Integrated Metabolomic and Transcriptomic Analysis of the Quinoa Seedling Response to High Relative Humidity Stress

Li, Xinyi; Zhang, Ping; Liu, Jia; Wang, Hongxin; Liu, Junna; Li, Hanxue; Xie, Heng; Wang, Qianchao; Li, Li; Zhang, Shan; Huang, Liubin; Liu, Chenghong; Qin, Peng

doi:10.3390/biom13091352

Cited by 4 publications

(1 citation statement)

References 83 publications

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“…An analysis of the differential expression of genes between the two groups was performed using DESeq2 v1.22.1, corrected p-values were calculated using the Benjamini-Hochberg method, and the threshold for significant differential expression was calculated using corrected p-values and the |log2foldchange|. Extensively targeted metabolomic analyses were performed using the method of Li et al [51], based on the self-built Metware database, lyophilized samples were analyzed for absorbed extracts using an LC-electrospray ionization-MS/MS system(CNWBOND Carbon-GCB SPE Cartridge, 250 mg, 3 mL; Shanghai Ampere Scientific Instruments, Shanghai, China), and metabolites were quantified using a multiple reaction monitoring method. Metabolites with a variable importance in projection score > 1 and with a difference of >2 times or <0.5 times between the control and experimental groups were considered to be significantly different [30].…”

Section: Data Acquisitionmentioning

confidence: 99%

Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA

Zhang,

Jiang,

Wang

et al. 2024

IJMS

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Quinoa is a nutritious crop that is tolerant to extreme environmental conditions; however, low-temperature stress can affect quinoa growth, development, and quality. Considering the lack of molecular research on quinoa seedlings under low-temperature stress, we utilized a Weighted Gene Co-Expression Network Analysis to construct weighted gene co-expression networks associated with physiological indices and metabolites related to low-temperature stress resistance based on transcriptomic data. We screened 11 co-expression modules closely related to low-temperature stress resistance and selected 12 core genes from the two modules that showed the highest associations with the target traits. Following the functional annotation of these genes to determine the key biological processes and metabolic pathways involved in low-temperature stress, we identified four important transcription factors involved in resistance to low-temperature stress: gene-LOC110731664, gene-LOC110736639, gene-LOC110684437, and gene-LOC110720903. These results provide insights into the molecular genetic mechanism of quinoa under low-temperature stress and can be used to breed lines with tolerance to low-temperature stress.

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Section: Data Acquisitionmentioning

confidence: 99%

Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA

Zhang,

Jiang,

Wang

et al. 2024

IJMS

Self Cite

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Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines

Huang,

Zhang,

Zhang

et al. 2024

BMC Genomics

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Background Quinoa, as a new food crop, has attracted extensive attention at home and abroad. However, the natural disaster of spike germination seriously threatens the quality and yield of quinoa. Currently, there are limited reports on the molecular mechanisms associated with spike germination in quinoa. Results In this study, we utilized transcriptome sequencing technology and successfully obtained 154.51 Gb of high-quality data with a comparison efficiency of more than 88%, which fully demonstrates the extremely high reliability of the sequencing results and lays a solid foundation for subsequent analysis. Using these data, we constructed a weighted gene co-expression network (WGCNA) related to starch, sucrose, α-amylase, and phenolic acid metabolites, and screened six co-expression modules closely related to spike germination traits. Two of the modules associated with physiological indicators were analyzed in depth, and nine core genes were finally predicted. Further functional annotation revealed four key transcription factors involved in the regulation of dormancy and germination processes: gene LOC110698065, gene LOC110696037, gene LOC110736224, and gene LOC110705759, belonging to the bHLH, NF-YA, MYB, and FAR1 gene families, respectively. Conclusions These results provide clues to identify the core genes involved in quinoa spike germination. This will ultimately provide a theoretical basis for breeding new quinoa varieties with resistance.

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Variability of morphological and phenological traits in Vigna unguiculata (L.) Walp. accessions contrasting by growth type in different ecological and geographical conditions

Krylova,

Chunikhina,

Boyko

et al. 2024

Biotehnologiâ i selekciâ rastenij

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Background. Cowpea (Vigna unguiculata (L.) Walp.) is a thermophilic crop that occupies the third place in the world in terms of cultivation area among leguminous crops. Vegetable cowpea cultivars are successfully cultivated in the open ground in Russia, in its southern regions and the south of the Far East. The creation of new cultivars adapted to cultivation in different regions and suitable for widespread industrial production, is extremely relevant. Materials and methods. The variability of 20 morphological and 3 phenological traits of six cowpea accessions with different growth habit types and architectonics was assessed in various ecological and geographical conditions at VIR experiment stations (in Astrakhan Province, Primorye Territory and Krasnodar Territory) in 2019-2022. The variability and interrelationships of the traits were estimated using basic and multivariate statistical methods. Results. The analysis revealed a significant influence of the factor complex (genotype/accession, research location) on the variability of traits. Phenological traits, the length of internodes and leaflets, depended most strongly on the research location. The range of variation in the number of nodes, branches, peduncles and beans per plant, stem thickness and bean size were determined by the genotype to a larger extent. The range of stem length variability was significantly influenced by the research location and the genotype, though the genotype had a stronger influence. The genotypes responded differently to changes in growing conditions. For the most of the studied accessions, an increase in the main stem length was noted in the monsoon climate conditions of the Primorye Territory, for some of them the type of growth habit changed from determinate to indeterminate. In our research, the plant length was positively correlated with the amount of precipitation and with the average relative air humidity. Excessive humidity and precipitation had minimal effect only on cv. ʻLyanchiheʼ, whose plants retained dwarfness and compact architectonics. Factor analysis (principal factors analysis) revealed 4 factors responsible for the main part of the variance of the analyzed traits. The characteristics of the leaf were combined in the first factor, those of architectonics and time of plant development in the second, features of the seedling and the juvenile stage in the third, and those of the bean in the fourth factor. These complexes of traits (factors) determined the variability of cowpea in our research. Conclusion. The performed analysis of morphological and phenological traits revealed a significant increase of stem length and changes in plant architectonics under conditions of high relative humidity and a large amount of precipitation. In some cases, even the type of growth habit was changed. The further research on the studied characters variability involving more accessions and the determination of molecular mechanisms that control stability of the growth habit type and length of the stem will allow us to proceed to a more efficient and rapid creation of new cultivars suitable for mechanized cultivation. This is extremely important for the development of new areas by cultivating species, the demand in which as a source of food and feed is increasing in the Russian Federation.

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Integrated Metabolomic and Transcriptomic Analysis of the Quinoa Seedling Response to High Relative Humidity Stress

Cited by 4 publications

References 83 publications

Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA

Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA

Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines

Variability of morphological and phenological traits in Vigna unguiculata (L.) Walp. accessions contrasting by growth type in different ecological and geographical conditions

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