Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq

Ma, Xiaolele; Zhao, Fangyuan; Lin, Hong; Guo, Yongfeng

doi:10.1186/s12864-022-08788-y

Cited by 14 publications

(9 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This overlap may be due to both intra- and interspecific variations being influenced by similar selective pressures in cold environments. AIL1 has been identified as an ethylene response factor and a transcription factor responsive to cold in grape ( Ma et al., 2022 ). CALS5 plays a crucial role in preserving the proper formation of callose walls during pollen development and responding to biotic stress ( Dong et al., 2005 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic basis of local adaptation in the cold-tolerant mangrove Kandelia obovata

Zou,

Wang,

Zhou

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

Understanding the genetic basis of local adaption is crucial in the context of global climate change. Mangroves, as salt-tolerant trees and shrubs in the intertidal zone of tropical and subtropical coastlines, are particularly vulnerable to climate change. Kandelia obovata, the most cold-tolerant mangrove species, has undergone ecological speciation from its cold-intolerant counterpart, Kandelia candel, with geographic separation by the South China Sea. In this study, we conducted whole-genome re-sequencing of K. obovata populations along China’s southeast coast, to elucidate the genetic basis responsible for mangrove local adaptation to climate. Our analysis revealed a strong population structure among the three K. obovata populations, with complex demographic histories involving population expansion, bottleneck, and gene flow. Genome-wide scans unveiled pronounced patterns of selective sweeps in highly differentiated regions among pairwise populations, with stronger signatures observed in the northern populations compared to the southern population. Additionally, significant genotype-environment associations for temperature-related variables were identified, while no associations were detected for precipitation. A set of 39 high-confidence candidate genes underlying local adaptation of K. obovata were identified, which are distinct from genes under selection detected by comparison between K. obovata and its cold-intolerant relative K. candel. These results significantly contribute to our understanding of the genetic underpinnings of local adaptation in K. obovata and provide valuable insights into the evolutionary processes shaping the genetic diversity of mangrove populations in response to climate change.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic basis of local adaptation in the cold-tolerant mangrove Kandelia obovata

Zou,

Wang,

Zhou

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…Our results indicate that there are complex mechanisms underlying the decrease in the supercooling ability of grape compound buds during deacclimation. Several transcriptomic studies have focused on deacclimating grape buds (Meitha et al, 2018; Kovaleski & Londo, 2019), although more studies have focused on the cold acclimation process (Xin et al, 2013; Fennell et al, 2015; Kim et al, 2017; Ma et al, 2022). Such comprehensive analyses may shed light on the factors contributing to the reduction in supercooling ability as well as dormancy release and growth resumption in grape buds.…”

Section: Discussionmentioning

confidence: 99%

Vessel development in compound buds of interspecific hybrid grape induced by artificial deacclimation treatments

Kasuga,

Kawase,

Kamigaki

et al. 2023

Physiologia Plantarum

View full text Add to dashboard Cite

Grape compound buds adapt to subfreezing temperatures in winter by supercooling, but the supercooling ability is thought to be lost upon formation of xylem connections between canes and buds. It was reported that compound buds of the Vitis vinifera variety 'Chardonnay' lack xylem cells in mid-winter, and that vessels differentiate during deacclimation. However, the pattern of vessel formation in compound buds may differ in cold-hardy Vitis species and interspecific hybrid varieties grown in colder regions.We investigated vessel formation in compound buds of the interspecific hybrid variety 'Yamasachi', which were harvested in mid-winter, during artificial deacclimation treatments. Before these treatments, 'Yamasachi' buds had a high supercooling ability (approx. À30 C) and contained cells with characteristics of vessel elements, that is, secondary wall thickening and lignification, at the basal parts. However, the cells still contained organelles and did not have a hydraulic conductivity function. Xylem continuity between the canes and buds was established from day 7 of deacclimation at 20 C. The different pattern of seasonal vessel formation in compound buds of 'Yamasachi' from that of V. vinifera may reflect the rapid development traits of Vitis species growing in cold regions with short growing seasons.

show abstract

“…Comparative transcriptional analysis using RNA-seq is a commonly used method to search for genes differentially expressed between two samples. This method is also generally used to mine plants for genes involved in disease resistance, as has been done in peanut [ 6 ], grape [ 7 ], pear [ 8 ] and apple [ 9 ]. Genomic analysis has been also used in sesame [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola

Jia,

Ni,

Zhao

et al. 2024

BMC Plant Biol

View full text Add to dashboard Cite

Background Corynespora leaf spot is a common leaf disease occurring in sesame, and the disease causes leaf yellowing and even shedding, which affects the growth quality of sesame. At present, the mechanism of sesame resistance to this disease is still unclear. Understanding the resistance mechanism of sesame to Corynespora leaf spot is highly important for the control of infection. In this study, the leaves of the sesame resistant variety (R) and the sesame susceptible variety (S) were collected at 0–48 hpi for transcriptome sequencing, and used a combined third-generation long-read and next-generation short-read technology approach to identify some key genes and main pathways related to resistance. Results The gene expression levels of the two sesame varieties were significantly different at 0, 6, 12, 24, 36 and 48 hpi, indicating that the up-regulation of differentially expressed genes in the R might enhanced the resistance. Moreover, combined with the phenotypic observations of sesame leaves inoculated at different time points, we found that 12 hpi was the key time point leading to the resistance difference between the two sesame varieties at the molecular level. The WGCNA identified two modules significantly associated with disease resistance, and screened out 10 key genes that were highly expressed in R but low expressed in S, which belonged to transcription factors (WRKY, AP2/ERF-ERF, and NAC types) and protein kinases (RLK-Pelle_DLSV, RLK-Pelle_SD-2b, and RLK-Pelle_WAK types). These genes could be the key response factors in the response of sesame to infection by Corynespora cassiicola. GO and KEGG enrichment analysis showed that specific modules could be enriched, which manifested as enrichment in biologically important pathways, such as plant signalling hormone transduction, plant-pathogen interaction, carbon metabolism, phenylpropanoid biosynthesis, glutathione metabolism, MAPK and other stress-related pathways. Conclusions This study provides an important resource of genes contributing to disease resistance and will deepen our understanding of the regulation of disease resistance, paving the way for further molecular breeding of sesame.

show abstract

Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq

Cited by 14 publications

References 90 publications

Genetic basis of local adaptation in the cold-tolerant mangrove Kandelia obovata

Genetic basis of local adaptation in the cold-tolerant mangrove Kandelia obovata

Vessel development in compound buds of interspecific hybrid grape induced by artificial deacclimation treatments

Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola

Contact Info

Product

Resources

About