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      Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach

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          Abstract

          Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot ( Prunus armeniaca) genotypes with contrasting bloom dates and peach ( Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box ( DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.

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          Molecular Regulation of CBF Signaling in Cold Acclimation

          Cold stress restricts plant growth, development, and distribution. Understanding how plants transduce and respond to cold signals has long been a topic of interest. Traditional genetic and molecular analyses have identified C-repeat/DREB binding factors (CBFs) as key transcription factors that function in cold acclimation. Recent studies revealed the involvement of pivotal protein kinases and transcription factors in CBF-dependent signaling, expanding our knowledge of cold signal transduction from perception to downstream gene expression events. In this review, we summarize recent advances in our understanding of the molecular regulation of these core components of the CBF cold signaling pathway. Knowledge of the mechanism underlying the ability of plants to survive freezing temperatures will facilitate the development of crop plants with increased freezing tolerance.
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            The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms.

            In tree species native to temperate and boreal regions, the activity-dormancy cycle is an important adaptive trait both for survival and growth. We discuss recent research on mechanisms controlling the overlapping developmental processes that define the activity-dormancy cycle, including cessation of apical growth, bud development, induction, maintenance and release of dormancy, and bud burst. The cycle involves an extensive reconfiguration of metabolism. Environmental control of the activity-dormancy cycle is based on perception of photoperiodic and temperature signals, reflecting adaptation to prevailing climatic conditions. Several molecular actors for control of growth cessation have been identified, with the CO/FT regulatory network and circadian clock having important coordinating roles in control of growth and dormancy. Other candidate regulators of bud set, dormancy and bud burst have been identified, such as dormancy-associated MADS-box factors, but their exact roles remain to be discovered. Epigenetic mechanisms also appear to factor in control of the activity-dormancy cycle. Despite evidence for gibberellins as negative regulators in growth cessation, and ABA and ethylene in bud formation, understanding of the roles that plant growth regulators play in controlling the activity-dormancy cycle is still very fragmentary. Finally, some of the challenges for further research in bud dormancy are discussed. © 2012 Blackwell Publishing Ltd.
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              Comparative mapping and marker-assisted selection in Rosaceae fruit crops.

              The development of saturated linkage maps using transferable markers, restriction fragment length polymorphisms, and micro-satellites has provided a foundation for fruit tree genetics and breeding. A Prunus reference map with 562 such markers is available, and a further set of 13 maps constructed with a subset of these markers has allowed genome comparison among seven Prunus diploid (x = 8) species (almond, peach, apricot, cherry, Prunus ferganensis, Prunus davidiana, and Prunus cerasifera); marker colinearity was the rule with all of them. Preliminary results of the comparison between apple and Prunus maps suggest a high level of synteny between these two genera. Conserved genomic regions have also been detected between Prunus and Arabidopsis. By using the data from different linkage maps anchored with the reference Prunus map, it has been possible to establish, in a general map, the position of 28 major genes affecting agronomic characters found in different species. Markers tightly linked to the major genes responsible for the expression of important traits (disease/pest resistances, fruit/nut quality, self-incompatibility, etc.) have been developed in apple and Prunus and are currently in use for marker-assisted selection in breeding programs. Quantitative character dissection using linkage maps and candidate gene approaches has already started. Genomic tools such as the Prunus physical map, large EST collections in both Prunus and Malus, and the establishment of the map position of high numbers of ESTs are required for a better understanding of the Rosaceae genome and to foster additional research and applications on fruit tree genetics.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                28 February 2020
                2020
                : 11
                : 180
                Affiliations
                [1] 1 Genome Science and Technology Program, University of Tennessee , Knoxville, TN, United States
                [2] 2 Forest Health Research and Education Center, University of Kentucky , Lexington, KY, United States
                [3] 3 Department of Plant Pathology, The Ohio State University , Columbus, OH, United States
                [4] 4 UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Universite de Bordeaux , Villenave d'Ornon, France
                [5] 5 Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, the Pennsylvania State University , University Park, PA, United States
                [6] 6 Center for Environmental Biotechnology, University of Tennessee , Knoxville, TN, United States
                [7] 7 Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service , Kearneysville, WV, United States
                [8] 8 GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA , Montfavet, France
                [9] 9 Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee , Knoxville, TN, United States
                Author notes

                Edited by: Michael James Considine, University of Western Australia, Australia

                Reviewed by: Hisayo Yamane, Kyoto University, Japan; Gabino Ríos, Instituto Valenciano de Investigaciones Agrarias, Spain; Carmen Leida, Fondazione Edmund Mach, Italy

                *Correspondence: Margaret E. Staton, mstaton1@ 123456utk.edu

                This article was submitted to Plant Physiology, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2020.00180
                7059448
                32180783
                728beace-fa4e-4a56-9aaa-c4a35a56a736
                Copyright © 2020 Yu, Conrad, Decroocq, Zhebentyayeva, Williams, Bennett, Roch, Audergon, Dardick, Liu, Abbott and Staton

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 05 November 2019
                : 06 February 2020
                Page count
                Figures: 9, Tables: 4, Equations: 0, References: 169, Pages: 24, Words: 13425
                Funding
                Funded by: National Institute of Food and Agriculture 10.13039/100005825
                Award ID: 2016–67014-24577
                Funded by: Agence Nationale de la Recherche 10.13039/501100001665
                Award ID: ANR-11-CHEX-0002
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                dormancy,prunus,floral buds,transcriptome,chill requirement,bloom date,co-expression network,rnaseq

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