Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

Khalil-Ur-Rehman, Muhammad; Sun, Long; Li, Chunxia; Faheem, Muhammad; Wu, Wei; Tao, Jianmin

doi:10.1186/s12870-016-0960-8

Cited by 103 publications

(67 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Significantly enriched gene ontology (GO) terms in clusters 1, 2, 4, and 7 constructed by cluster analysis (Fig. 3) changes, such as dormancy release , Khalil-Ur-Rehman et al, 2017, Liu et al, 2012, cold hardening or both (John et al, 2016).…”

Section: Levels In Terminal Flower Budsmentioning

confidence: 99%

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

Takeuchi¹,

Matsushita²,

Nishiyama³

et al. 2018

J. Amer. Soc. Hort. Sci.

View full text Add to dashboard Cite

Endodormancy release and the fulfillment of the chilling requirement (CR) are critical physiological processes that enable uniform blooming in fruit tree species, including apple (Malus ×domestica). However, the molecular mechanisms underlying these traits have not been fully characterized. The objective of this study was to identify potential master regulators of endodormancy release and the CR in apple. We conducted RNA-Sequencing (RNA-seq) analyses and narrowed down the number of candidates among the differentially expressed genes (DEGs) based on the following two strict screening criteria: 1) the gene must be differentially expressed between endodormant and ecodormant buds under different environmental conditions and 2) the gene must exhibit chill unit (CU)–correlated expression. The results of our cluster analysis suggested that global expression patterns varied between field-grown buds and continuously chilled buds, even though they were exposed to similar amounts of chilling and were expected to have a similar dormancy status. Consequently, our strict selection strategy resulted in narrowing down the number of possible candidates and identified the DEGs strongly associated with the transition between dormancy stages. The genes included four transcription factor genes, PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), FLOWERING LOCUS C (FLC)-LIKE, APETALLA2 (AP2)/ETHYLENE-RESPONSIVE 113 (ERF113), and MYC2. Their expressions were upregulated during endodormancy release, and were correlated with the CU, suggesting that these transcription factors are closely associated with chilling-mediated endodormancy release in apple.

show abstract

Section: Levels In Terminal Flower Budsmentioning

confidence: 99%

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

Takeuchi¹,

Matsushita²,

Nishiyama³

et al. 2018

J. Amer. Soc. Hort. Sci.

View full text Add to dashboard Cite

show abstract

“…Insufficient cold accumulation during this period generally results in non-uniform flowering and reduced fruit set. The grape buds in southeast China can achieve their chilling requirement at the end of February and bloom in the following spring ( Khalil-Ur-Rehman et al, 2017 ). Therefore, to allow coordinated and early production of economically viable yields, artificial substitutes are required for chilling to avoid prolonged dormancy in these regions ( Zheng et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Study on Reagents Involved in Grape Bud Break and Their Effects on Different Metabolites and Related Gene Expression during Winter

Khalil-Ur-Rehman

et al. 2017

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

To elucidate promoting and inhibiting effects of hydrogen cynamide (HC) and abscisic acid (ABA) on quiescence release of grape buds, physiological and molecular approaches were used to explore the mechanisms of quiescence based on metabolic and gene expression analysis. Physiological and molecular mechanisms involved in bud quiescence of grape were studied before and after application of HC, ABA, and ABA-HC. The data showed that ABA inhibited proclamation of quiescence in grape buds and attenuated the influence of HC. Bud quiescence was promoted and regulated by HC and ABA pre-treatment on buds of grape cultivar “Shine Muscat” with 5% HC, 100 μM ABA and combination of ABA-HC (5% HC+100 μM ABA) during quiescence under forcing condition. Exogenous application of ABA elevated superoxide dismutase (SOD), peroxidase (POD) and ascorbate peroxidase (APX) related specific activities, while catalase (CAT) activity was increased during initial period of forcing and then decreased. The concentration of plant growth hormones including gibberellins (GA) and indole acetic acid increased by HC application but decreased the ABA contents under forcing condition. ABA increased the fructose content during quiescence under forcing condition while sucrose and total soluble sugars peaked in HC treated buds as compared to control. Genes related to ABA pathway, protein phosphatase 2C (PP2C family) were down regulated in the buds treated with HC, ABA and ABA-HC as compared to control while two genes related to GA pathway (GID1 family), out of which one gene showed down regulation during initial period of forcing while other gene was up regulated in response to HC and ABA-HC treatments as compared to control. Exogenous ABA application up regulated genes related to antioxidant enzymes as compared to control. The gene probable fructose-bisphosphate aldolase 1, chloroplastic-like, was up regulated in response to ABA treatment as compared to control. Analysis of metabolites and related gene expression pattern would provide a comprehensive view of quiescence after HC, ABA, and ABA-HC treatments in grape buds which may helpful for ultimate improvement in table grape production.

show abstract

“…In the presence of gibberellin, the stable GID1-GA-DELLA complex is recognized by the SCF SLY1 complex which ubiquintylates the DELLA proteins and causes their degradation by the 26S proteasome [71,72]. It has been reported previously that GID1-transcripts are upregulated during bud dormancy in grapevine while transcripts of DELLA are downregulated [73]. Similarly, we found that the GID1B receptor transcript is upregulated during bud dormancy while the DELLA-protein SLR1-like (SLENDER RICE 1 LIKE) are downregulated.…”

Section: Discussionmentioning

confidence: 99%

Characterization of genes and alleles involved in the control of flowering time in grapevine

Kamal

Ochßner

Schwandner

et al. 2019

Preprint

View full text Add to dashboard Cite

34 Grapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. 35 Understanding of developmental processes like flowering, which impact quality and quantity of yield 36 in this species is therefore of high interest. This gets even more important when considering some of 37 the expected consequences of climate change. Earlier bud burst and flowering, for example, may 38 result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine 39 quality. Knowledge of interactions between a genotype or allele combination and the environment 40 can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this 41 end, we have generated a list of more than 500 candidate genes that may play a role in the timing of 42 flowering. The grapevine genome was exploited for flowering time control gene homologs on the 43 basis of functional data from model organisms like A. thaliana. In a previous study, a mapping 44 population derived from early flowering GF.GA-47-42 and late flowering 'Villard Blanc' was 45 analyzed for flowering time QTLs. In a second step we have now established a workflow combining 46 amplicon sequencing and bioinformatics to follow alleles of selected candidate genes in the F 1 47 individuals and the parental genotypes. Allele combinations of these genes in individuals of the 48 mapping population were correlated with early or late flowering phenotypes. Specific allele 49 combinations of flowering time candidate genes within and outside of the QTL regions for flowering 50 time on chromosome 1, 4, 14, 17, and 18 were found to be associated with an early flowering 51 phenotype. In addition, expression of many of the flowering candidate genes was analyzed over 52 consecutive stages of bud and inflorescence development indicating functional roles of these genes in 53 the flowering control network. 54 Introduction 55 The reproductive developmental cycle of grapevine spans two years (S1 Figure). Grapevine plants 56 need intense light and high temperatures to initiate inflorescences during spring, which develop and 57 flower during the subsequent summer [1]. The ongoing tendency to higher temperatures in spring 58 due to global warming causes earlier bud burst and flowering [2]. As a consequence, late spring 59 frost is an increasing risk to viticulture, which may cause significant crop loss [3]. Together with 60 flowering the onset of ripening is shifted towards earlier dates [4,5] and the ripening process occurs 61 under warmer conditions. This influences berry composition [6], affects wine quality and promotes 62 e.g. fungi infection. Grapevine breeding programs aim to keep the production of high quality grapes 63 in a changing environment consistent. Making use of late flowering genotypes may be one approach 64 to compensate for earlier ripening. Understanding the flowering process in grapevine and 65 determining factors that lead to early or late flowering may help to control variation in berry 66 production [7]....

show abstract

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

Cited by 103 publications

References 48 publications

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

Comparative Study on Reagents Involved in Grape Bud Break and Their Effects on Different Metabolites and Related Gene Expression during Winter

Characterization of genes and alleles involved in the control of flowering time in grapevine

Contact Info

Product

Resources

About