Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis
Physical dormancy (PY) commonly present in the seeds of higher plants is believed to be responsible for the germination failure by impermeable seed coat in hard seeds of legume species, instead of physiological dormancy (PD). In this study, a non-destructive approach involving multispectral imaging...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2023-10-01
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| Series: | Crop Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S221451412300034X |
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| author | Xuemeng Wang Han Zhang Rui Song Ming Sun Ping Liu Peixin Tian Peisheng Mao Shangang Jia |
| author_facet | Xuemeng Wang Han Zhang Rui Song Ming Sun Ping Liu Peixin Tian Peisheng Mao Shangang Jia |
| author_sort | Xuemeng Wang |
| collection | DOAJ |
| description | Physical dormancy (PY) commonly present in the seeds of higher plants is believed to be responsible for the germination failure by impermeable seed coat in hard seeds of legume species, instead of physiological dormancy (PD). In this study, a non-destructive approach involving multispectral imaging was used to successfully identify hard seeds from non-hard seeds in Medicago sativa, with accuracy as high as 96.8%–99.0%. We further adopted multiple-omics strategies to investigate the differences of physiology, metabolomics, methylomics, and transcriptomics in alfalfa hard seeds, with non-hard seeds as control. The hard seeds showed dramatically increased antioxidants and 125 metabolites of significant differences in non-targeted metabolomics analysis, which are enriched in the biosynthesis pathways of flavonoids, lipids and hormones, especially with significantly higher ABA, a hormone known to induce dormancy. In our transcriptomics results, the enrichment pathway of “response to abscisic acid” of differential expressed genes (DEG) supported the key role of ABA in metabolomics results. The methylome analysis identified 54,899, 46,216 and 54,452 differential methylation regions for contexts of CpG, CHG and CHH, and 344 DEGs might be regulated by hypermethylation and hypomethylation of promoter and exon regions, including four ABA- and JA-responsive genes. Among 8% hard seeds in seed lots, 24.5% still did not germinate after scarifying seed coat, and were named as non-PY hard seeds. Compared to hard seeds, significantly higher contents of ABA/IAA and ABA/JA were identified in non-PY hard seeds, which indicated the potential presence of PD. In summary, the significantly changed metabolites, gene expressions, and methylations all suggested involvement of ABA responses in hard seeds, and germination failure of alfalfa hard seeds was caused by combinational dormancy (PY + PD), rather than PY alone. |
| first_indexed | 2024-03-11T18:19:16Z |
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| institution | Directory Open Access Journal |
| issn | 2214-5141 |
| language | English |
| last_indexed | 2024-03-11T18:19:16Z |
| publishDate | 2023-10-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Crop Journal |
| spelling | doaj.art-9730844eb2cd412aad6716cb5f6d9b4f2023-10-16T04:12:20ZengKeAi Communications Co., Ltd.Crop Journal2214-51412023-10-0111514581468Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysisXuemeng Wang0Han Zhang1Rui Song2Ming Sun3Ping Liu4Peixin Tian5Peisheng Mao6Shangang Jia7College of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCorresponding authors.; College of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaCorresponding authors.; College of Grassland Science and Technology, China Agricultural University, Beijing 100193, ChinaPhysical dormancy (PY) commonly present in the seeds of higher plants is believed to be responsible for the germination failure by impermeable seed coat in hard seeds of legume species, instead of physiological dormancy (PD). In this study, a non-destructive approach involving multispectral imaging was used to successfully identify hard seeds from non-hard seeds in Medicago sativa, with accuracy as high as 96.8%–99.0%. We further adopted multiple-omics strategies to investigate the differences of physiology, metabolomics, methylomics, and transcriptomics in alfalfa hard seeds, with non-hard seeds as control. The hard seeds showed dramatically increased antioxidants and 125 metabolites of significant differences in non-targeted metabolomics analysis, which are enriched in the biosynthesis pathways of flavonoids, lipids and hormones, especially with significantly higher ABA, a hormone known to induce dormancy. In our transcriptomics results, the enrichment pathway of “response to abscisic acid” of differential expressed genes (DEG) supported the key role of ABA in metabolomics results. The methylome analysis identified 54,899, 46,216 and 54,452 differential methylation regions for contexts of CpG, CHG and CHH, and 344 DEGs might be regulated by hypermethylation and hypomethylation of promoter and exon regions, including four ABA- and JA-responsive genes. Among 8% hard seeds in seed lots, 24.5% still did not germinate after scarifying seed coat, and were named as non-PY hard seeds. Compared to hard seeds, significantly higher contents of ABA/IAA and ABA/JA were identified in non-PY hard seeds, which indicated the potential presence of PD. In summary, the significantly changed metabolites, gene expressions, and methylations all suggested involvement of ABA responses in hard seeds, and germination failure of alfalfa hard seeds was caused by combinational dormancy (PY + PD), rather than PY alone.http://www.sciencedirect.com/science/article/pii/S221451412300034XHard seedMultispectral imagingTranscriptomicsMetabolomicsABA |
| spellingShingle | Xuemeng Wang Han Zhang Rui Song Ming Sun Ping Liu Peixin Tian Peisheng Mao Shangang Jia Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis Crop Journal Hard seed Multispectral imaging Transcriptomics Metabolomics ABA |
| title | Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis |
| title_full | Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis |
| title_fullStr | Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis |
| title_full_unstemmed | Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis |
| title_short | Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis |
| title_sort | multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis |
| topic | Hard seed Multispectral imaging Transcriptomics Metabolomics ABA |
| url | http://www.sciencedirect.com/science/article/pii/S221451412300034X |
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