Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq
Abstract Background Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of the molecular mechanism of alfalfa defoliation traits remains unclear...
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5180-1 |
| _version_ | 1828446558498062336 |
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| author | Qiming Cheng Shiqie Bai Gentu Ge Ping Li Liying Liu Chengdong Zhang Yushan Jia |
| author_facet | Qiming Cheng Shiqie Bai Gentu Ge Ping Li Liying Liu Chengdong Zhang Yushan Jia |
| author_sort | Qiming Cheng |
| collection | DOAJ |
| description | Abstract Background Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of the molecular mechanism of alfalfa defoliation traits remains unclear. The transcriptome database created by RNA-Seq is used to identify critical genes related to defoliation traits. Results In this study, we sequenced the transcriptomes of the Zhungeer variety (with easy leaf abscission) and WL319HQ variety (without easy leaf abscission). Among the identified 66,734 unigenes, 706 differentially expressed genes (DEGs) upregulated, and 392 unigenes downregulated in the Zhungeer vs WL319HQ leaf. KEGG pathway annotations showed that 8,414 unigenes were annotated to 87 pathways and contained 281 DEGs. Six DEGs belonging to the “Carotenoid biosynthesis”, “Plant hormone signal transduction” and “Circadian rhythm-plant” pathways involved in defoliation traits were identified and validated by RT-qPCR analyses. Conclusions This study used RNA-Seq to discover genes associated with defoliation traits between two alfalfa varieties. Our transcriptome data dramatically enriches alfalfa functional genomic studies. In addition, these data provide theoretical guidance for field production practice and genetic breeding, as well as references for future study of defoliation traits in alfalfa. |
| first_indexed | 2024-12-10T22:14:08Z |
| format | Article |
| id | doaj.art-a4fc9b310b5e41f48b1ba2ddbfd8ee4c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T22:14:08Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-a4fc9b310b5e41f48b1ba2ddbfd8ee4c2022-12-22T01:31:31ZengBMCBMC Genomics1471-21642018-11-011911810.1186/s12864-018-5180-1Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-SeqQiming Cheng0Shiqie Bai1Gentu Ge2Ping Li3Liying Liu4Chengdong Zhang5Yushan Jia6College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural UniversitySichuan Academy of Grassland SciencesCollege of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural UniversitySichuan Academy of Grassland SciencesInner Mongolia Academy of Forestry ScienceSchool of Biotechnology and Biomolecular Sciences, University of New South WalesCollege of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural UniversityAbstract Background Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of the molecular mechanism of alfalfa defoliation traits remains unclear. The transcriptome database created by RNA-Seq is used to identify critical genes related to defoliation traits. Results In this study, we sequenced the transcriptomes of the Zhungeer variety (with easy leaf abscission) and WL319HQ variety (without easy leaf abscission). Among the identified 66,734 unigenes, 706 differentially expressed genes (DEGs) upregulated, and 392 unigenes downregulated in the Zhungeer vs WL319HQ leaf. KEGG pathway annotations showed that 8,414 unigenes were annotated to 87 pathways and contained 281 DEGs. Six DEGs belonging to the “Carotenoid biosynthesis”, “Plant hormone signal transduction” and “Circadian rhythm-plant” pathways involved in defoliation traits were identified and validated by RT-qPCR analyses. Conclusions This study used RNA-Seq to discover genes associated with defoliation traits between two alfalfa varieties. Our transcriptome data dramatically enriches alfalfa functional genomic studies. In addition, these data provide theoretical guidance for field production practice and genetic breeding, as well as references for future study of defoliation traits in alfalfa.http://link.springer.com/article/10.1186/s12864-018-5180-1AlfalfaTranscriptomeDifferentially expressed genes (DEGs)Defoliation |
| spellingShingle | Qiming Cheng Shiqie Bai Gentu Ge Ping Li Liying Liu Chengdong Zhang Yushan Jia Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq BMC Genomics Alfalfa Transcriptome Differentially expressed genes (DEGs) Defoliation |
| title | Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq |
| title_full | Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq |
| title_fullStr | Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq |
| title_full_unstemmed | Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq |
| title_short | Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq |
| title_sort | study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on rna seq |
| topic | Alfalfa Transcriptome Differentially expressed genes (DEGs) Defoliation |
| url | http://link.springer.com/article/10.1186/s12864-018-5180-1 |
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