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Ecological indicator values of understorey plants perform poorly to infer forest microclimate temperature

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Ecological indicator values of understorey plants perform poorly to infer forest microclimate temperature

For the first time, we test whether ecological indicator values (EIVs) of forest plant communities are solely able to capture macroclimate or also microclimate temperature. Vascular plant and bryophyte communities successfully inferred macroclimatic differences across forests but largely failed to do so for microclimate variation within forests. Refined temperature EIVs are needed to capture microclimates experienced by understorey species.


Abstract

Question

Ecological indicator values (EIVs) reflect species‘ optimal conditions on an environmental gradient, such as temperature. Averaged over a community, they are used to quantify thermophilization stemming from climate change, i.e. the reshuffling of communities toward more warm-adapted species. In forests, understorey plant communities do not keep up with global warming and accumulate a climatic debt. Although the causes are still debated, this thermal lag may be partly explained by forest microclimate buffering. For the first time, we test whether community means of EIVs are able to capture microclimate (here, under forest canopies) temperature across, or also within forests.

Location

157 forest plots across three French deciduous forests covering a large macroclimatic gradient.

Methods

To assess whether EIVs can be used to infer the mean and range of microclimate temperature in forests, we measured understorey air temperature for ca. 1 year (10 months) with sensors located 1 m above the ground. We surveyed bryophytes and vascular plants within 400-m2 plots, and computed floristic temperature from ordinal-scale EIVs (Ellenberg, Julve) and degree-scale EIVs (ClimPlant, Bryophytes of Europe Traits) for both temperature and continentality, i.e. temperature annual range. Finally, we fitted linear models to assess whether EIVs could explain the mean and range of microclimate temperature in forests.

Results

Vascular plant and bryophyte communities successfully reflected differences in mean annual temperatures across forests but largely failed to do so for microclimate variation within forests. Bryophytes did not perform better than vascular plants to infer microclimate conditions. The annual range of microclimate temperatures was poorly associated with ordinal-scale EIVs for continentality but was positively correlated with degree-scale EIVs for annual range within lowland forests, especially for vascular plant communities.

Conclusion

Overall, the capabilities of EIVs to infer microclimate was inconsistent. Refined EIVs for temperature are needed to capture forest microclimates experienced by understorey species.

Identification and pathogenicity of Colletotrichum species associated with twig dieback of citrus in Western Australia

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Identification and pathogenicity of Colletotrichum species associated with twig dieback of citrus in Western Australia

Citrus twig dieback in Western Australia was shown to be caused by Colletotrichum gloeosporioides, C. karstii and C. novae-zelandiae.


Abstract

Up to 32 Colletotrichum species have been reported to be associated with pre- or postharvest diseases of citrus globally, while in Australia, six species have been reported to cause citrus leaf and fruit disease. Twig or shoot dieback has recently been observed as an emerging disease in citrus orchards in Western Australia. Colletotrichum species were isolated from diseased twigs showing dieback (withertip) or lesions, with or without gummosis, collected from 12 varieties of orange, mandarin and lemon. Colletotrichum gloeosporioides sensu stricto, Colletotrichum karstii and Colletotrichum novae-zelandiae were identified using a polyphasic approach that included multigene phylogenetic analysis using sequences of internal transcribed spacer and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (gapdh), β-tubulin (tub2), actin (act) and histone (his3) for isolates in the boninense species complex, and Apn2–Mat1–2 intergenic spacer and partial mating type (Mat1–2) (ApMat) and glutamine synthetase (gs) for isolates in the gloeosporioides species complex, as well as morphological characteristics. C. gloeosporioides was the most prevalent species associated with twig dieback in Western Australia, while C. novae-zelandiae was reported for the first time in Australia. Pathogenicity tests on shoot twigs from lemon and orange trees confirmed C. gloeosporioides, C. karstii and C. novae-zelandiae as the cause of twig dieback, with C. gloeosporioides being the most aggressive species. Knowledge of the species causing twig dieback and their lifestyle will assist the development of integrated control methods.

Comparative genomics identifies genetic markers linked to structural variations that differentiate Puccinia graminis tritici and secalis formae speciales

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Comparative genomics identifies genetic markers linked to structural variations that differentiate Puccinia graminis tritici and secalis formae speciales

Newly available genome sequence data were harnessed to design four simple PCR-based assays able to distinguish Puccina graminis formae speciales.


Abstract

Stem rust is a serious disease of many gramineous plants including small grain staples such as wheat, barley, rye and triticale. Separate formae speciales (ff. spp.) of the causal fungus, Puccinia graminis, predominantly infect certain host plant genera. However, despite these taxonomic subdivisions, many P. graminis ff. spp. are genetically too similar to distinguish using existing genetic markers. For those infecting cereals, this is particularly challenging for P. graminis f. sp. tritici (Pgt) and P. graminis f. sp. secalis (Pgs). Herein we harnessed newly available genomic data for 39 Pgt and Pgs isolates and identified four regions of structural variation that were used to design four simple PCR-based assays to distinguish the aforementioned formae speciales. These genomic regions display large presence/absence variation between Pgt and Pgs isolates, and yet a high degree of sequence conservation within shared neighbouring regions, facilitating primer design. We also confirmed lack of amplification in host plant genera analysed, which included assessment of the shared alternate host of Pgt and Pgs, Berberis vulgaris. Accurate classification of P. graminis ff. spp. infections on B. vulgaris is exceptionally valuable to rapidly define plants harbouring P. graminis inoculum when adjacent to cereal crops. Finally, we demonstrated utility of these four genetic markers to correctly distinguish a genetically diverse array of Pgt and Pgs isolates. This strategy could now be readily applied to other pathogens of interest, which will be of increasing value as genomic resources continue to rapidly expand for many key biotic threats to agricultural productivity.

The Ralstonia solanacearum effector RipV1 acts as a novel E3 ubiquitin ligase to suppress plant PAMP‐triggered immunity responses and promote susceptibility in potato

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The Ralstonia solanacearum effector RipV1 acts as a novel E3 ubiquitin ligase to suppress plant PAMP-triggered immunity responses and promote susceptibility in potato

Ralstonia solanacearum requires the type III effector RipV1 to exhibit its virulence role, which acts as a novel E3 ubiquitin ligase to suppress plant PAMP-triggered immunity responses and promote susceptibility.


Abstract

Bacterial wilt caused by Ralstonia solanacearum is a destructive plant disease, particularly in potato (Solanum tuberosum). R. solanacearum deploys a diverse and potent arsenal of type III effectors to inhibit the plant immune system. However, the understanding of individual effectors promoting susceptibility in host plants and interfering with plant immunity responses is still limited. Here, we demonstrated that the type III effector RipV1 functioned as a novel E3 ubiquitin ligase (NEL) effector and exhibited E3 ubiquitin ligase activity in vitro. Transient expression of RipV1 suppressed plant pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) responses in Nicotiana benthamiana, such as the expression of PTI-related genes and the reactive oxygen species (ROS) burst. Prolonged expression of RipV1 induced cell death in N. benthamiana leaves. Notably, mutating the conserved cysteine residue of RipV1 abolished its E3 ligase activity and its ability to suppress plant PTI responses. This study also revealed the indispensability of RipV1 for R. solanacearum's full virulence in potato. Transgenic potato plants overexpressing ripV1 but not the catalytic mutant ripV1-C444A displayed enhanced susceptibility to R. solanacearum. RipV1 was observed to localize specifically to the plant plasma membrane, with its N-terminus being pivotal in determining this localization. These findings showcase that RipV1 acts as a NEL effector and contributes to R. solanacearum virulence by suppressing plant PTI responses through its E3 activity.

Development and application of a codominant marker of the melon rind colour gene CmAPRR2

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Abstract

Rind colour is an important quality attribute of melon appearance. Identifying target genes and developing functional molecular markers is significant for rind colour breeding in melon. This study involved a genetic analysis of the fruit rind colours of two inbred lines: H185 (with black green melon rind) and H160 (with white rind) alongside a fruit rind colour gene, CmAPRR2. The purpose was to discover the variation sites of the CmAPRR2 gene and develop specific molecular marker for rind colour in melon. The results showed that the black green rind is dominant over white, and single gene controls the colours. A mutation of the G856T base occurred in the eighth exon of the CmAPRR2 coding DNA region in H160, suggesting that this mutation is the key factor for the white rind colour. Thus, a codominant molecular marker, FC, for gene CmAPRR2 was developed and used for molecular identification of 189 F2 individuals. The marker revealed a complete correspondence between genotype and phenotype. Additionally, the marker revealed that the other four white rinds had G856T mutations. This study provides a basis for targeted improvement of melon rind colours, offering a technical means for molecular marker-assisted breeding of melon rind colours.

Validation of sorghum quality control (QC) markers across African breeding lines

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Abstract

Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (H o) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and H o of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.