Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization

Leida, Carmen; Terol, Javier; Martí, Gracia; Agustí, Manuel; Llácer, G.; Badenes, M. L.; Ríos, Gabino

doi:10.1093/treephys/tpq008

Cited by 98 publications

(143 citation statements)

References 37 publications

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“…Initial attempts to discover genes related to bud dormancy release used strategies of relatively small-scale expression profiling at the genomic level. These included the cDNA-AFLP technique in apricot (Čechová et al, 2012) and the RNA subtraction technique in Japanese apricot (Yamane et al, 2008) and peach (Leida et al, 2010(Leida et al, , 2012. Then, strategies moved to a more comprehensive genome-wide basis that used RNA sequencing with SGS (RNA-seq) …”

Section: ) Identification Of Dormancy-associated Madsbox Genes In Prmentioning

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: ) Identification Of Dormancy-associated Madsbox Genes In Prmentioning

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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“…Such ESTs and other related to plant dormancy for the first time in this work provide insight into the signals and processes regulating bud dormancy in general, and offer a series of gene sequences susceptible to be used for marker-assisted selection in peach breeding. DAM1 and DAM6 are up-regulated during bud growth cessation, following a change from long to short day photoperiod (Jiménez et al, 2010a), and down-regulated during dormancy release in two different peach cultivars (Leida et al, 2010). In a recent work, the expression of DAM5 and DAM6…”

Section: Discussionmentioning

confidence: 94%

“…We have performed a genome-wide search for peach genes related to bud dormancy by hybridizing a cDNA microarray containing bud-enriched probes (Leida et al, 2010) with RNA samples from cultivars showing diverse dormancy behaviour, followed by an expression correlation analysis. The DAM6 gene identified in this study was subjected to a detailed analysis by localizing histone H3 modifications associated to dormancy release in its promoter and coding region.…”

Section: Discussionmentioning

confidence: 99%

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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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“…The most stable genes were TEF2, UBQ10, and RPII for different tissues, genotypes and environmental conditions. Some studies used other genes as reference genes, including Act (Leida et al, 2010(Leida et al, , 2012 and Tua5 (Li et al, 2009).…”

Section: Description and Expression Profiling Of Candidate Reference mentioning

confidence: 99%

Identification of reference genes for RT-qPCR analysis in peach genotypes with contrasting chilling requirements

et al. 2017

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ABSTRACT. Selecting and validating reference genes are the first steps in studying gene expression by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The present study aimed to evaluate the stability of five reference genes for the purpose of normalization when studying gene expression in various cultivars of Prunus persica with different chilling requirements. Flower bud tissues of nine peach genotypes from Embrapa's peach breeding program with different chilling requirements were used, and five candidate reference genes based on the RT-qPCR that were useful for studying the relative quantitative gene expression and stability were evaluated using geNorm, NormFinder, and bestKeeper software packages. The results indicated that among the genes tested, the most stable genes to be used as reference genes are Act and UBQ10. This study is the first survey of the stability of reference genes in peaches under chilling stress and provides guidelines for more accurate RT-qPCR results.

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Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization

Cited by 98 publications

References 37 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.)

Identification of reference genes for RT-qPCR analysis in peach genotypes with contrasting chilling requirements

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