Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage
Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the env...
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MDPI AG
2024-03-01
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| author | Ning Chen Tianze Ma Sijia Xia Chengxin Li Yinuo Liu Jiaqi Wang Guize Qu Hualong Liu Hongliang Zheng Luomiao Yang Detang Zou Jingguo Wang Wei Xin |
| author_facet | Ning Chen Tianze Ma Sijia Xia Chengxin Li Yinuo Liu Jiaqi Wang Guize Qu Hualong Liu Hongliang Zheng Luomiao Yang Detang Zou Jingguo Wang Wei Xin |
| author_sort | Ning Chen |
| collection | DOAJ |
| description | Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (<i>Os01g0159250</i>, <i>Os02g0618200</i>, <i>Os02g0618400</i>, <i>Os02g0630300</i>, and <i>Os06g0619000</i>) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice. |
| first_indexed | 2024-04-24T18:15:06Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-04-24T18:15:06Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
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| series | Genes |
| spelling | doaj.art-cb293444516545b9ae8e3bf419cf4bbb2024-03-27T13:43:05ZengMDPI AGGenes2073-44252024-03-0115332710.3390/genes15030327Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling StageNing Chen0Tianze Ma1Sijia Xia2Chengxin Li3Yinuo Liu4Jiaqi Wang5Guize Qu6Hualong Liu7Hongliang Zheng8Luomiao Yang9Detang Zou10Jingguo Wang11Wei Xin12College of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaHarbin Academy of Agricultural Sciences, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaNitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (<i>Os01g0159250</i>, <i>Os02g0618200</i>, <i>Os02g0618400</i>, <i>Os02g0630300</i>, and <i>Os06g0619000</i>) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.https://www.mdpi.com/2073-4425/15/3/327rice (<i>Oryza sativa</i> L.)GWASRNA-seqQTLsnitrogen |
| spellingShingle | Ning Chen Tianze Ma Sijia Xia Chengxin Li Yinuo Liu Jiaqi Wang Guize Qu Hualong Liu Hongliang Zheng Luomiao Yang Detang Zou Jingguo Wang Wei Xin Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage Genes rice (<i>Oryza sativa</i> L.) GWAS RNA-seq QTLs nitrogen |
| title | Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage |
| title_full | Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage |
| title_fullStr | Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage |
| title_full_unstemmed | Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage |
| title_short | Mapping of Candidate Genes for Nitrogen Uptake and Utilization in <i>Japonica</i> Rice at Seedling Stage |
| title_sort | mapping of candidate genes for nitrogen uptake and utilization in i japonica i rice at seedling stage |
| topic | rice (<i>Oryza sativa</i> L.) GWAS RNA-seq QTLs nitrogen |
| url | https://www.mdpi.com/2073-4425/15/3/327 |
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