Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton

Zhang, Yihao; Zhang, Yaning; Ge, Xianping; Yuán, Yǒulù; Jin, Yang; Wang, Ye; Zhao, Lihong; Han, Xiao; Hu, Wei; Liu, Yang; Gao, Chenxu; Xi, Wei; Li, Fuguang; Yang, Zhaoen

doi:10.1186/s13059-023-02950-9

Cited by 14 publications

(3 citation statements)

References 86 publications

(110 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…tomato ( Pst ) DC3000. V. dahliae is a soil‐borne fungal pathogen responsible for severe losses of biomass, yield and quality in plenty of economically important crops including tomato and cotton (Zhang et al ., 2023 ), while P. syringae represents a model biotrophic bacterial pathogen that has been extensively investigated in tomato and Arabidopsis (Xin and He, 2013 ). Three‐week‐old tomato seedlings of wild‐type and sldml2 mutants that display non‐differential stem lengths were inoculated with V. dahliae and the disease response was observed at 18 days post‐inoculation (dpi) (Figure S5a,b ).…”

Section: Resultsmentioning

confidence: 99%

The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

Zhou

Gao

et al. 2023

Plant Biotechnology Journal

View full text Add to dashboard Cite

SummaryFruit ripening and disease resistance are two essential biological processes for quality formation and maintenance. DNA methylation, in the form of 5‐methylcytosine (5mC), has been elucidated to modulate fruit ripening, but its role in regulating fruit disease resistance remains poorly understood. In this study, we show that mutation of SlDML2, the DNA demethylase gene essential for fruit ripening, affects multiple developmental processes of tomato besides fruit ripening, including seed germination, leaf length and width and flower branching. Intriguingly, loss of SlDML2 function decreased the resistance of tomato fruits against the necrotrophic fungal pathogen Botrytis cinerea. Comparative transcriptomic analysis revealed an obvious transcriptome reprogramming caused by SlDML2 mutation during B. cinerea invasion. Among the thousands of differentially expressed genes, SlβCA3 encoding a β‐carbonic anhydrase and SlFAD3 encoding a ω‐3 fatty acid desaturase were demonstrated to be transcriptionally activated by SlDML2‐mediated DNA demethylation and positively regulate tomato resistance to B. cinerea probably in the same genetic pathway with SlDML2. We further show that the pericarp tissue surrounding B. cinerea infection exhibited a delay in ripening with singnificant decrease in expression of ripening genes that are targeted by SlDML2 and increase in expression of SlβCA3 and SlFAD3. Taken together, our results uncover an essential layer of gene regulation mediated by DNA methylation upon B. cinerea infection and raise the possible that the DNA demethylase gene SlDML2, as a multifunctional gene, participates in modulating the trade‐off between fruit ripening and disease resistance.

show abstract

Section: Resultsmentioning

confidence: 99%

The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

Zhou

Gao

et al. 2023

Plant Biotechnology Journal

View full text Add to dashboard Cite

show abstract

“…cDNAs were synthesized using the PrimeScript RT reagent kit with gDNA Eraser (Takara). Reverse transcriptase quantitative PCR (RT‐qPCR) was performed using the SuperReal PreMix Plus Kit (Tiangen), with the following amplification parameters: 94 °C for 5 min, followed by 27 cycles of 98 °C for 15 s, 60 °C for 15 s, and 68 °C for 30 s. The detailed quantitative reverse transcriptase PCR analysis refers to our previous research (Zhang et al ., 2023 ). The gene‐specific primers used for RT‐qPCR were designed using the Primer Database (Lu et al ., 2018 ), which were listed in Table S4 .…”

Section: Methodsmentioning

confidence: 99%

GhRCD1 promotes cotton tolerance to cadmium by regulating the GhbHLH12–GhMYB44–GhHMA1 transcriptional cascade

Wei,

Geng,

Yuan

et al. 2024

Plant Biotechnology Journal

Self Cite

View full text Add to dashboard Cite

SummaryHeavy metal pollution poses a significant risk to human health and wreaks havoc on agricultural productivity. Phytoremediation, a plant‐based, environmentally benign, and cost‐effective method, is employed to remove heavy metals from contaminated soil, particularly in agricultural or heavy metal‐sensitive lands. However, the phytoremediation capacity of various plant species and germplasm resources display significant genetic diversity, and the mechanisms underlying these differences remain hitherto obscure. Given its potential benefits, genetic improvement of plants is essential for enhancing their uptake of heavy metals, tolerance to harmful levels, as well as overall growth and development in contaminated soil. In this study, we uncover a molecular cascade that regulates cadmium (Cd2+) tolerance in cotton, involving GhRCD1, GhbHLH12, GhMYB44, and GhHMA1. We identified a Cd2+‐sensitive cotton T‐DNA insertion mutant with disrupted GhRCD1 expression. Genetic knockout of GhRCD1 by CRISPR/Cas9 technology resulted in reduced Cd2+ tolerance in cotton seedlings, while GhRCD1 overexpression enhanced Cd2+ tolerance. Through molecular interaction studies, we demonstrated that, in response to Cd2+ presence, GhRCD1 directly interacts with GhbHLH12. This interaction activates GhMYB44, which subsequently activates a heavy metal transporter, GhHMA1, by directly binding to a G‐box cis‐element in its promoter. These findings provide critical insights into a novel GhRCD1–GhbHLH12–GhMYB44–GhHMA1 regulatory module responsible for Cd2+ tolerance in cotton. Furthermore, our study paves the way for the development of elite Cd2+‐tolerant cultivars by elucidating the molecular mechanisms governing the genetic control of Cd2+ tolerance in cotton.

show abstract

“…GWASs are an effective strategy for uncovering the genetic architecture of complex traits by associating genetic variations with phenotypic variations at the population level [13][14][15]. Over the last decade, many genetic loci/genes have been identified by using this approach in rice [16], maize [17,18], wheat [19], soybean [20], cotton [21], tomato [22], melon [23], watermelon [24], etc. Thus, GWASs have been widely used to study important traits that are related to plant genetics and breeding, thus effectively promoting germplasm innovation and molecular breeding.…”

Section: Introductionmentioning

confidence: 99%

Identification of Loci for Four Important Agronomic Traits in Loose-Curd Cauliflower Based on Genome-Wide Association Studies

Zhang,

Wen,

Jiang

et al. 2023

Horticulturae

View full text Add to dashboard Cite

Cauliflower is a nutritious vegetable with inflorescences that are specialized to form the edible organs called curds. Uncovering key genes underlying important traits is crucial for the genetic improvement of this important crop. However, the genetic basis of many important agronomic traits, including curd performance and plant architecture in cauliflower, remains unclear. GWASs have proved to be powerful tools to study agronomic traits in many crops. To reveal the genetic basis of four important agronomic traits, namely, the main stem height (MSH), purplish curd (PC), external leaf wing (ELW) and weight of a single curd (WSC), we selected 220 core accessions of loose-curd cauliflower for resequencing, phenotypic investigation and GWAS. The approach revealed significant novel loci. We detected several significant associations: on C02 for MSH and PC, on C06 for ELW and on C01 for WSC. More interestingly, we identified a significant single-peak signal for the weight of a single curd (WSC), an important yield trait, and within this signal interval, we identified the BOB01G136670 gene with five SNPs encoding nonsynonymous mutations in the CDS region; these mutations resulted in two haplotypes with significant differences in curd weight. The weight of a single curd was significantly increased in the varieties with the BOB01G136670 Hap1 allele compared to those with BOB01G136670 Hap2. BOB01G136670 was highly conserved with the homologous genes that encode serine carboxypeptidase and belong to the S10 family in other species, including GS5, which functions as a positive regulator of grain size in rice, wheat and maize. Additionally, BOB01G136670 was highly expressed specifically at the curd enlargement stage, with low or even no expression at all in other tissues and stages, indicating that BOB01G136670 is a plausible candidate gene for WSC. Overall, this study identified genomic loci for four important agronomic traits that are relevant for accelerating biological breeding and the improvement of cauliflower varieties.

show abstract

Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton

Cited by 14 publications

References 86 publications

The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato

GhRCD1 promotes cotton tolerance to cadmium by regulating the GhbHLH12–GhMYB44–GhHMA1 transcriptional cascade

Identification of Loci for Four Important Agronomic Traits in Loose-Curd Cauliflower Based on Genome-Wide Association Studies

Contact Info

Product

Resources

About