Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)

Hedley, Pete E.; Russell, Joanne; Jorgensen, Linzi; Gordon, Sandra; Morris, Jenny; Hackett, Christine A.; Cardle, Linda; Brennan, Rex

doi:10.1186/1471-2229-10-202

Cited by 60 publications

(45 citation statements)

References 49 publications

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“…Examples of recently published omics studies using agronomically important fruit tree species include: grapevine (Vitis spp.) (Diaz-Riquelme et al, 2012;Mathiason et al, 2009); Japanese pear (Pyrus pyrifolia) Liu et al, 2012;Nishitani et al, 2012); chestnut (Castanea sativa) (Santamaría et al, 2011); raspberry (Rubus idaeus) (Mazzitelli et al, 2007); blackcurrant (Ribes nigrum L.) (Hedley et al, 2010); and Prunus spp. (described in detail below).…”

Section: Introductionmentioning

confidence: 99%

Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold ^|^amp; Zucc.) and Peach [Prunus persica (L.) Batsch]: A Summary of Recent Studies

Yamane

2014

J. Japan. Soc. Hort. Sci.

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Bud dormancy allows most deciduous fruit tree species to avoid injury in unsuitable environments, synchronize their annual growth, and adapt to a temperate zone climate. Because bud dormancy affects next season's fruit production and vegetative growth, it is considered one of the most important physiological factors that control fruit production. Recent global climate changes require us to better understand the genetic factors regulating bud dormancy, especially those that induce dormancy release and subsequent bud break. In this review, environmental factors that affect the seasonal dormancy depth of Japanese apricot (P. mume Siebold & Zucc.) and peach [P. persica (L.) Batsch] are first outlined. Next, recent progress of genetic, biochemical, and molecular biological studies of Prunus dormancy regulation is described. Recent advances in functional genomics have promoted the discovery of gene function and gene networks associated with bud dormancy regulation. A group of candidate genes for bud dormancy regulation, the DORMANCY-ASSOCIATED MADS-box (DAM) genes in Prunus, are focused. Recently reported expressional analysis suggests a significant role for DAMs in dormancy release and bud break of Japanese apricot and peach vegetative buds. Transformation studies of PmDAM6 have demonstrated that it has an inhibitory effect on the apical growth of poplar (Populus spp.). As bud dormancy is a quantitative polygenic trait, not only DAMs, but also other genes and gene networks appear to regulate bud dormancy. Ongoing and future studies will undoubtedly facilitate the unveiling of the molecular aspects of bud dormancy regulation in temperate fruit tree species of Prunus.

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Section: Introductionmentioning

confidence: 99%

Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold ^|^amp; Zucc.) and Peach [Prunus persica (L.) Batsch]: A Summary of Recent Studies

Yamane

2014

J. Japan. Soc. Hort. Sci.

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“…MADS-box genes named DORMANCY ASSOCIATED MADS-box (DAM) have been found related to dormancy processes in poplar (Ruttink et al, 2007), raspberry (Mazzitelli et al, 2007), japanese apricot (Yamane et al, 2008), leafy spurge (Horvath et al, 2008) and blackcurrant (Hedley et al, 2010), suggesting similar mechanisms of dormancy control in perennial plants.…”

Section: In Perennial Plants Short Vegetative Phase (Svp)-like/agamoumentioning

confidence: 99%

“…The relevance of these transcription factors is highlighted by the abundant literature showing dormancy-dependent regulation of DAM-like genes in other species as poplar (Ruttink et al, 2007;Druart et al, 2004), raspberry (Mazzitelli et al, 2007), Japanese apricot (Yamane et al, 2008), leafy spurge (Horvath et al, 2008), blackcurrant (Hedley et al, 2010) as well as in peach fruit tissue after cold storage (Ogundiwin et al, 2008). The seasonal expression pattern of DAM genes in peach indicates that they are induced at different stages: DAM3, DAM5 and DAM6 during dormancy entrance, and DAM1, DAM2 and DAM4 during terminal bud formation (Li et al, 2009).…”

Section: Regulation Of Gene Expression Dam-like Transcription Factorsmentioning

confidence: 99%

Molecular aspects of dormancy in peach (Prunus persica [L.] Batsch.)

Leida¹

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En estos cuatros años en los que he estado trabajando, he conocido a mucha gente que me ha ayudado en distintas formas para la realización de esta tesis y por eso he pensado en agradecerlos.En primer lugar quería dar las gracias a mis directores por la dedicación que me han prestado. A Gerardo y Marisa por darme la oportunidad de trabajar en el IVIA y de desarrollar esta tesis. A Gabino por haber estado ahí en todo momento, para enseñar y contestar a mis preguntas, sin su apoyo no habría podido llegar hasta aquí. ABSTRACTDormancy is one of the most important adaptive mechanisms developed by perennial plants, in order to survive the low temperatures of autumn and winter in temperate climates. The study of the genes regulated during dormancy release is crucial to understand the process, with the final objective of the development of new varieties with a better adaptation to certain environments; and this is particularly important considering the increasing economical weight of fruit crops in low and medium chilling regions as the Mediterranean area. We focused on the molecular and physiological mechanisms underlying the maintenance and release of seasonal dormancy in peach. In order to achieve this we first used suppression subtractive hybridization (SSH) to identify genes expressed in dormant and dormancy-released buds in two cultivars with different chilling requirements, 'Zincal-5' and 'Springlady', and subsequently validated their differential expression utilizing a peach cDNA microarray platform containing transcripts enriched in flower buds. Additionally, we carried out a genome-wide search of peach genes related to dormancy release by hybridizing the previous cDNA microarray with mRNA samples from 10 cultivars showing different dormancy behaviour, followed by an expression correlation analysis.Among the most relevant genes identified in these two first works, we found the DORMANCY ASSOCIATED MADS-box genes DAM4, DAM5 and DAM6, described independently by other groups working in peach and other species. The central role of DAM genes in dormancy regulation has also been confirmed by additional functional approaches as the analysis of the non-dormant evg mutant, QTL analysis, and transgenic approaches.In our second work we focused on the molecular mechanisms of DAM6 down-regulation concomitant with dormancy release in flower buds. A ChIP analysis of DAM6 promoter and structural gene revealed chromatin modification events similar to those observed in vernalization of Arabidopsis and cereals. We showed that DAM6 is transcriptionally active in dormant buds collected in October, when a short chromatin region around its ATG was trimethylated in histone H3 at K4 (H3K4) and acetylated at the N-terminal tail of H3. Concomitantly with DAM6 repression, H3K4 became demethylated and H3 deacetylated. Later H3K27 was found trimethylated along a genomic region larger than 4kb, including promoter, coding sequence and intron. Due to their relevance in dormancy regulation, DAM genes could be used as expression markers to assess...

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“…(Ko et al, 2011;Ruttink et al, 2007), raspberry (Rubus idaeus L.) (Mazzitelli et al, 2007), grapevine (Vitis riparia Michx.) (Mathiason et al, 2009), blackcurrant (Ribes nigrum L.) (Hedley et al, 2010), and leafy spurge (Euphobia esula L.) (Doğramaci et al, 2010). A substantial amount of the target transcriptome is required for microarray-based gene expression analysis and, at present, the expressed sequence tag (EST) information is insufficient for analyses of gene expression in dormant buds of Prunus species.…”

Section: Introductionmentioning

confidence: 99%

454-Pyrosequencing of the Transcriptome in Leaf and Flower Buds of Japanese Apricot (Prunus mume Sieb. et Zucc.) at Different Dormant Stages

Habu

Yamane

Igarashi

et al. 2012

J. Japan. Soc. Hort. Sci.

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Bud dormancy in temperate woody perennials is a complex process consisting of three different stages; paradormancy, endodormancy, and ecodormancy. Endodormant buds differ from the other types of dormant buds in that they cannot resume growth under favorable conditions. Because endodormant buds require a certain amount of chilling accumulation for the transition to ecodormancy, genes showing chilling-mediated differential expression patterns are candidates for internal factors controlling endodormancy. To search for genes controlling the endodormancy of Japanese apricot (Prunus mume Sieb. et Zucc.), we performed 454-pyrosequencing to examine gene expression patterns of the dormant leaf and flower buds of Japanese apricot at three different stages of dormancy. We also used buds from branches that had been collected at the endodormant stage and treated with cold or non-cold temperatures. From 485,376 reads generated, we obtained 28,382 contigs and 85,247 singletons, of which 47,401 (41.7%) were annotated by BLAST searches against the non-redundant NCBI protein/ nucleotide database. Among them, only 2,530 sequences showed high sequence similarity to Prunus genes in the database, while the remaining 44,871 sequences showed similarity to known genes of other genera and were novel in Prunus. Functional classification by the gene ontology (GO) term indicated that the genes obtained in this study function in a relatively wide range of biological processes. We searched for up-regulated genes in endodormant leaf and flower buds and found that 74 and 82 genes, respectively, were up-regulated at the endodormant stage as compared with the paradormant stage. About one-third of them, 21 and 25 genes in the leaf and flower buds, respectively, were down-regulated at the ecodormant stage as compared with the endodormant stage. P. mume DORMANCY-ASSOCIATED MADS (PmDAM) genes were among those that were up-regulated preferentially in endodormant buds. From the EST data obtained, we constructed a "Japanese apricot dormant bud EST database" (JADB) for future studies on dormancy in Prunus.

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Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)

Cited by 60 publications

References 49 publications

Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold ^|^amp; Zucc.) and Peach [Prunus persica (L.) Batsch]: A Summary of Recent Studies

Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold ^|^amp; Zucc.) and Peach [Prunus persica (L.) Batsch]: A Summary of Recent Studies

Molecular aspects of dormancy in peach (Prunus persica [L.] Batsch.)

454-Pyrosequencing of the Transcriptome in Leaf and Flower Buds of Japanese Apricot (Prunus mume Sieb. et Zucc.) at Different Dormant Stages

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