Populations of European ash trees (Fraxinus excelsior) are being devastated by the invasive alien fungus Hymenoscyphus fraxineus, which causes ash dieback. We sequenced whole genomic DNA from 1,250 ash trees in 31 DNA pools, each pool containing trees with the same ash dieback damage status in a screening trial and from the same seed-source zone. A genome-wide association study identified 3,149 single nucleotide polymorphisms (SNPs) associated with low versus high ash dieback damage. Sixty-one of the 192 most significant SNPs were in, or close to, genes with putative homologues already known to be involved in pathogen responses in other plant species. We also used the pooled sequence data to train a genomic prediction model, cross-validated using individual whole genome sequence data generated for 75 healthy and 75 damaged trees from a single seed source. The model's genomic estimated breeding values (GEBVs) allocated these 150 trees to their observed health statuses with 67% accuracy using 10,000 SNPs. Using the top 20% of GEBVs from just 200 SNPs, we could predict observed tree health with over 90% accuracy. We infer that ash dieback resistance in F. excelsior is a polygenic trait that should respond well to both natural selection and breeding, which could be accelerated using genomic prediction.

/pdf/genomic-basis-of-european-ash-tree-resistance-to-ash-dieback-3ia4ftu2a1.pdf

Genomic basis of European ash tree resistance to ash dieback fungus.

Color and pigment contents are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops. Further analyses establish the link between sequence or expression level variations in the CmAPRR2 gene and pigment content in the rind and flesh of mature melon fruits. A genome-wide association study (GWAS) of young fruit rind color in a panel composed of 177 diverse melon accessions did not result in any significant association, leading to an earlier assumption that multiple genes are involved in shaping the overall phenotypic variation in this trait. Through resequencing of 25 representative accessions and allelism tests between light rind accessions, we show that multiple independent single nucleotide polymorphisms in the CmAPRR2 gene are causative of the light rind phenotype. The multi-haplotypic nature of this gene explains the lack of detection power obtained through genotyping by sequencing-based GWAS and confirms the pivotal role of this gene in shaping fruit color variation in melon. This study demonstrates the power of combining bi- and multi-allelic designs with deep sequencing, to resolve lack of power due to high haplotypic diversity and low allele frequencies. Due to its central role and broad effect on pigment accumulation in fruits, the APRR2 gene is an attractive target for carotenoid bio-fortification of cucurbit crops.

The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon.

Anthocyanins, sugars, and organic acids contribute to the appearance, health benefits, and taste of strawberries. However, their spatial distribution in the ripe fruit has been fully unrevealed. Therefore, we performed matrix-assisted laser desorption/ionization, MALDI-IMS, analysis to investigate their spatial distribution in ripe strawberries. The detection sensitivity was improved by using the TM-Sprayer for matrix application. In the receptacle, pelargonidins were distributed in the skin, cortical, and pith tissues, whereas cyanidins and delphinidins were slightly localized in the skin. In the achene, mainly cyanidins were localized in the outside of the skin. Citric acid was mainly distributed in the upper and bottom side of cortical tissue. Although hexose was distributed almost equally throughout the fruits, sucrose was mainly distributed in the upper side of cortical and pith tissues. These results suggest that using the TM-Sprayer in MALDI-IMS was useful for microscopic distribution analysis of a...

Distribution Analysis of Anthocyanins, Sugars, and Organic Acids in Strawberry Fruits Using Matrix-Assisted Laser Desorption/Ionization-Imaging Mass Spectrometry.

Pathogen recognition by the plant immune system leads to defense responses that are often accompanied by a form of regulated cell death known as the hypersensitive response (HR). HR shares some features with regulated necrosis observed in animals. Genetically, HR can be uncoupled from local defense responses at the site of infection and its role in immunity may be to activate systemic responses in distal parts of the organism. Recent advances in the field reveal conserved cell death-specific signaling modules that are assembled by immune receptors in response to pathogen-derived effectors. The structural elucidation of the plant resistosome-an inflammasome-like structure that may attach to the plasma membrane on activation-opens the possibility that HR cell death is mediated by the formation of pores at the plasma membrane. Necrotrophic pathogens that feed on dead tissue have evolved strategies to trigger the HR cell death pathway as a survival strategy. Ectopic activation of immunomodulators during autoimmune reactions can also promote HR cell death. In this perspective, we discuss the role and regulation of HR in these different contexts.

/pdf/cell-death-in-plant-immunity-11dpznflcw.pdf

Cell Death in Plant Immunity.

A BIN2-GLK1 Signaling Module Integrates Brassinosteroid and Light Signaling to Repress Chloroplast Development in the Dark.

Strawberry fruits (cv. Benihoppe, Tochiotome, Sachinoka, and Guimeiren) were harvested and evaluated the flavor and nutritional parameters. By principal component analysis and hierarchical clustering analysis, differences were observed based on the volatile compounds composition, sugar and acid concentration, sweetness, and total soluble sugars/total organic acids of the four varieties. A total of 37, 48, 65, and 74 volatile compounds were identified and determined in cv. Benihoppe, Tochiotome, Sachinoka, and Guimeiren strawberry fruits extracted by head-space solid-phase microextraction (HS-SPME), respectively. Esters significantly dominated the chemical composition of the four varieties. Furaneol was detected in cultivars of Sachinoka and Guimeiren, but mesifuran was only found in cv. Tochiotome. Tochiotome and Sachinoka showed higher content of linalool and (E)-nerolidol. Sachinoka showed the highest content of total sugars and total acids. Guimeiren showed higher sweetness index than the other three cultivars. Firmness of Tochiotome was highest among all the varieties. The highest total soluble solids TSS value was found in cv. Sachinoka, followed by the Guimeiren and Tochiotome varieties. Sachinoka had the highest titratable acidity TA value. The content of ascorbic acid (AsA) of cv. Tochiotome was higher than the others, but there was no significant difference in cultivars of Benihoppe, Tochiotome, and Sachinoka. Fructose and glucose were the major sugars in all cultivars. Citric acid was the major organic acid in cv. Tochiotome, cv. Sachinoka, and cv. Guimeiren. Tochiotome had higher ratios of TSS/TA and total sugars/total organic acids than others, arising from its lower acid content. The order of the comprehensive evaluation score was Sachinoka>Guimeiren>Tochiotome>Benihoppe.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/fsn3.346

The flavor and nutritional characteristic of four strawberry varieties cultured in soilless system.

Transcriptome analysis of ripe peach (Prunus persica) fruit under low-dose UVB radiation

We previously showed that PHB3 regulates auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates LR development mainly through influencing lateral root primordia (LRP) initiation via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 was largely rescued by exogenous NO donor SNAP treatment. The decreased NO accumulation in phb3 caused a lower expression of GATA23 and LBD16 through inhibiting the degradation of IAA14/28. Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced LRP number phenotype. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signaling through regulating the degradation of IAA14/28.

PHB3 Regulates Lateral Root Primordia Formation via NO-mediated Degradation of AUX/IAAs.

Golden2-like (GLK) transcription factors are members of the GARP family of Myb transcription factors with an established relationship to chloroplast development in the plant kingdom. In the last century, Golden2 was proposed as a second golden producing factor and identified as controlling cellular differentiation in maize leaves. Then, GLKs were also found to play roles in disease defense and their function is conserved in regulating chloroplast development. Recently, research on GLKs has rapidly increased and shown that GLKs control chloroplast development in green and non-green tissues. Moreover, links between phytohormones and GLKs were verified. In this mini-review, we summarize the history, conservation, function, potential targets and degradation of GLKs.

/pdf/golden-2-like-transcription-factors-of-plants-3c9ym5ix8j.pdf

GOLDEN 2-LIKE Transcription Factors of Plants.

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Papers

The flavor and nutritional characteristic of four strawberry varieties cultured in soilless system.

Transcriptome analysis of ripe peach (Prunus persica) fruit under low-dose UVB radiation

PHB3 Regulates Lateral Root Primordia Formation via NO-mediated Degradation of AUX/IAAs.

GOLDEN 2-LIKE Transcription Factors of Plants.