QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice
Low temperature is a serious threat to the seed emergence of rice, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination and study their functions...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-07-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/13/7379 |
| _version_ | 1797479570875613184 |
|---|---|
| author | Nari Kim Rahmatullah Jan Jae-Ryoung Park Saleem Asif Dan-Dan Zhao Eun-Gyeong Kim Yoon-Hee Jang Gyu-Hyeon Eom Gang-Seob Lee Kyung-Min Kim |
| author_facet | Nari Kim Rahmatullah Jan Jae-Ryoung Park Saleem Asif Dan-Dan Zhao Eun-Gyeong Kim Yoon-Hee Jang Gyu-Hyeon Eom Gang-Seob Lee Kyung-Min Kim |
| author_sort | Nari Kim |
| collection | DOAJ |
| description | Low temperature is a serious threat to the seed emergence of rice, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination and study their functions for breeding new rice cultivars with immense low-temperature tolerance during seed germination. In the current experiment, 120 lines of the Cheongcheong Nagdong Double Haploid (CNDH) population were used for quantitative trait locus (QTL) analysis of low-temperature germinability. The results showed a significant difference in germination under low different temperature (LDT) (15 °C, 20 °C) conditions. In total, four QTLs were detected on chromosome 3, 6, and 8. A total of 41 genes were identified from all the four QTLs, among them, 25 genes were selected by gene function annotation and further screened through quantitative real-time polymerase chain reaction (qRT-PCR). Based on gene function annotation and level of expression under low-temperature, our study suggested the <i>OsGPq3</i> gene as a candidate gene controlling viviparous germination, ABA and GA signaling under low-temperature. This study will provide a theoretical basis for marker-assisted breeding and lay the basis for further mining molecular mechanisms of low-temperature germination tolerance in rice. |
| first_indexed | 2024-03-09T21:47:41Z |
| format | Article |
| id | doaj.art-1f7833a4ae884849a42baadbc65d911b |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T21:47:41Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1f7833a4ae884849a42baadbc65d911b2023-11-23T20:12:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-07-012313737910.3390/ijms23137379QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in RiceNari Kim0Rahmatullah Jan1Jae-Ryoung Park2Saleem Asif3Dan-Dan Zhao4Eun-Gyeong Kim5Yoon-Hee Jang6Gyu-Hyeon Eom7Gang-Seob Lee8Kyung-Min Kim9Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaCrop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaLow temperature is a serious threat to the seed emergence of rice, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination and study their functions for breeding new rice cultivars with immense low-temperature tolerance during seed germination. In the current experiment, 120 lines of the Cheongcheong Nagdong Double Haploid (CNDH) population were used for quantitative trait locus (QTL) analysis of low-temperature germinability. The results showed a significant difference in germination under low different temperature (LDT) (15 °C, 20 °C) conditions. In total, four QTLs were detected on chromosome 3, 6, and 8. A total of 41 genes were identified from all the four QTLs, among them, 25 genes were selected by gene function annotation and further screened through quantitative real-time polymerase chain reaction (qRT-PCR). Based on gene function annotation and level of expression under low-temperature, our study suggested the <i>OsGPq3</i> gene as a candidate gene controlling viviparous germination, ABA and GA signaling under low-temperature. This study will provide a theoretical basis for marker-assisted breeding and lay the basis for further mining molecular mechanisms of low-temperature germination tolerance in rice.https://www.mdpi.com/1422-0067/23/13/7379low-temperatureseed germinationCheongcheong Nagdong double haploidquantitative trait locusviviparous germinationmarker-assisted breeding |
| spellingShingle | Nari Kim Rahmatullah Jan Jae-Ryoung Park Saleem Asif Dan-Dan Zhao Eun-Gyeong Kim Yoon-Hee Jang Gyu-Hyeon Eom Gang-Seob Lee Kyung-Min Kim QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice International Journal of Molecular Sciences low-temperature seed germination Cheongcheong Nagdong double haploid quantitative trait locus viviparous germination marker-assisted breeding |
| title | QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice |
| title_full | QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice |
| title_fullStr | QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice |
| title_full_unstemmed | QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice |
| title_short | QTL Mapping and Candidate Gene Analysis for Seed Germination Response to Low Temperature in Rice |
| title_sort | qtl mapping and candidate gene analysis for seed germination response to low temperature in rice |
| topic | low-temperature seed germination Cheongcheong Nagdong double haploid quantitative trait locus viviparous germination marker-assisted breeding |
| url | https://www.mdpi.com/1422-0067/23/13/7379 |
| work_keys_str_mv | AT narikim qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT rahmatullahjan qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT jaeryoungpark qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT saleemasif qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT dandanzhao qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT eungyeongkim qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT yoonheejang qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT gyuhyeoneom qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT gangseoblee qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice AT kyungminkim qtlmappingandcandidategeneanalysisforseedgerminationresponsetolowtemperatureinrice |