Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice
Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the <i>indica</i> cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold respon...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-07-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/12/14/2675 |
| _version_ | 1797587701228109824 |
|---|---|
| author | Tao Yan Meng Sun Rui Su Xiaozhong Wang Xuedan Lu Yunhua Xiao Huabing Deng Xiong Liu Wenbang Tang Guilian Zhang |
| author_facet | Tao Yan Meng Sun Rui Su Xiaozhong Wang Xuedan Lu Yunhua Xiao Huabing Deng Xiong Liu Wenbang Tang Guilian Zhang |
| author_sort | Tao Yan |
| collection | DOAJ |
| description | Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the <i>indica</i> cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two <i>indica</i> cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including <i>WRKY</i>, <i>NAC</i>, <i>bHLH</i>, <i>ERF</i>, <i>bZIP</i>, <i>MYB</i>, <i>C2H2</i>, and <i>GRAS</i>, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the “response to cold” category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as “Pyruvate metabolism”, “Glycolysis/Gluconeogenesis”, and “Starch and sucrose metabolism”, contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the <i>indica</i> cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible <i>indica</i> rice cultivars. |
| first_indexed | 2024-03-11T00:42:37Z |
| format | Article |
| id | doaj.art-0933543c9c3c42ed89638a94476ef1ad |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T00:42:37Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-0933543c9c3c42ed89638a94476ef1ad2023-11-18T21:00:26ZengMDPI AGPlants2223-77472023-07-011214267510.3390/plants12142675Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> RiceTao Yan0Meng Sun1Rui Su2Xiaozhong Wang3Xuedan Lu4Yunhua Xiao5Huabing Deng6Xiong Liu7Wenbang Tang8Guilian Zhang9College of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the <i>indica</i> cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two <i>indica</i> cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including <i>WRKY</i>, <i>NAC</i>, <i>bHLH</i>, <i>ERF</i>, <i>bZIP</i>, <i>MYB</i>, <i>C2H2</i>, and <i>GRAS</i>, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the “response to cold” category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as “Pyruvate metabolism”, “Glycolysis/Gluconeogenesis”, and “Starch and sucrose metabolism”, contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the <i>indica</i> cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible <i>indica</i> rice cultivars.https://www.mdpi.com/2223-7747/12/14/2675cold stressRNA-seqricecold-transcription factorsgene ontologyKEGG pathway analysis |
| spellingShingle | Tao Yan Meng Sun Rui Su Xiaozhong Wang Xuedan Lu Yunhua Xiao Huabing Deng Xiong Liu Wenbang Tang Guilian Zhang Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice Plants cold stress RNA-seq rice cold-transcription factors gene ontology KEGG pathway analysis |
| title | Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice |
| title_full | Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice |
| title_fullStr | Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice |
| title_full_unstemmed | Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice |
| title_short | Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of <i>Indica</i> Rice |
| title_sort | transcriptomic profiling of cold stress induced differentially expressed genes in seedling stage of i indica i rice |
| topic | cold stress RNA-seq rice cold-transcription factors gene ontology KEGG pathway analysis |
| url | https://www.mdpi.com/2223-7747/12/14/2675 |
| work_keys_str_mv | AT taoyan transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT mengsun transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT ruisu transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT xiaozhongwang transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT xuedanlu transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT yunhuaxiao transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT huabingdeng transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT xiongliu transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT wenbangtang transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice AT guilianzhang transcriptomicprofilingofcoldstressinduceddifferentiallyexpressedgenesinseedlingstageofiindicairice |