Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Malus × domestica Borkh.)

Miotto, Yohanna Evelyn; Tessele, Carolina; Czermainski, A. B. C.; Porto, Diogo Denardi; Falavigna, Vítor da Silveira; Sartor, Tiago; Cattani, Amanda Malvessi; Delatorre, Carla Andréa; Alencar, Sérgio Amorim de; Silva‐Junior, Orzenil B.; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Pappas, George J.; Grynberg, Priscila; Oliveira, P. R. D. de; Kvitschal, Marcus Vinícius; Denardi, Frederico; Buffon, Vanessa; Revers, L. F.

doi:10.3389/fpls.2019.00033

Cited by 30 publications

(26 citation statements)

References 83 publications

(140 reference statements)

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“…Next, we investigated the function of apple MADS TFs during dormancy, as previous genetic and molecular evidence highlighted their roles during the dormancy cycle [4,5,16,25,46,47]. To gain insights whether the observed physical interactions between apple MADS TFs have biological relevance during dormancy, the transcript levels of their encoding genes were quantified during an annual time course (Figure 2D).…”

Section: Resultsmentioning

confidence: 99%

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

Falavigna

Severing

Lai

et al. 2021

Preprint

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Background: The effect of global warming on dormancy and flowering patterns of crop trees threatens world-wide fruit production and food security. In Rosaceous tree species, it is believed that a group of genes encoding MADS transcription factors (TFs) controls temperature-mediated dormancy cycle. These genes are similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis thaliana and referred as DORMANCY-ASSOCIATED MADS-BOX (DAM) genes. Results: By making use of apple tree (Malus x domestica) as a model for Rosaceous species, we have investigated the function of MADS TFs during the dormancy cycle. We found that MdDAM and other dormancy related MADS TFs form multimeric complexes with MdSVPa, and that MdSVPa is essential for the transcriptional complex activity. Then, for the first time in non-model plant species, we performed sequential DNA Affinity Purification sequencing (seq-DAP-seq) to define the genome-wide binding sites of these MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained by the inducible glucocorticoid receptor expression system, and reanalyzing preexisting data related to dormancy cycle in apple trees. Conclusion: We have determined a gene regulatory network formed by MdSVPa-containing complexes that regulate the dormancy cycle in apple trees in response to environmental cues. Key genes identified with our genomic approach and the elucidated regulatory relationships provide leads for breeding fruit trees better adapted to changing climate conditions. Moreover, we provide novel molecular evidence on the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae family.

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Section: Resultsmentioning

confidence: 99%

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

Falavigna

Severing

Lai

et al. 2021

Preprint

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“…By examining the transcript level of PmDAM6 in the mapping population, they proposed that DAM6 may act as a repressor for bud break in a dose-dependent manner in P. mume (Kitamura et al, 2018). A similar QTL study on apple identified a major QTL related to timing of bud break on LG9 that contained orthologs of ICE1, FLOWERING LOCUS C (FLC), and PACLOBUTRAZOL RESISTANCE 1 (PRE1) that are possibly involved in mediating bud break in apple trees (Miotto et al, 2019). With the development of next-generation sequencing, genome-wide association mapping has become an alternative for genetic linkage mapping (Jackson et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume

et al. 2021

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Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.

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“…Even the mechanism of chemicals known to help overcome dormancy and promote budbreak (i.e., hydrogen cyanamide) is yet to be described (35). It is possible that this is due to the fact that most studies compare species and genotypes with "low chill" and "high chill" requirement based on time to budbreak [e.g., (36)(37)(38)]. The results presented here suggest that those chill requirements are mostly a result of a genotype's response to forcing (r = -0.78) and not different stages of dormancy.…”

Section: Implications Of a Conserved Dormancy Progressionmentioning

confidence: 99%

“…However, there are still questions about which temperatures promote chilling and how much chilling they provide (26,27), leading to multiple methods for estimation of chill accumulation based on temperature (28)(29)(30)(31)(32). This is in part due to the fact that a mechanism for dormancy has yet to be resolved, despite a growing list of dormancy related genes and chemicals that promote dormancy transitions (33)(34)(35)(36)(37)(38). Recent work has shown that rates of cold hardiness loss (deacclimation) increase with chilling accumulation, which can be used to study dormancy progression (24).…”

Section: Introductionmentioning

confidence: 99%

Woody species do not differ in dormancy progression: differences in time to budbreak due to forcing and cold hardiness

Kovaleski

2021

Preprint

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Budbreak is one of the most observed and studied phenological phases in perennial plants. Two dimensions of exposure to temperature are generally used to model budbreak: accumulation of time spent at low temperatures (chilling); and accumulation of heat units (forcing). These two effects have a well-established negative correlation: the more chilling, the less forcing required for budbreak. Furthermore, temperate plant species are assumed to vary in amount of chilling required to complete endodormancy and begin the transition to breaking bud. Still, prediction of budbreak remains a challenge. The present work demonstrates across a wide range of species how bud cold hardiness must be accounted for to study dormancy and accurately predict time to budbreak. Cold hardiness defines the path length to budbreak, meaning the difference between the cold hardiness buds attain during the winter, and the cold hardiness at which deacclimated buds are predicted to open. This distance varies among species and throughout winter within a species. Increases in rate of cold hardiness loss (deacclimation) measured throughout winter show that chilling controls deacclimation potential – the proportion of the maximum rate response attained at high chill accumulation – which has a sigmoid relationship to chilling accumulation. For forcing, rates of deacclimation increase non-linearly in response to temperature. Comparisons of deacclimation potential show a dormancy progresses similarly for all species. This observation suggests that comparisons of physiologic and genetic control of dormancy requires an understanding of cold hardiness dynamics and the necessity for an update of the framework for studying dormancy and its effects on spring phenology.

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Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Malus × domestica Borkh.)

Cited by 30 publications

References 83 publications

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume

Woody species do not differ in dormancy progression: differences in time to budbreak due to forcing and cold hardiness

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