Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties
Abstract Background Salinity, a major abiotic stress, significantly impairs crop productivity by inducing osmotic, ionic, and secondary stresses that disrupt metabolic processes. Chickpea (Cicer arietinum L.), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated...
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2025-07-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06910-2 |
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| author | Guangxia Duan Chaoni Liang Jundong Su Yan Liang Wanming Li Jinbo Zhang Yigong Zhang |
| author_facet | Guangxia Duan Chaoni Liang Jundong Su Yan Liang Wanming Li Jinbo Zhang Yigong Zhang |
| author_sort | Guangxia Duan |
| collection | DOAJ |
| description | Abstract Background Salinity, a major abiotic stress, significantly impairs crop productivity by inducing osmotic, ionic, and secondary stresses that disrupt metabolic processes. Chickpea (Cicer arietinum L.), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated by farmers with limited resources. While previous studies have explored salt tolerance in chickpeas, this study provides a comprehensive multi-omics perspective. Exploring the mechanism of chickpea adaptation to the saline environment can effectively supplement the problem of single source of plant protein. Results The present study analyzed the transcriptomic and metabolomic profiles of two distinct chickpea varieties, DY3 and DY1, with contrasting salinity tolerance capacities. The salinity tolerance of DY3 was associated with greater biomass, higher antioxidant enzyme activity, and higher photosynthetic efficiency. Transcriptomic analysis revealed that the genes induced in DY3 under salinity stress were associated with ion homeostasis, antioxidant defense system, and plant hormone signaling. Metabolomics analysis revealed significant enrichment of components of diverse secondary metabolites pathways, as well as carbohydrate metabolism. Integrated multi-omics analysis highlighted the anthocyanin biosynthesis pathway, functioning within the broader flavonoid metabolic network, as a key regulator of salt tolerance in the chickpea. Subsequent, RT-qPCR confirmed the upregulation of key genes associated with anthocyanin metabolism. Conclusions These findings reveal the key regulatory role of the flavonoid pathway in salt tolerance of chickpeas, offering insights for breeding improved varieties. |
| format | Article |
| id | doaj-art-7149614cbe4d4e96a8b564bc83c0000c |
| institution | DOAJ |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-7149614cbe4d4e96a8b564bc83c0000c2025-08-20T03:04:24ZengBMCBMC Plant Biology1471-22292025-07-0125111710.1186/s12870-025-06910-2Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varietiesGuangxia Duan0Chaoni Liang1Jundong Su2Yan Liang3Wanming Li4Jinbo Zhang5Yigong Zhang6Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang UniversityXinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang UniversityInstitute of Crop Sciences, Xinjiang Academy of Agricultural SciencesXinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang UniversityXinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang UniversityXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesXinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang UniversityAbstract Background Salinity, a major abiotic stress, significantly impairs crop productivity by inducing osmotic, ionic, and secondary stresses that disrupt metabolic processes. Chickpea (Cicer arietinum L.), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated by farmers with limited resources. While previous studies have explored salt tolerance in chickpeas, this study provides a comprehensive multi-omics perspective. Exploring the mechanism of chickpea adaptation to the saline environment can effectively supplement the problem of single source of plant protein. Results The present study analyzed the transcriptomic and metabolomic profiles of two distinct chickpea varieties, DY3 and DY1, with contrasting salinity tolerance capacities. The salinity tolerance of DY3 was associated with greater biomass, higher antioxidant enzyme activity, and higher photosynthetic efficiency. Transcriptomic analysis revealed that the genes induced in DY3 under salinity stress were associated with ion homeostasis, antioxidant defense system, and plant hormone signaling. Metabolomics analysis revealed significant enrichment of components of diverse secondary metabolites pathways, as well as carbohydrate metabolism. Integrated multi-omics analysis highlighted the anthocyanin biosynthesis pathway, functioning within the broader flavonoid metabolic network, as a key regulator of salt tolerance in the chickpea. Subsequent, RT-qPCR confirmed the upregulation of key genes associated with anthocyanin metabolism. Conclusions These findings reveal the key regulatory role of the flavonoid pathway in salt tolerance of chickpeas, offering insights for breeding improved varieties.https://doi.org/10.1186/s12870-025-06910-2ChickpeaTranscriptomeMetabolomeFlavonoidsSalt stress |
| spellingShingle | Guangxia Duan Chaoni Liang Jundong Su Yan Liang Wanming Li Jinbo Zhang Yigong Zhang Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties BMC Plant Biology Chickpea Transcriptome Metabolome Flavonoids Salt stress |
| title | Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties |
| title_full | Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties |
| title_fullStr | Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties |
| title_full_unstemmed | Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties |
| title_short | Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties |
| title_sort | integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea cicer arietinum l varieties |
| topic | Chickpea Transcriptome Metabolome Flavonoids Salt stress |
| url | https://doi.org/10.1186/s12870-025-06910-2 |
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