Leveraging Discarded Sequencing Reads to Uncover Natural Variation in Pest Resistance in the Emerging Crop Thlaspi arvense

Centrala begrepp

Non-target sequencing reads from plant DNA can be leveraged as proxies to quantify natural variation in plant resistance to pests such as aphids and powdery mildew.

Sammanfattning

The study explored the possibility of using non-target sequencing reads from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (Thlaspi arvense) to estimate intensities of plant-pest interactions. The plants had been grown in a common environment and spontaneously colonized by aphids, mildew and other microbes.
Key highlights:

Classified sequencing reads into target (T. arvense), ambiguous (mapping to both T. arvense and pests) and exogenous (non-target) reads. Removed ambiguous reads to avoid false variant calls.
Taxonomically classified the exogenous reads using MG-RAST and competitive mapping, identifying the aphid Myzus persicae and the powdery mildew Erysiphe cruciferarum as the main pests.
Found significant population differences and moderate heritability (>15%) for the abundances of these pests and other microbes, suggesting genetic determination of plant resistance.
Pest loads were associated with climate of origin, with plants from colder and more thermally fluctuating habitats showing higher aphid and mildew DNA loads, likely due to lower resistance.
Pest loads also correlated with baseline glucosinolate levels, with benzyl glucosinolates negatively associated with aphid abundance.
Genome-wide association analyses identified genetic variants near known defense genes, as well as novel regions associated with variation in aphid and mildew DNA loads.
Epigenome-wide association analyses revealed differentially methylated regions associated with pathogen loads, including hypomethylation in the promoter of a gene involved in stomatal closure, potentially induced by pathogens.

Statistik

The climate of origin of the Thlaspi arvense lines was negatively correlated with annual minimum temperature (r = -0.41, p < 0.001) and positively correlated with temperature variability (mean diurnal range: r = 0.37, p < 0.001; temperature annual range: r = 0.35, p < 0.001).
The abundance of the aphid Myzus persicae was positively correlated with the total glucosinolate content (r = 0.26, p < 0.001) and the most abundant glucosinolate sinigrin (r = 0.25, p < 0.001), but negatively correlated with benzyl glucosinolates (r = -0.32, p < 0.001).

Citat

"Plants from colder and more thermally fluctuating climates, which are less favorable to aphids, were less well defended and performed worse in our glasshouse."
"Benzyl glucosinolates might have a deterrent effect, while sinigrin might on the contrary attract M. persicae or act as a stimulant."
"Hypomethylation of the MAPKKK20 promoter might induce its overexpression and consequent stomatal closure, thereby preventing mildew access to the leaf blade."

Viktiga insikter från

Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense

by Gala... på www.biorxiv.org 10-20-2023

https://www.biorxiv.org/content/10.1101/2023.10.17.562203v2

Djupare frågor

How could the insights from this study on natural variation in pest resistance be leveraged to develop more pest-resistant Thlaspi arvense cultivars for biofuel and cover crop applications

The insights gained from this study on natural variation in pest resistance in Thlaspi arvense can be instrumental in developing more pest-resistant cultivars for biofuel and cover crop applications. By identifying genetic variants associated with pest resistance through Genome-Wide Association (GWA) analyses, researchers can pinpoint specific genes and alleles that contribute to resistance against pests like aphids and powdery mildew. These genetic markers can then be used in breeding programs to selectively breed Thlaspi arvense cultivars with enhanced pest resistance. By incorporating these resistance alleles into breeding strategies, it is possible to develop new cultivars that are better equipped to withstand pest pressures, leading to increased crop yields and reduced reliance on pesticides. Additionally, understanding the role of glucosinolates in pest resistance, as highlighted in the study, can further guide breeding efforts by focusing on enhancing the production of specific glucosinolates that are effective against pests.

What other plant-pest interactions beyond aphids and powdery mildew could be quantified using this approach of leveraging non-target sequencing reads

Beyond aphids and powdery mildew, the approach of leveraging non-target sequencing reads can be applied to quantify a wide range of other plant-pest interactions. For example, this method can be used to study interactions with other herbivorous insects, such as caterpillars, beetles, or mites, by identifying non-target reads associated with these pests in plant sequencing data. Additionally, it can be extended to investigate interactions with fungal pathogens, bacterial pathogens, or viruses that affect plant health. By analyzing the abundance of non-target reads corresponding to different pests or pathogens, researchers can gain insights into the prevalence and intensity of these interactions in plant populations. This information is valuable for understanding the genetic basis of plant defense mechanisms and for developing strategies to enhance resistance against a broader range of pests and pathogens.

Could the observed associations between DNA methylation and pest loads provide insights into the epigenetic regulation of plant defense mechanisms

The observed associations between DNA methylation and pest loads in the study provide valuable insights into the epigenetic regulation of plant defense mechanisms. The differential methylation patterns identified in response to pest infestations, such as hypomethylation of specific genomic regions associated with pest resistance, suggest that epigenetic modifications play a role in modulating plant responses to biotic stressors. These findings indicate that plants may dynamically adjust their DNA methylation profiles in response to pest attacks, potentially activating defense-related genes or pathways through demethylation. By linking specific DNA methylation changes to pest resistance traits, researchers can uncover the epigenetic mechanisms underlying plant defense responses and explore how these mechanisms contribute to the adaptation of plants to biotic stress. Understanding the epigenetic regulation of plant defense can provide new avenues for improving pest resistance in crops through targeted manipulation of DNA methylation patterns.