Genetic Mapping Combined with a Transcriptome Analysis to Screen for Candidate Genes Responsive to Abscisic Acid Treatment in <i>Brassica napus</i> Embryos During Seed Germination

Di, Feifei; Wang, Tengyue; Ding, Yiran; Chen, Xueping; Wang, Hao; Li, Jiana; Liu, Liezhao

doi:10.1089/dna.2019.5169

Cited by 5 publications

(2 citation statements)

References 58 publications

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“…Importantly, the up-regulated DEGs were largely enriched in "phenylpropanoid metabolic" and "phenylpropanoid biosynthetic" processes. Our GO terms results were highly consistent with previous publication, many candidate genes were related to "response to stimuli", "response to oxygen-containing compounds", "lipid response", as well as "transport and seed dormancy processes" in brassica during seed germination [28]. As significant enrichment in down-regulated DEGs was observed in GO-BP terms related to "cell wall organization or biogenesis", "external encapsulating structure organization", "polysaccharide metabolic process".…”

Section: Identification Of Aba-responsive Genes By Transcriptomesupporting

confidence: 91%

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Chen,

Wu,

et al. 2024

BMC Plant Biol

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Seed germination is an important development process in plant growth. The phytohormone abscisic acid (ABA) plays a critical role during seed germination. However, the mechanism of rapeseed in response to ABA is still elusive. In order to understand changes of rapeseed under exogenous ABA treatment, we explored differentially expressed metabolites (DEMs) and the differentially expressed genes (DEGs) between mock- and ABA-treated seedlings. A widely targeted LC-MS/MS based metabolomics were used to identify and quantify metabolic changes in response to ABA during seed germination, and a total of 186 significantly DEMs were identified. There are many compounds which are involved in ABA stimuli, especially some specific ABA transportation-related metabolites such as starches and lipids were screened out. Meanwhile, a total of 4440 significantly DEGs were identified by transcriptomic analyses. There was a significant enrichment of DEGs related to phenylpropanoid and cell wall organization. It suggests that exogenous ABA mainly affects seed germination by regulating cell wall loosening. Finally, the correlation analysis of the key DEMs and DEGs indicates that many DEGs play a direct or indirect regulatory role in DEMs metabolism. The integrative analysis between DEGs and DEMs suggests that the starch and sucrose pathways were the key pathway in ABA responses. The two metabolites from starch and sucrose pathways, levan and cellobiose, both were found significantly down-regulated in ABA-treated seedlings. These comprehensive metabolic and transcript analyses provide useful information for the subsequent post-transcriptional modification and post germination growth of rapeseed in response to ABA signals and stresses.

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Section: Identification Of Aba-responsive Genes By Transcriptomesupporting

confidence: 91%

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Chen,

Wu,

et al. 2024

BMC Plant Biol

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“…In several studies, combined forward and reverse genetics have been applied for gene detection and mining [ 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 ]. Our study has joined BSA, fine mapping, transcriptome, and polymorphism to detect candidate genes associated with drought tolerance in watermelon.…”

Section: Discussionmentioning

confidence: 99%

Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon

Mahmoud,

Qi,

Chi

et al. 2023

IJMS

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Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.

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Meta-analysis of QTLs controlling seed quality traits based on QTL alignment in Brassica napus

Bilgrami

Liu

Farokhzadeh

et al. 2022

Industrial Crops and Products

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Genetic Mapping Combined with a Transcriptome Analysis to Screen for Candidate Genes Responsive to Abscisic Acid Treatment in Brassica napus Embryos During Seed Germination

Cited by 5 publications

References 58 publications

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon

Meta-analysis of QTLs controlling seed quality traits based on QTL alignment in Brassica napus

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