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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

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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.

Prospects for developing allergen‐depleted food crops

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Abstract

In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio-molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentially life-threatening consequences. The relentless working lifestyles of the modern era often incorporate poor eating habits that include readymade prepackaged and processed foods, which contain additives such as peanuts, tree nuts, wheat, and soy-based products, rather than traditional home cooking. Of the predominant allergenic foods (soybean, wheat, fish, peanut, shellfish, tree nuts, eggs, and milk), peanuts (Arachis hypogaea) are the best characterized source of allergens, followed by tree nuts (Juglans regia, Prunus amygdalus, Corylus avellana, Carya illinoinensis, Anacardium occidentale, Pistacia vera, Bertholletia excels), wheat (Triticum aestivum), soybeans (Glycine max), and kidney beans (Phaseolus vulgaris). The prevalence of food allergies has risen significantly in recent years including chance of accidental exposure to such foods. In contrast, the standards of detection, diagnosis, and cure have not kept pace and unfortunately are often suboptimal. In this review, we mainly focus on the prevalence of allergies associated with peanut, tree nuts, wheat, soybean, and kidney bean, highlighting their physiological properties and functions as well as considering research directions for tailoring allergen gene expression. In particular, we discuss how recent advances in molecular breeding, genetic engineering, and genome editing can be used to develop potential low allergen food crops that protect consumer health.

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

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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

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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.

Skim exome capture genotyping in wheat

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Abstract

Next-generation sequencing (NGS) technology advancements continue to reduce the cost of high-throughput genome-wide genotyping for breeding and genetics research. Skim sequencing, which surveys the entire genome at low coverage, has become feasible for quantitative trait locus (QTL) mapping and genomic selection in various crops. However, the genome complexity of allopolyploid crops such as wheat (Triticum aestivum L.) still poses a significant challenge for genome-wide genotyping. Targeted sequencing of the protein-coding regions (i.e., exome) reduces sequencing costs compared to whole genome re-sequencing and can be used for marker discovery and genotyping. We developed a method called skim exome capture (SEC) that combines the strengths of these existing technologies and produces targeted genotyping data while decreasing the cost on a per-sample basis compared to traditional exome capture. Specifically, we fragmented genomic DNA using a tagmentation approach, then enriched those fragments for the low-copy genic portion of the genome using commercial wheat exome baits and multiplexed the sequencing at different levels to achieve desired coverage. We demonstrated that for a library of 48 samples, ∼7–8× target coverage was sufficient for high-quality variant detection. For higher multiplexing levels of 528 and 1056 samples per library, we achieved an average coverage of 0.76× and 0.32×, respectively. Combining these lower coverage SEC sequencing data with genotype imputation using a customized wheat practical haplotype graph database that we developed, we identified hundreds of thousands of high-quality genic variants across the genome. The SEC method can be used for high-resolution QTL mapping, genome-wide association studies, genomic selection, and other downstream applications.

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

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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

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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.

Integrating de novo QTL‐seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean

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Abstract

White mold (WM), caused by the ubiquitous fungus Sclerotinia sclerotiorum, is a devastating disease that limits production and quality of dry bean globally. In the present study, classic linkage mapping combined with QTL-seq were employed in two recombinant inbred line (RIL) populations, “Montrose”/I9365-25 (M25) and “Raven”/I9365-31 (R31), with the initial goal of fine-mapping QTL WM5.4 and WM7.5 that condition WM resistance. The RILs were phenotyped for WM reactions under greenhouse (straw test) and field environments. The general region of WM5.4 and WM7.5 were reconfirmed with both mapping strategies within each population. Combining the results from both mapping strategies, WM5.4 was delimited to a 22.60–36.25 Mb interval in the heterochromatic regions on Pv05, while WM7.5 was narrowed to a 0.83 Mb (3.99–4.82 Mb) region on the Pv07 chromosome. Furthermore, additional QTL WM2.2a (3.81–7.24 Mb), WM2.2b (11.18–17.37 Mb, heterochromatic region), and WM2.2c (23.33–25.94 Mb) were mapped to a narrowed genomic interval on Pv02 and WM4.2 in a 0.89 Mb physical interval at the distal end of Pv04 chromosome. Gene models encoding gibberellin 2-oxidase proteins regulating plant architecture are likely candidate genes associated with WM2.2a resistance. Nine gene models encoding a disease resistance protein (quinone reductase family protein and ATWRKY69) found within the WM5.4 QTL interval are putative candidate genes. Clusters of 13 and 5 copies of gene models encoding cysteine-rich receptor-like kinase and receptor-like protein kinase-related family proteins, respectively, are potential candidate genes associated with WM7.5 resistance and most likely trigger physiological resistance to WM. Acquired knowledge of the narrowed major QTL intervals, flanking markers, and candidate genes provides promising opportunities to develop functional molecular markers to implement marker-assisted selection for WM resistant dry bean cultivars.