| Pepper is one of the most important vegetable crops widely cultivated in the world and has a high economic value.Fruit is the most important economic product of pepper,and the development of fruit involves many physiological,biochemical and internal molecular mechanism regulation changes.At present,the rapid development of transcriptomics and proteomics technology has provided important help for the analysis of fruit development mechanism and quality formation regulation mechanism of tomato,apple,grape and many other economic crops.In this study,the physiological and biochemical indexes,microRNA identification,transcriptome and proteome sequencing of peppers at different stages of development were determined.At the level of gene and protein,the response and regulation mechanism of capsicum fruit development were studied in combination with the physiological phenotypes.The main results are as follows:(1)Through the study on the change of quality related physical and chemical properties of five different genotype pepper fruits in four different development stages,the quality change rule was discussed.The results showed that the contents of total soluble sugar,fructose,sucrose,glucose,soluble protein,total amino acid,vitamin C,vitamin E,capsaicin and lignin all increased with the development of fruit,while cellulose and hemicellulose decreased.The change from green stage to breaker stage was the most important stage in the whole fruit development process,in which fructose,sucrose,glucose,total soluble sugar,soluble protein,total amino acid,vitamin C,capsanthin and capsaicin increased significantly from green stage to breaker stage.Correlation analysis showed that there was a positive correlation between other qualities except cellulose and hemicellulose.(2)Through the identification and analysis of small RNAs in four samples at 30 days,40 days,50 days of SJ11-3 and 30 days of 06g19-1-1-1 pepper fruit,we identified 59 known miRNAs by mirdeep2 software,belonging to 17 miRNA families;meanwhile,310 novel miRNAs were alos identified,from which 656 novel miRNA target genes were predicted,and 402 of them were identified Annotations.The results of KEGG annotation showed that the target genes were mainly involved in RNA degradation,ribosome,cysteine and methionine metabolism during the development of pepper fruit;at 30 days of capsicum fruit development,there were significant differences between the two capsicum materials in amino acid and ribose metabolism,starch and sucrose metabolism.(3)Through the transcriptome sequencing of SJ11-3 and 06g19-1-1-1 pepper fruits,23349 genes were identified in four different developmental stages.Among these genes,17361 and 17083 were identified to express in all four different developmental stages of SJ11-3 and 06g19-1-1-1,respectively.In the comparison of adjacent development stages,the number of differentially expressed genes in Br/MG stage was the largest,and there were 8160 and 5252 differentially expressed genes in SJ11-3’and 06g19-1-1-1,respectively.SJ11-3 and 06g19-1-1-1 showed the lowest number of differentially expressed genes in MR/Br and MG/IMG stages,with 1782 and 1490,respectively.GO functional enrichment analysis showed that these differentially expressed genes are largely enriched in oxidation-reduction process,membrane and integral component of membrane.KEGG functional enrichment analysis showed that the differentially expressed genes were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites.(4)On the basis of transcriptome studies,the proteomic analysis on the fruits of two pepper materials at four different stages of development was carried out by using label free technology,and a total of 5455 proteins were identified.Of these proteins,2568 and 2139 were identified to express in all four different developmental stages of SJ11-3 and 06g19-1-1-1,respectively.In the comparison of adjacent development stages,the number of differentially expressed proteins in Br/MG stage was the largest,and there were 408 and 634 differentially expressed proteins in SJ11-3 and06g19-1-1-1,respectively.The number of differentially expressed proteins in MG/IMG stage was the least,only 181 and 193,respectively.GO functional enrichment analysis showed that the differentially expressed proteins were mainly enriched in photosynthesis of molecular function and thylakoid of cell component in the late stage of fruit development.KEGG functional enrichment analysis showed that a large number of differentially expressed proteins were enriched in endoplasmic reticulum,photosynthesis and photosynthesis-antenna proteins pathways during fruit development.(5)Through the correlation analysis of transcriptome and proteome data,we found that more than 95% of the identified proteins can be correlated to the corresponding transcriptome genes,but the proportion of differentially expressed proteins that can be correlated to the differentially expressed genes in the transcriptome decreased significantly.Those proteins that can be correlated to differentially expressed genes can be annotated into 41 go functional groups,and the main annotation term is metabolic process,cell physiological process,stimulation response,catalytic activity,binding,cell,cell component and organelle.KEGG functional enrichment analysis also showed that these correlated differentially expressed genes/proteins could be enriched in endoplasmic reticulum,photosynthesis and photosynthesis antenna proteins.(6)In this study,integration of the transcriptome and proteome profiles uncovered a number of candidate transcripts/proteins that might be involved in capsanthin,vitamin E,and vitamin C biosynthesis and cell wall metabolism during fruit development and ripening.In peppers,the synthesis of capsanthin is mainly regulated by key proteins especially geranylgeranyl diphosphate synthase 1(Capana04g000412)and capsanthin/capsorubin synthase 1(Capana06g000615).The synthesis of vitamin E is mainly regulated by proteins GGPS1,geranylgeranyl diphosphate reductase(Capana03g000791)and tocopherol cyclase(Capana08g000837).GGPS1 is involved not only in the regulation of capsanthin synthesis,but also in the regulation of tocopherol synthesis.In early stages of pepper fruit development,the catalytic products of GGPS1 are mainly used in the synthesis of tocopherol,while in later stages,they are mainly used in the synthesis of capsanthin.The synthetic pathway of vitamin C is mainly regulated by proteins GDP-L-galactose phosphorylase(Capana06g000722)and GDP-mannose pyrophosphorylase(Capana03g002806). |
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