Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes
Abstract Background The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quali...
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | BMC Genomic Data |
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| Online Access: | https://doi.org/10.1186/s12863-022-01098-y |
| _version_ | 1797863396642652160 |
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| author | Xingfei Fu Guiping Li Faguang Hu Jiaxiong Huang Yuqiang Lou Yaqi Li Yanan Li Hongyan He YuLan Lv Jinhuan Cheng |
| author_facet | Xingfei Fu Guiping Li Faguang Hu Jiaxiong Huang Yuqiang Lou Yaqi Li Yanan Li Hongyan He YuLan Lv Jinhuan Cheng |
| author_sort | Xingfei Fu |
| collection | DOAJ |
| description | Abstract Background The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quality are yet largely unknown in peaberry. A transcriptome analysis was performed by using peaberry and regular coffee beans in this study. Results The result of phenotypic analysis stated a difference in the physical attributes of both coffee beans. In addition, transcriptome analysis revealed low genetic differences. Only 139 differentially expressed genes were detected in which 54 genes exhibited up-regulation and 85 showed down-regulations in peaberry beans compared to regular beans. The majority of differentially expressed genes had functional annotation with cell wall modification, lipid binding, protein binding, oxidoreductase activity, and transmembrane transportation. Many fold lower expression of Ca25840-PMEs1, Ca30827-PMEs2, Ca30828-PMEs3, Ca25839-PMEs4, Ca36469-PGs. and Ca03656-Csl genes annotated with cell wall modification might play a critical role to develop different bean shape patterns in Arabica. The ERECTA family genes Ca15802-ERL1, Ca99619-ERL2, Ca07439-ERL3, Ca97226-ERL4, Ca89747-ERL5, Ca07056-ERL6, Ca01141-ERL7, and Ca32419-ERL8 along lipid metabolic pathway genes Ca06708-ACOX1, Ca29177-ACOX2, Ca01563-ACOX3, Ca34321-CPFA1, and Ca36201-CPFA2 are predicted to regulate different shaped bean development. In addition, flavonoid biosynthesis correlated genes Ca03809-F3H, Ca95013-CYP75A1, and Ca42029-CYP75A2 probably help to generate rarely formed peaberry beans. Conclusion Our results provide molecular insights into the formation of peaberry. The data resources will be important to identify candidate genes correlated with the different bean shape patterns in Arabica. |
| first_indexed | 2024-04-09T22:34:55Z |
| format | Article |
| id | doaj.art-5cf17482ea64496db0e61da3c19934f8 |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-04-09T22:34:55Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-5cf17482ea64496db0e61da3c19934f82023-03-22T12:31:24ZengBMCBMC Genomic Data2730-68442023-02-0124111310.1186/s12863-022-01098-yComparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genesXingfei Fu0Guiping Li1Faguang Hu2Jiaxiong Huang3Yuqiang Lou4Yaqi Li5Yanan Li6Hongyan He7YuLan Lv8Jinhuan Cheng9Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural SciencesAbstract Background The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quality are yet largely unknown in peaberry. A transcriptome analysis was performed by using peaberry and regular coffee beans in this study. Results The result of phenotypic analysis stated a difference in the physical attributes of both coffee beans. In addition, transcriptome analysis revealed low genetic differences. Only 139 differentially expressed genes were detected in which 54 genes exhibited up-regulation and 85 showed down-regulations in peaberry beans compared to regular beans. The majority of differentially expressed genes had functional annotation with cell wall modification, lipid binding, protein binding, oxidoreductase activity, and transmembrane transportation. Many fold lower expression of Ca25840-PMEs1, Ca30827-PMEs2, Ca30828-PMEs3, Ca25839-PMEs4, Ca36469-PGs. and Ca03656-Csl genes annotated with cell wall modification might play a critical role to develop different bean shape patterns in Arabica. The ERECTA family genes Ca15802-ERL1, Ca99619-ERL2, Ca07439-ERL3, Ca97226-ERL4, Ca89747-ERL5, Ca07056-ERL6, Ca01141-ERL7, and Ca32419-ERL8 along lipid metabolic pathway genes Ca06708-ACOX1, Ca29177-ACOX2, Ca01563-ACOX3, Ca34321-CPFA1, and Ca36201-CPFA2 are predicted to regulate different shaped bean development. In addition, flavonoid biosynthesis correlated genes Ca03809-F3H, Ca95013-CYP75A1, and Ca42029-CYP75A2 probably help to generate rarely formed peaberry beans. Conclusion Our results provide molecular insights into the formation of peaberry. The data resources will be important to identify candidate genes correlated with the different bean shape patterns in Arabica.https://doi.org/10.1186/s12863-022-01098-yCoffea arabicaTranscriptome analysisGene expressionBean qualityBean components |
| spellingShingle | Xingfei Fu Guiping Li Faguang Hu Jiaxiong Huang Yuqiang Lou Yaqi Li Yanan Li Hongyan He YuLan Lv Jinhuan Cheng Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes BMC Genomic Data Coffea arabica Transcriptome analysis Gene expression Bean quality Bean components |
| title | Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes |
| title_full | Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes |
| title_fullStr | Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes |
| title_full_unstemmed | Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes |
| title_short | Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes |
| title_sort | comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes |
| topic | Coffea arabica Transcriptome analysis Gene expression Bean quality Bean components |
| url | https://doi.org/10.1186/s12863-022-01098-y |
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