Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]
Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in ter...
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Frontiers Media S.A.
2021-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.612131/full |
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| author | Mu-Chien Lai Zheng-Yuan Lai Li-Hsin Jhan Ya-Syuan Lai Chung-Feng Kao Chung-Feng Kao |
| author_facet | Mu-Chien Lai Zheng-Yuan Lai Li-Hsin Jhan Ya-Syuan Lai Chung-Feng Kao Chung-Feng Kao |
| author_sort | Mu-Chien Lai |
| collection | DOAJ |
| description | Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean. |
| first_indexed | 2024-12-16T13:14:54Z |
| format | Article |
| id | doaj.art-4721bc07f2f140f2a5ddc7f68c35e715 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-16T13:14:54Z |
| publishDate | 2021-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-4721bc07f2f140f2a5ddc7f68c35e7152022-12-21T22:30:29ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.612131612131Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]Mu-Chien Lai0Zheng-Yuan Lai1Li-Hsin Jhan2Ya-Syuan Lai3Chung-Feng Kao4Chung-Feng Kao5Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, TaiwanDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, TaiwanDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, TaiwanDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, TaiwanDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, TaiwanAdvanced Plant Biotechnology Center, National Chung Hsing University, Taichung, TaiwanSoybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.https://www.frontiersin.org/articles/10.3389/fgene.2020.612131/fullsoybeanflooding tolerancegenomic data meta-analysisgene prioritizationgene-set enrichment analysis |
| spellingShingle | Mu-Chien Lai Zheng-Yuan Lai Li-Hsin Jhan Ya-Syuan Lai Chung-Feng Kao Chung-Feng Kao Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.] Frontiers in Genetics soybean flooding tolerance genomic data meta-analysis gene prioritization gene-set enrichment analysis |
| title | Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.] |
| title_full | Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.] |
| title_fullStr | Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.] |
| title_full_unstemmed | Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.] |
| title_short | Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.] |
| title_sort | prioritization and evaluation of flooding tolerance genes in soybean glycine max l merr |
| topic | soybean flooding tolerance genomic data meta-analysis gene prioritization gene-set enrichment analysis |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.612131/full |
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