Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings
Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and e...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2022-10-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-022-00597-x |
| _version_ | 1811238854585221120 |
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| author | Jia Li Wei Xin Weiping Wang Shijiao Zhao Lu Xu Xingdong Jiang Yuxuan Duan Hongliang Zheng Luomiao Yang Hualong Liu Yan Jia Detang Zou Jingguo Wang |
| author_facet | Jia Li Wei Xin Weiping Wang Shijiao Zhao Lu Xu Xingdong Jiang Yuxuan Duan Hongliang Zheng Luomiao Yang Hualong Liu Yan Jia Detang Zou Jingguo Wang |
| author_sort | Jia Li |
| collection | DOAJ |
| description | Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency. |
| first_indexed | 2024-04-12T12:48:17Z |
| format | Article |
| id | doaj.art-7e1b6c1024f0482eb05ff76f012d08e2 |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-12T12:48:17Z |
| publishDate | 2022-10-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-7e1b6c1024f0482eb05ff76f012d08e22022-12-22T03:32:32ZengSpringerOpenRice1939-84251939-84332022-10-0115111610.1186/s12284-022-00597-xMapping of Candidate Genes in Response to Low Nitrogen in Rice SeedlingsJia Li0Wei Xin1Weiping Wang2Shijiao Zhao3Lu Xu4Xingdong Jiang5Yuxuan Duan6Hongliang Zheng7Luomiao Yang8Hualong Liu9Yan Jia10Detang Zou11Jingguo Wang12College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationCollege of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of EducationAbstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.https://doi.org/10.1186/s12284-022-00597-xRiceGenome-wide association studyRNA-seqLow-nitrogen tolerance |
| spellingShingle | Jia Li Wei Xin Weiping Wang Shijiao Zhao Lu Xu Xingdong Jiang Yuxuan Duan Hongliang Zheng Luomiao Yang Hualong Liu Yan Jia Detang Zou Jingguo Wang Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings Rice Rice Genome-wide association study RNA-seq Low-nitrogen tolerance |
| title | Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings |
| title_full | Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings |
| title_fullStr | Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings |
| title_full_unstemmed | Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings |
| title_short | Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings |
| title_sort | mapping of candidate genes in response to low nitrogen in rice seedlings |
| topic | Rice Genome-wide association study RNA-seq Low-nitrogen tolerance |
| url | https://doi.org/10.1186/s12284-022-00597-x |
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