The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance
Abstract Background Pineapple (Ananas comosus L.) is a major tropical fruit crop with considerable economic importance, and its growth and development are significantly impacted by low temperatures. The plant-specific GRAS gene family plays crucial roles in diverse processes, including flower and fr...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-12-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-024-05913-9 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846112666477658112 |
|---|---|
| author | Jinting Lin Jiahao Wu Dan Zhang Xinkai Cai Lumiao Du Lin Lu Chaojia Liu Shengzhen Chen Qinglong Yao Shiyu Xie Xiaowen Xu Xiaomei Wang Ruoyu Liu Yuan Qin Ping Zheng |
| author_facet | Jinting Lin Jiahao Wu Dan Zhang Xinkai Cai Lumiao Du Lin Lu Chaojia Liu Shengzhen Chen Qinglong Yao Shiyu Xie Xiaowen Xu Xiaomei Wang Ruoyu Liu Yuan Qin Ping Zheng |
| author_sort | Jinting Lin |
| collection | DOAJ |
| description | Abstract Background Pineapple (Ananas comosus L.) is a major tropical fruit crop with considerable economic importance, and its growth and development are significantly impacted by low temperatures. The plant-specific GRAS gene family plays crucial roles in diverse processes, including flower and fruit development, as well as in stress responses. However, the role of the GRAS family in pineapple has not yet been systematically analyzed. Results In this study, 43 AcGRAS genes were identified in the pineapple genome; these genes were distributed unevenly across 19 chromosomes and 6 scaffolds and were designated as AcGRAS01 to AcGRAS43 based on their chromosomal locations. Phylogenetic analysis classified these genes into 14 subfamilies: OS19, HAM-1, HAM-2, SCL4/7, LISCL, SHR, PAT1, DLT, LAS, SCR, SCL3, OS43, OS4, and DELLA. Gene structure analysis revealed that 60.5% of the AcGRAS genes lacked introns. Expression profiling demonstrated tissue-specific expression, with most AcGRAS genes predominantly expressed in specific floral organs, fruit tissues, or during particular developmental stages, suggesting functional diversity in pineapple development. Furthermore, the majority of AcGRAS genes were induced by cold stress, but different members seemed to play distinct roles in short-term or long-term cold adaptation in pineapple. Notably, most members of the PAT1 subfamily were preferentially expressed during late petal development and were upregulated under cold stress, suggesting their special roles in petal development and the cold response. In contrast, no consistent expression patterns were observed among genes in other subfamilies, suggesting that various regulatory factors, such as miRNAs, transcription factors, and cis-regulatory elements, may contribute to the diverse functions of AcGRAS members, even within the same subfamily. Conclusions This study provides the first comprehensive analysis of GRAS genes in pineapple, offers valuable insights for further functional investigations of AcGRASs and provides clues for improving pineapple cold resistance breeding. |
| format | Article |
| id | doaj-art-e2cef0a0a4b84d1cb874ce0cc93173e0 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-e2cef0a0a4b84d1cb874ce0cc93173e02024-12-22T12:25:11ZengBMCBMC Plant Biology1471-22292024-12-0124111910.1186/s12870-024-05913-9The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold toleranceJinting Lin0Jiahao Wu1Dan Zhang2Xinkai Cai3Lumiao Du4Lin Lu5Chaojia Liu6Shengzhen Chen7Qinglong Yao8Shiyu Xie9Xiaowen Xu10Xiaomei Wang11Ruoyu Liu12Yuan Qin13Ping Zheng14Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry UniversityAbstract Background Pineapple (Ananas comosus L.) is a major tropical fruit crop with considerable economic importance, and its growth and development are significantly impacted by low temperatures. The plant-specific GRAS gene family plays crucial roles in diverse processes, including flower and fruit development, as well as in stress responses. However, the role of the GRAS family in pineapple has not yet been systematically analyzed. Results In this study, 43 AcGRAS genes were identified in the pineapple genome; these genes were distributed unevenly across 19 chromosomes and 6 scaffolds and were designated as AcGRAS01 to AcGRAS43 based on their chromosomal locations. Phylogenetic analysis classified these genes into 14 subfamilies: OS19, HAM-1, HAM-2, SCL4/7, LISCL, SHR, PAT1, DLT, LAS, SCR, SCL3, OS43, OS4, and DELLA. Gene structure analysis revealed that 60.5% of the AcGRAS genes lacked introns. Expression profiling demonstrated tissue-specific expression, with most AcGRAS genes predominantly expressed in specific floral organs, fruit tissues, or during particular developmental stages, suggesting functional diversity in pineapple development. Furthermore, the majority of AcGRAS genes were induced by cold stress, but different members seemed to play distinct roles in short-term or long-term cold adaptation in pineapple. Notably, most members of the PAT1 subfamily were preferentially expressed during late petal development and were upregulated under cold stress, suggesting their special roles in petal development and the cold response. In contrast, no consistent expression patterns were observed among genes in other subfamilies, suggesting that various regulatory factors, such as miRNAs, transcription factors, and cis-regulatory elements, may contribute to the diverse functions of AcGRAS members, even within the same subfamily. Conclusions This study provides the first comprehensive analysis of GRAS genes in pineapple, offers valuable insights for further functional investigations of AcGRASs and provides clues for improving pineapple cold resistance breeding.https://doi.org/10.1186/s12870-024-05913-9PineappleGRAS transcription factorGene expressionGenome-wide analysis |
| spellingShingle | Jinting Lin Jiahao Wu Dan Zhang Xinkai Cai Lumiao Du Lin Lu Chaojia Liu Shengzhen Chen Qinglong Yao Shiyu Xie Xiaowen Xu Xiaomei Wang Ruoyu Liu Yuan Qin Ping Zheng The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance BMC Plant Biology Pineapple GRAS transcription factor Gene expression Genome-wide analysis |
| title | The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance |
| title_full | The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance |
| title_fullStr | The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance |
| title_full_unstemmed | The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance |
| title_short | The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance |
| title_sort | gras gene family and its roles in pineapple ananas comosus l developmental regulation and cold tolerance |
| topic | Pineapple GRAS transcription factor Gene expression Genome-wide analysis |
| url | https://doi.org/10.1186/s12870-024-05913-9 |
| work_keys_str_mv | AT jintinglin thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT jiahaowu thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT danzhang thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT xinkaicai thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT lumiaodu thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT linlu thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT chaojialiu thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT shengzhenchen thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT qinglongyao thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT shiyuxie thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT xiaowenxu thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT xiaomeiwang thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT ruoyuliu thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT yuanqin thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT pingzheng thegrasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT jintinglin grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT jiahaowu grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT danzhang grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT xinkaicai grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT lumiaodu grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT linlu grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT chaojialiu grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT shengzhenchen grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT qinglongyao grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT shiyuxie grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT xiaowenxu grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT xiaomeiwang grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT ruoyuliu grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT yuanqin grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance AT pingzheng grasgenefamilyanditsrolesinpineappleananascomosusldevelopmentalregulationandcoldtolerance |