Transcriptome analysis of fruit development of a citrus late-ripening mutant by microarray

Zeng, Jiwu; Gao, Chongyang; Deng, Guiming; Jiang, Bo; XinXiang, Peng; Zhong, Yun; Zhou, Birong; Li, Kai

doi:10.1016/j.scienta.2011.10.018

Cited by 10 publications

(8 citation statements)

References 41 publications

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“…Accumulation of PR proteins has also been demonstrated during ripening of other fruits [ 8 , 53 , 54 ]. For example, large-scale analysis of gene expression differences in peels between late ripening cultivar of citrus and its wild type revealed that 7 genes were significantly differentially expressed, including two disease resistance-responsive protein-related genes and one chitinase gene [ 55 ]. The two disease resistance-responsive protein-related genes and chitinase gene were all up-regulated in the late ripening cultivar.…”

Section: Discussionmentioning

confidence: 99%

Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Guo

et al. 2016

BMC Genomics

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BackgroundEarly ripening is an important desirable attribute for fruit crops. ‘Kyoho’ is a popular table grape cultivar in many Asian countries. ‘Fengzao’ is a bud mutant of ‘Kyoho’ and ripens nearly 30 days earlier than ‘Kyoho’. To identify genes controlling early fruit development and ripening in ‘Fengzao’, RNA-Seq profiles of the two cultivars were compared at 8 different berry developmental stages in both berry peel and flesh tissues.MethodsRNA-Seq profiling of berry development between ‘Kyoho’ and ‘Fenzhao’ were obtained using the Illumina HiSeq system and analyzed using various statistical methods. Expression patterns of several selected genes were validated using qRT-PCR.ResultsAbout 447 millions of RNA-Seq sequences were generated from 40 RNA libraries covering various different berry developmental stages of ‘Fengzao’ and ‘Kyoho’. These sequences were mapped to 23,178 and 22,982 genes in the flesh and peel tissues, respectively. While most genes in ‘Fengzao’ and ‘Kyoho’ shared similar expression patterns over different berry developmental stages, there were many genes whose expression were detected only in ‘Fengzao’ or ‘Kyoho’. We observed 10 genes in flesh tissue and 22 genes in peel tissue were differentially expressed at FDR ≤ 0.05 when the mean expression of ‘Fengzao’ and ‘Kyoho’ were compared. The most noticeable one was VIT_214s0030g00950 (a superoxide dismutase gene). This ROS related gene showed lower expression levels in ‘Fengzao’ than ‘Kyoho’ in both peel and flesh tissues across various berry developmental stages with the only exception at véraison. VIT_200s0238g00060 (TMV resistance protein n-like) and VIT_213s0067g01100 (disease resistance protein at3g14460-like) were the two other noticeable genes which were found differentially expressed between the two cultivars in both peel and flesh tissues. GO functional category and KEGG enrichment analysis of DEGs indicated that gene activities related to stress and ROS were altered between the two cultivars in both flesh and peel tissues. Several differentially expressed genes of interest were successfully validated using qRT-PCR.ConclusionsComparative profiling analysis revealed a few dozens of genes which were differentially expressed in the developing berries of ‘Kyoho’ and its early ripening mutant ‘Fengzao’. Further analysis of these differentially expressed genes suggested that gene activities related to ROS and pathogenesis were likely involved in contributing to the early ripening in ‘Fengzao’.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3051-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Guo

et al. 2016

BMC Genomics

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“…The bud mutant and its original cultivar are excellent materials to identify and describe the molecular mechanisms involved in citrus fruit maturation [5]. Some mutants display changes in fruit color, like the ‘Tardivo’ mandarin, a late ripening mutant of the ‘Comune’ clementine and Mingliutianju, a late-ripening mutant of Chuntianju, that have been analyzed at the transcriptome level [27, 28]. More recently, RNA-Seq technique has been used for transcriptome comparative studies between wild sweet orange cultivars and several mutants: Hong Angliu orange that displays a red flesh phenotype [29]; and mutant oranges Fengwan [30], and Jincheng [31] that produce late ripening fruits.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness

et al. 2019

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BackgroundHarvest time is a relevant economic trait in citrus, and selection of cultivars with different fruit maturity periods has a remarkable impact in the market share. Generation of early- and late-maturing cultivars is an important target for citrus breeders, therefore, generation of knowledge regarding the genetic mechanisms controlling the ripening process and causing the early and late phenotypes is crucial. In this work we analyze the evolution of the transcriptome during fruit ripening in 3 sport mutations derived from the Fina clementine (Citrus clementina) mandarin: Clemenules (CLE), Arrufatina (ARR) and Hernandina (HER) that differ in their harvesting periods. CLE is considered a mid-season cultivar while ARR and HER are early- and late-ripening mutants, respectively.ResultsWe used RNA-Seq technology to carry out a time course analysis of the transcriptome of the 3 mutations along the ripening period. The results indicated that in these mutants, earliness and lateness during fruit ripening correlated with the advancement or delay in the expression of a set of genes that may be implicated in the maturation process. A detailed analysis of the transcription factors known to be involved in the regulation of fruit ripening identified a member of the MADS box family whose expression was lower in ARR, the early-ripening mutant, and higher in HER, the late-ripening mutant. The pattern of expression of this gene during the maturation period was basically contrary to those of the ethylene biosynthetic genes, SAM and ACC synthases and ACC oxidase. The gene was present in hemizygous dose in the early-ripening mutant.ConclusionsOur analysis provides new clues about the genetic control of fruit ripening in citrus and allowed the identification of a transcription factor that could be involved in the early phenotype.Electronic supplementary materialThe online version of this article (10.1186/s12870-019-1651-z) contains supplementary material, which is available to authorized users.

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“…Mingliutianju), as a late-ripening mutant of Chuntianju, was analyzed at the transcriptome level, revealing 18 different biological processes including flavonols' metabolism. And these 18 processes may be related to its mutation [7] . The ‘Fengwan’ orange ( Citrus sinensis L. Osbeck), as a late ripening mutant of the ‘Fengjie 72-1’ orange, was analyzed at the transcriptome and proteome levels during three fruit ripening stages, indicating the importance of sucrose and abscisic acid to fruit ripening [8] .…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analyses between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild Type Suggest the Functions of ABA, Sucrose and JA during Citrus Fruit Ripening

Zhang

Wang

et al. 2014

PLoS ONE

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A spontaneous late-ripening mutant of ‘Jincheng’ (C. sinensis L. Osbeck) sweet orange exhibited a delay of fruit pigmentation and harvesting. In this work, we studied the processes of orange fruit ripening through the comparative analysis between the Jincheng mutant and its wild type. This study revealed that the fruit quality began to differ on 166th days after anthesis. At this stage, fruits were subjected to transcriptome analysis by RNA sequencing. 13,412 differentially expressed unigenes (DEGs) were found. Of these unigenes, 75.8% were down-regulated in the wild type, suggesting that the transcription level of wild type was lower than that of the mutant during this stage. These DEGs were mainly clustered into five pathways: metabolic pathways, plant-pathogen interaction, spliceosome, biosynthesis of plant hormones and biosynthesis of phenylpropanoids. Therefore, the expression profiles of the genes that are involved in abscisic acid, sucrose, and jasmonic acid metabolism and signal transduction pathways were analyzed during the six fruit ripening stages. The results revealed the regulation mechanism of sweet orange fruit ripening metabolism in the following four aspects: First, the more mature orange fruits were, the lower the transcription levels were. Second, the expression level of PME boosted with the maturity of the citrus fruit. Therefore, the expression level of PME might represent the degree of the orange fruit ripeness. Third, the interaction of PP2C, PYR/PYL, and SnRK2 was peculiar to the orange fruit ripening process. Fourth, abscisic acid, sucrose, and jasmonic acid all took part in orange fruit ripening process and might interact with each other. These findings provide an insight into the intricate process of sweet orange fruit ripening.

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Transcriptome analysis of fruit development of a citrus late-ripening mutant by microarray

Cited by 10 publications

References 41 publications

Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness

Comparative Transcriptome Analyses between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild Type Suggest the Functions of ABA, Sucrose and JA during Citrus Fruit Ripening

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