeted recombination, the number of recombinations on a given chromosome was correlated (r = 0.76–0.91) with the chromosome size (in cM). Simulation results suggested that previous results on gains from targeted recombination relative to nontargeted recombination were too optimistic by around 20%. Because the underlying QTL are unknown, studies on targeted recombination have relied on genomewide marker effects as proxies for QTL information. The simulation results indicated a 25% (for 10 recombinations) to 33% (for 20 recombinations) reduction in response due to the use of genomewide marker effects as proxies for QTL information. Overall, the results indicated that the integer programming model we developed is useful for increasing both the predicted and true gains from targeted recombination, but the predicted gains are likely to overestimate the true gains.

Evaluation of Ascochyta resistance in chickpea genotypes with quantitative polymerase chain reaction assay

Posted on by

Abstract

Ascochyta blight caused by Ascochyta rabiei is a globally important chickpea disease. Host resistance to Ascochyta blight is considered the most practical and effective means of control, but breeding has been hindered by a lack of effective resistance sources, and time-consuming, labour-intensive traditional methods to screen the resistance level of chickpea genotypes. This paper evaluated the progression of pathogen infection and the disease reaction of chickpea genotypes to Ascochyta blight by traditional and molecular methods. The resistance level of 84 chickpea genotypes was assessed by a quantitative polymerase chain reaction assay (qPCR) using a standard curve produced by various known amounts of pathogen DNA and compared with disease scores based on visual assessments 8 days after inoculation. Disease assessments revealed statistically significant differences between the resistance levels of chickpea genotypes, while the quantity of target DNA in the samples inoculated with the pathogen ranged from 0.004 to 83.37 ng. Our results showed a close relationship between the visual assessment of disease severity and the quantification of the target DNA in chickpea genotypes. The genotypes Tüb-35, Tüb-47, Tüb-26, Tüb-82, Tüb-65 and Tüb-69 were classified as highly resistant to Ascochyta blight based on the results of both assays used for screening chickpea genotypes. This qPCR analysis could be used to quantify disease progression in plant tissues and screen chickpea genotypes as a potential alternative to visual assessment of resistance levels in breeding programmes.

Genetic diversity of an effector gene, AvrPi9, of rice blast pathogen in Thailand and characterization of its promoter

Posted on by
Genetic diversity of an effector gene, AvrPi9, of rice blast pathogen in Thailand and characterization of its promoter

MoHox6, a transcription factor, binds to the AvrPi9 promoter and helps the expression of the AvrPi9 gene in the rice blast fungus during infection and in rice protoplasts.


Abstract

Rice blast is one of the most destructive diseases of rice and is caused by the fungus Magnaporthe oryzae. The disease causes enormous yield losses in rice production worldwide. The rice blast fungus delivers effector proteins into rice cells. The effector proteins play an essential role in fungal virulence by manipulating and controlling host cellular pathways and inhibiting host immune responses to enhance pathogenicity. An effector gene, AvrPi9, which corresponds to the resistance gene Pi9, was cloned and characterized. However, a regulatory molecular mechanism for AvrPi9 gene expression has not been determined. In this study, the genetic variation of the AvrPi9 and its promoter function were characterized. The results showed that 98% (116/118) of the samples carried the AvrPi9 gene without any sequence variation, whilst two isolates, 10576 from Kalasin and NYK56003 from Nakhon Nayok, lacked the AvrPi9 gene. A homeobox domain-containing protein (MoHOX6) was identified as a candidate transcription factor. The AvrPi9 gene expression was delayed in the MoHOX6 knockout mutant. Moreover, the AvrPi9 promoter was able to drive the expression of a luciferase gene in rice protoplasts. This study provides the first insight into the function and regulation of the AvrPi9 promoter of rice blast fungus.

Intracellular and mitochondrial proteomic analysis reveals antifungal mechanisms of borate on mango black spot pathogen Alternaria alternata

Posted on by
Intracellular and mitochondrial proteomic analysis reveals antifungal mechanisms of borate on mango black spot pathogen Alternaria alternata

The antifungal effect of potassium tetraborate on the proteomics of Alternaria alternata involves multiple metabolic pathways and could be used as a potential substitute for fungicides to control postharvest diseases of mango.


Abstract

Boron, in the form of potassium tetraborate, has previously been found to be effective at inhibiting mango black spot disease, caused by Alternaria alternata. However, the mechanisms involved in this inhibition are largely unknown. In this study, A. alternata was treated in vitro with potassium tetraborate at a concentration of 5–10 mM for 48 or 72 h. The intracellular and mitochondrial proteins were extracted from mycelium and separated using two-dimensional electrophoresis (2-DE). Differentially expressed proteins (DEPs) were identified using bioinformatics tools and differences between protein spots were derived from mass spectrometry (MS). Using matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-ToF-MS/MS), 96 intracellular and 56 mitochondrial DEPs were identified. The intracellular proteins identified were found to be involved in posttranslational modifications, protein turnover and chaperones, while the mitochondrial proteins were involved in electron transport chains. Our results demonstrate that various metabolic pathways are involved in the antifungal activity of boron. The differential expression of 20 genes was also verified at the mRNA level by reverse transcription-quantitative PCR. Our study suggests that borate could be used as a potential substitute for synthetic fungicides to control this postharvest disease of mango fruits.

Breeding dryland legumes for diverse needs: Using multi‐location trials and participatory variety selection to develop farmer‐preferred groundnut (Arachis hypogaea) and pigeon pea (Cajanus cajan) varieties

Posted on by

Abstract

Agriculture in Sub-Saharan Africa is primarily smallholder-based, employing up to 60% of the workforce and accounting for 14%–23% of GDP. The smallholders grow crops for domestic and off-farm markets, necessitating crop variety attributes for which trait mismatches may limit adoption. Indeed, improved variety adoption is varied and limited, especially for self-pollinated crops, in part due to the mismatch in characteristics of commercialised varieties. The international research community leads breeding of varieties for under-invested crops, especially legumes. These varieties are often resilient and productive, but the dynamisms in target agri-food systems may limit their relevance. Gaining a better understanding of the trait profiles that crop value chain actors consider will increase their adoption. This study combined multi-location trials and participatory variety selection (PVS) of pigeon pea and groundnut across different environments to evaluate the efficacy of both processes in the breeding of desired varieties. The present study shows improvement in the new materials regarding performance and preference by farmers. Additionally, PVS showed that men prioritised productivity and market-enhancing traits, whereas women ranked food security traits highest.

Postmeiotic irregular anther1 (PIA1) is required for anther cuticle and pollen exine development in maize (Zea mays L.)

Posted on by

Abstract

Male sterile lines are valuable germplasm resources for hybrid seed production in maize (Zea mays L.). The structures of the anther cuticle and pollen exine are associated with male sterility. We obtained a completely male sterile mutant (postmeiotic irregular anther1, pia1), which has closed glumes and relatively small and wilted anthers (compared with the wild-type control). Cytological analysis revealed the normal meiosis and premature tapetal degradation in pia1. Additionally, formation of the pia1 anther cuticle and Ubisch bodies was abnormal, and the pollen exine was discontinuous. Genetic analysis showed that the pia1 mutant was the result of a single recessive mutation of a nuclear gene. On the basis of fine mapping, PIA1 was mapped between the W07051 and W07124 molecular markers on chromosome 1. This region does not contain known genes associated with male sterility. Furthermore, transcriptome analysis indicated genes implicated in transmembrane transport, amino acid transmembrane transport, amino acid transport, and carboxylic acid transmembrane transport are differentially expressed in pia1 mutant anthers. The study findings suggest PIA1 is a novel regulator of anther cuticle and pollen exine development.

Genome‐wide association of dry (Tamar) date palm fruit color

Posted on by

Abstract

Date palm (Phoenix dactylifera) fruit (dates) are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some date palm traits have been performed, including sex determination, sugar content, and fresh fruit color. In this study, we used genome sequences and image data of 199 dry dates (Tamar) collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover both the previously identified VIRESCENS (VIR) genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of date color phenotype, especially at the most commercially important Tamar stage.

Multiscale temporal and spatiotemporal analysis of wheat blast infection‐like dynamics using vertical plant stratification, regression and Markov chain approaches

Posted on by
Multiscale temporal and spatiotemporal analysis of wheat blast infection-like dynamics using vertical plant stratification, regression and Markov chain approaches

Deterministic and stochastic methods identified how WB intensity varies across scales. Temporally, WSB presented a higher disease intensity than WLB. At the spatiotemporal level, four types of infection-like changes were estimated.


Abstract

The spatiotemporal progress of wheat blast (WB) epidemics within the plant canopy remains poorly known due to complex pathogen–host–environment interactions. Although deterministic methods are popular and useful, robust stochastic methods, such as generalized additive models for location, scale and shape (GAMLSS) and probability matrix or Markov transition model (MTM), have seldom been used to analyse plant disease epidemics. Hence, both methods were employed to derive valuable insights into WB epidemiology at the vertical canopy level. We conducted experiments in three climatic zones in Bolivia, using three wheat cultivars, with disease data corresponding to different canopy positions (lower, L; middle, M; flag leaf, F; and spike, S). Using WB severity data (AUDPC, progress rate and maximum severity [K max]), we implemented the GAMLSS and MTM to test our hypothesis that WB is affected by host resistance, location and canopy level. Results showed that the AUDPC, progress rate and K max differed across sites, cultivars and canopy positions. Clearly, L and M canopies showed a lower progress rate than F and S. The disease showed an ascending movement from L and M canopies to F and S across locations and cultivars. However, descending transitions also occurred from M to L early or F to M canopy later in the season. Both ascending and descending movements can arise at a single state or several recurrent states, indicating indirect evidence of autoinfection within the canopy before and after spike emergence. Our findings contribute knowledge to improve monitoring and managing WB.

The antifungal activity of trans‐cinnamic acid and its priming effect in apple in response to Valsa mali

Posted on by
The antifungal activity of trans-cinnamic acid and its priming effect in apple in response to Valsa mali

Trans-cinnamic acid not only plays a significant role in inhibiting the growth of Valsa mali, a fungus causing apple Valsa canker disease, but also in priming host defence.


Abstract

Valsa mali causes Valsa canker, one of the most destructive diseases on apple trees, leading to severe losses for the apple industry in China. Considering the development of fungicide resistance and the harmful effects of chemical residues, it is urgent to identify alternatives to control this disease. Trans-cinnamic acid (t-CA), a compound with good antibacterial, antitumour and anti-inflammatory properties, is widely used in food, medicine and other industries. However, the antifungal activity of t-CA against V. mali and its regulatory role in apple defence against biotic stresses are unclear. Based on a metabolomic assay, we found that Malus yunnaensis (Valsa canker-resistant) twigs infected with V. mali dramatically accumulated t-CA. Exogenous application of t-CA effectively inhibited V. mali growth on potato dextrose agar. The EC50 value of t-CA inhibiting mycelial growth was 200 μg/mL. Malus prunifolia (Valsa canker-susceptible) leaves and twigs pretreated with t-CA had significantly enhanced V. mali resistance. The t-CA application increased salicylic acid but reduced jasmonic acid levels in leaves and twigs. Moreover, the contents of phenolic acids and flavonoids increased in t-CA-treated samples. In addition, t-CA increased the activities of phenylalanine ammonia-lyase, β-1,3-glucanase and chitinase. These results indicate that t-CA plays a significant role in inhibiting V. mali growth and priming apple defence.