The Dormancy-associated MADS-box(DAM)gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit,chilling response and floral bud developmental p...The Dormancy-associated MADS-box(DAM)gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit,chilling response and floral bud developmental pace.Yet,how different temperature regimes interact with and regulate the six linked DAM genes remains unclear.Here,we demonstrate that chilling downregulates DAM1 and DAM3–6 in dormant floral buds with distinct patterns and identify DAM4 as the most abundantly expressed one.We reveal multiple epigenetic events,with tri-methyl histone H3 lysine 27(H3K27me3)induced by chilling specifically in DAM1 and DAM5,a 21-nt sRNA in DAM3 and a ncRNA induced in DAM4.Such induction is inversely correlated with downregulation of their cognate DAMs.We also show that the six DAMs were hypermethylated,associating with the production of 24-nt sRNAs.Hence,the chilling-responsive dynamic of the different epigenetic elements and their interactions likely define distinct expression abundance and downregulation pattern of each DAM.We further show that the expression of the five DAMs remains steadily unchanged or continuously downregulated at the ensuing warm temperature after chilling,and this state of regulation correlates with robust increase of sRNA expression,H3K27me3 and CHH methylation,which is particularly pronounced in DAM4.Such robust increase of repressive epigenetic marks may irreversibly reinforce the chillingimposed repression of DAMs to ensure flower-developmental programming free from any residual DAM inhibition.Taken together,we reveal novel information about genetic and epigenetic regulation of the DAM cluster in peach,which will be of fundamental significance in understanding of the regulatory mechanisms underlying chilling requirement and dormancy release,and of practical application for improvement of plasticity of flower time and bud break in fruit trees to adapt changing climates.展开更多
Cucumber,Cucumis sativus L.(2n=2x=14),is an important vegetable crop worldwide.It was the first specialty crop with a publicly available draft genome.Its relatively small,diploid genome,short life cycle,and selfcompat...Cucumber,Cucumis sativus L.(2n=2x=14),is an important vegetable crop worldwide.It was the first specialty crop with a publicly available draft genome.Its relatively small,diploid genome,short life cycle,and selfcompatible mating system offers advantages for genetic studies.In recent years,significant progress has been made in molecular mapping,and identification of genes and QTL responsible for key phenotypic traits,but a systematic review of the work is lacking.Here,we conducted an extensive literature review on mutants,genes and QTL that have been molecularly mapped or characterized in cucumber.We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped.For each gene,detailed information was compiled including chromosome locations,allelic variants and associated polymorphisms,predicted functions,and diagnostic markers that could be used for marker-assisted selection in cucumber breeding.We also documented 322 QTL for 42 quantitative traits,including 109 for disease resistances against seven pathogens.By alignment of these QTL on the latest version of cucumber draft genomes,consensus QTL across multiple studies were inferred,which provided insights into heritable correlations among different traits.Through collaborative efforts among public and private cucumber researchers,we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber.This is the first attempt to systematically summarize,analyze and inventory cucumber mutants,cloned or mapped genes and QTL,which should be a useful resource for the cucurbit research community.展开更多
The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivat...The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health benefits.The recent publication of the first highquality chromosome-scale octoploid strawberry genome(cv.Camarosa)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research questions.In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture.Among these are the origins of the genome,characterization of genetic variants,and big data approaches to breeding.Key areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen interactions.In order to realize this potential as a global community,investments in genome resources must be continually augmented.展开更多
基金funded by the ARS-INHouse fund,USDA-NIFA grant(3200000379-16-182)the National Natural Science Foundation of China(31772371)and AoE grant(AoE/M-403/16).
文摘The Dormancy-associated MADS-box(DAM)gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit,chilling response and floral bud developmental pace.Yet,how different temperature regimes interact with and regulate the six linked DAM genes remains unclear.Here,we demonstrate that chilling downregulates DAM1 and DAM3–6 in dormant floral buds with distinct patterns and identify DAM4 as the most abundantly expressed one.We reveal multiple epigenetic events,with tri-methyl histone H3 lysine 27(H3K27me3)induced by chilling specifically in DAM1 and DAM5,a 21-nt sRNA in DAM3 and a ncRNA induced in DAM4.Such induction is inversely correlated with downregulation of their cognate DAMs.We also show that the six DAMs were hypermethylated,associating with the production of 24-nt sRNAs.Hence,the chilling-responsive dynamic of the different epigenetic elements and their interactions likely define distinct expression abundance and downregulation pattern of each DAM.We further show that the expression of the five DAMs remains steadily unchanged or continuously downregulated at the ensuing warm temperature after chilling,and this state of regulation correlates with robust increase of sRNA expression,H3K27me3 and CHH methylation,which is particularly pronounced in DAM4.Such robust increase of repressive epigenetic marks may irreversibly reinforce the chillingimposed repression of DAMs to ensure flower-developmental programming free from any residual DAM inhibition.Taken together,we reveal novel information about genetic and epigenetic regulation of the DAM cluster in peach,which will be of fundamental significance in understanding of the regulatory mechanisms underlying chilling requirement and dormancy release,and of practical application for improvement of plasticity of flower time and bud break in fruit trees to adapt changing climates.
基金supported by grants from the National Institute of Food and Agriculture,U.S.Department of Agriculture,under award numbers and 2015-51181-24285 and 2017-67013-26195(to Y.Q.W.)。
文摘Cucumber,Cucumis sativus L.(2n=2x=14),is an important vegetable crop worldwide.It was the first specialty crop with a publicly available draft genome.Its relatively small,diploid genome,short life cycle,and selfcompatible mating system offers advantages for genetic studies.In recent years,significant progress has been made in molecular mapping,and identification of genes and QTL responsible for key phenotypic traits,but a systematic review of the work is lacking.Here,we conducted an extensive literature review on mutants,genes and QTL that have been molecularly mapped or characterized in cucumber.We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped.For each gene,detailed information was compiled including chromosome locations,allelic variants and associated polymorphisms,predicted functions,and diagnostic markers that could be used for marker-assisted selection in cucumber breeding.We also documented 322 QTL for 42 quantitative traits,including 109 for disease resistances against seven pathogens.By alignment of these QTL on the latest version of cucumber draft genomes,consensus QTL across multiple studies were inferred,which provided insights into heritable correlations among different traits.Through collaborative efforts among public and private cucumber researchers,we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber.This is the first attempt to systematically summarize,analyze and inventory cucumber mutants,cloned or mapped genes and QTL,which should be a useful resource for the cucurbit research community.
基金funding from USDA National Institute of Food and Agriculture Specialty Crop Research Initiative projects[2014-51181-22376,2014-51181-22378]USDA National Institute of Food and Agriculture National Research Support Project 10+1 种基金NSF Plant Genome Research Program award#444573,NSF CIF21 Data infrastructure Building Blocks award#1443040USDA Hatch project 1014919,California Strawberry Commission,Florida Strawberry Growers Association,Washington Tree Fruit Research Commission,and Washington State University.
文摘The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health benefits.The recent publication of the first highquality chromosome-scale octoploid strawberry genome(cv.Camarosa)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research questions.In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture.Among these are the origins of the genome,characterization of genetic variants,and big data approaches to breeding.Key areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen interactions.In order to realize this potential as a global community,investments in genome resources must be continually augmented.
