Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis
Soil salinity is a major abiotic stress that causes disastrous losses in crop yields. To identify favorable alleles that enhance the salinity resistance of rice (<i>Oryza sativa</i> L.) crops, a set of 120 Cheongcheong Nagdong double haploid (CNDH) lines derived from a cross between the...
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MDPI AG
2022-09-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/19/2467 |
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| author | Saleem Asif Eun-Gyeong Kim Yoon-Hee Jang Rahmatullah Jan Nari Kim Sajjad Asaf Lubna Muhammad Farooq Kyung-Min Kim |
| author_facet | Saleem Asif Eun-Gyeong Kim Yoon-Hee Jang Rahmatullah Jan Nari Kim Sajjad Asaf Lubna Muhammad Farooq Kyung-Min Kim |
| author_sort | Saleem Asif |
| collection | DOAJ |
| description | Soil salinity is a major abiotic stress that causes disastrous losses in crop yields. To identify favorable alleles that enhance the salinity resistance of rice (<i>Oryza sativa</i> L.) crops, a set of 120 Cheongcheong Nagdong double haploid (CNDH) lines derived from a cross between the <i>Indica</i> variety Cheongcheong and the <i>Japonica</i> variety Nagdong were used. A total of 23 QTLs for 8 different traits related to salinity resistance on chromosomes 1–3 and 5–12 were identified at the seedling stage. A QTL related to the salt injury score (SIS), qSIS-3b, had an LOD score of six within the interval RM3525–RM15904 on chromosome 3, and a phenotypic variation of 31% was further examined for the candidate genes. Among all the CNDH populations, five resistant lines (CNDH 27, CNDH 34-1, CNDH 64, CNDH 78, and CNDH 112), five susceptible lines (CNDH 52-1, CNDH 67, CNDH 69, CNDH 109, and CNDH 110), and the parent lines Cheongcheong and Nagdong were selected for relative gene expression analysis. Among all the genes, two candidate genes were highly upregulated in resistant lines, including the auxin-responsive protein IAA13 (Os03g0742900) and the calmodulin-like protein 4 (Os03g0743500-1). The calmodulin-like protein 4 (Os03g0743500-1) showed a higher expression in all the resistant lines than in the susceptible lines and a high similarity with other species in sequence alignment and phylogenetic tree, and it also showed a protein–protein interaction with other important proteins. The genes identified in our study will provide new genetic resources for improving salt resistance in rice using molecular breeding strategies in the future. |
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| last_indexed | 2024-03-09T21:18:06Z |
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| series | Plants |
| spelling | doaj.art-ac7bcfbbff71427aa3287ea4fc35670f2023-11-23T21:27:56ZengMDPI AGPlants2223-77472022-09-011119246710.3390/plants11192467Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL AnalysisSaleem Asif0Eun-Gyeong Kim1Yoon-Hee Jang2Rahmatullah Jan3Nari Kim4Sajjad Asaf5Lubna6Muhammad Farooq7Kyung-Min Kim8Department 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, KoreaNatural and Medical Science Research Center, University of Nizwa, Nizwa 616, OmanDepartment of Botany, Garden Campus, Abdul Wali Khan University, Mardan 23200, PakistanDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaDepartment of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, KoreaSoil salinity is a major abiotic stress that causes disastrous losses in crop yields. To identify favorable alleles that enhance the salinity resistance of rice (<i>Oryza sativa</i> L.) crops, a set of 120 Cheongcheong Nagdong double haploid (CNDH) lines derived from a cross between the <i>Indica</i> variety Cheongcheong and the <i>Japonica</i> variety Nagdong were used. A total of 23 QTLs for 8 different traits related to salinity resistance on chromosomes 1–3 and 5–12 were identified at the seedling stage. A QTL related to the salt injury score (SIS), qSIS-3b, had an LOD score of six within the interval RM3525–RM15904 on chromosome 3, and a phenotypic variation of 31% was further examined for the candidate genes. Among all the CNDH populations, five resistant lines (CNDH 27, CNDH 34-1, CNDH 64, CNDH 78, and CNDH 112), five susceptible lines (CNDH 52-1, CNDH 67, CNDH 69, CNDH 109, and CNDH 110), and the parent lines Cheongcheong and Nagdong were selected for relative gene expression analysis. Among all the genes, two candidate genes were highly upregulated in resistant lines, including the auxin-responsive protein IAA13 (Os03g0742900) and the calmodulin-like protein 4 (Os03g0743500-1). The calmodulin-like protein 4 (Os03g0743500-1) showed a higher expression in all the resistant lines than in the susceptible lines and a high similarity with other species in sequence alignment and phylogenetic tree, and it also showed a protein–protein interaction with other important proteins. The genes identified in our study will provide new genetic resources for improving salt resistance in rice using molecular breeding strategies in the future.https://www.mdpi.com/2223-7747/11/19/2467QTLsalinityCheongcheong Nagdong double haploidcalmodulin-like proteinrice seedling |
| spellingShingle | Saleem Asif Eun-Gyeong Kim Yoon-Hee Jang Rahmatullah Jan Nari Kim Sajjad Asaf Lubna Muhammad Farooq Kyung-Min Kim Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis Plants QTL salinity Cheongcheong Nagdong double haploid calmodulin-like protein rice seedling |
| title | Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis |
| title_full | Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis |
| title_fullStr | Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis |
| title_full_unstemmed | Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis |
| title_short | Identification of the <i>OsCML4</i> Gene in Rice Related to Salt Stress Using QTL Analysis |
| title_sort | identification of the i oscml4 i gene in rice related to salt stress using qtl analysis |
| topic | QTL salinity Cheongcheong Nagdong double haploid calmodulin-like protein rice seedling |
| url | https://www.mdpi.com/2223-7747/11/19/2467 |
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