Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size
Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.958808/full |
| _version_ | 1811209711798714368 |
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| author | Yue Wu Yue Wu Ziqi Sun Feiyan Qi Mengdi Tian Juan Wang Ruifang Zhao Xiao Wang Xiaohui Wu Xinlong Shi Hongfei Liu Wenzhao Dong Bingyan Huang Zheng Zheng Xinyou Zhang |
| author_facet | Yue Wu Yue Wu Ziqi Sun Feiyan Qi Mengdi Tian Juan Wang Ruifang Zhao Xiao Wang Xiaohui Wu Xinlong Shi Hongfei Liu Wenzhao Dong Bingyan Huang Zheng Zheng Xinyou Zhang |
| author_sort | Yue Wu |
| collection | DOAJ |
| description | Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts. |
| first_indexed | 2024-04-12T04:44:08Z |
| format | Article |
| id | doaj.art-dc445c5ff4af4a7cb24a79d125773756 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T04:44:08Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-dc445c5ff4af4a7cb24a79d1257737562022-12-22T03:47:33ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-09-011310.3389/fpls.2022.958808958808Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed sizeYue Wu0Yue Wu1Ziqi Sun2Feiyan Qi3Mengdi Tian4Juan Wang5Ruifang Zhao6Xiao Wang7Xiaohui Wu8Xinlong Shi9Hongfei Liu10Wenzhao Dong11Bingyan Huang12Zheng Zheng13Xinyou Zhang14School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou, Henan, ChinaCollege of Agriculture, Henan University of Science and Technology, Luoyang, ChinaSchool of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaHenan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, ChinaPod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts.https://www.frontiersin.org/articles/10.3389/fpls.2022.958808/fullpeanutphytohormoneMAPK signaling pathwaytranscription factorpod developmentpod size |
| spellingShingle | Yue Wu Yue Wu Ziqi Sun Feiyan Qi Mengdi Tian Juan Wang Ruifang Zhao Xiao Wang Xiaohui Wu Xinlong Shi Hongfei Liu Wenzhao Dong Bingyan Huang Zheng Zheng Xinyou Zhang Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size Frontiers in Plant Science peanut phytohormone MAPK signaling pathway transcription factor pod development pod size |
| title | Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size |
| title_full | Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size |
| title_fullStr | Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size |
| title_full_unstemmed | Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size |
| title_short | Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size |
| title_sort | comparative transcriptomics analysis of developing peanut arachis hypogaea l pods reveals candidate genes affecting peanut seed size |
| topic | peanut phytohormone MAPK signaling pathway transcription factor pod development pod size |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.958808/full |
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