Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i>
Grain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in <i>japonica</i> rice, which severely limits the improvement of japonica rice yields. Here, we systemical...
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MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/14/11447 |
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| author | Luomiao Yang Peng Li Jingguo Wang Hualong Liu Hongliang Zheng Wei Xin Detang Zou |
| author_facet | Luomiao Yang Peng Li Jingguo Wang Hualong Liu Hongliang Zheng Wei Xin Detang Zou |
| author_sort | Luomiao Yang |
| collection | DOAJ |
| description | Grain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in <i>japonica</i> rice, which severely limits the improvement of japonica rice yields. Here, we systemically measured the GL of 667 F<sub>2</sub> and 1570 BC<sub>3</sub>F<sub>3</sub> individuals derived from two cultivated rice cultivars, Pin20 and Songjing15, in order to identify the major genomic regions associated with GL. A novel major QTL, <i>qGL9.1</i>, was mapped on chromosome 9, which is associated with the GL, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F<sub>2</sub> and fine mapping with the recombinant plant revealed a 93-kb core region on <i>qGL9.1</i> encoding 15 protein-coding genes. Only the expression level of <i>LOC_Os09g26970</i> was significantly different between the two parents at different stages of grain development. Moreover, haplotype analysis revealed that the alleles of Pin20 contribute to the optimal GL (9.36 mm) and GL/W (3.31), suggesting that Pin20 is a cultivated species carrying the optimal GL variation of <i>LOC_Os09g26970</i>. Furthermore, a functional-type mutation (16398989-bp, G>A) located on an exon of <i>LOC_Os09g26970</i> could be used as a molecular marker to distinguish between long and short grains. Our experiments identified <i>LOC_Os09g26970</i> as a novel gene associated with GL in <i>japonica</i> rice. This result is expected to further the exploration of the genetic mechanism of rice GL and improve GL in rice <i>japonica</i> varieties by marker-assisted selection. |
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| language | English |
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| publishDate | 2023-07-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-dd59ca84ffb04005b240a75abf812df32023-11-18T19:39:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-07-0124141144710.3390/ijms241411447Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i>Luomiao Yang0Peng Li1Jingguo Wang2Hualong Liu3Hongliang Zheng4Wei Xin5Detang Zou6Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaKey Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaKey Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaKey Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaKey Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaKey Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaKey Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, ChinaGrain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in <i>japonica</i> rice, which severely limits the improvement of japonica rice yields. Here, we systemically measured the GL of 667 F<sub>2</sub> and 1570 BC<sub>3</sub>F<sub>3</sub> individuals derived from two cultivated rice cultivars, Pin20 and Songjing15, in order to identify the major genomic regions associated with GL. A novel major QTL, <i>qGL9.1</i>, was mapped on chromosome 9, which is associated with the GL, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F<sub>2</sub> and fine mapping with the recombinant plant revealed a 93-kb core region on <i>qGL9.1</i> encoding 15 protein-coding genes. Only the expression level of <i>LOC_Os09g26970</i> was significantly different between the two parents at different stages of grain development. Moreover, haplotype analysis revealed that the alleles of Pin20 contribute to the optimal GL (9.36 mm) and GL/W (3.31), suggesting that Pin20 is a cultivated species carrying the optimal GL variation of <i>LOC_Os09g26970</i>. Furthermore, a functional-type mutation (16398989-bp, G>A) located on an exon of <i>LOC_Os09g26970</i> could be used as a molecular marker to distinguish between long and short grains. Our experiments identified <i>LOC_Os09g26970</i> as a novel gene associated with GL in <i>japonica</i> rice. This result is expected to further the exploration of the genetic mechanism of rice GL and improve GL in rice <i>japonica</i> varieties by marker-assisted selection.https://www.mdpi.com/1422-0067/24/14/11447<i>Oryza sativa</i> L.grain lengthre-sequencingfine mappingP450 protein |
| spellingShingle | Luomiao Yang Peng Li Jingguo Wang Hualong Liu Hongliang Zheng Wei Xin Detang Zou Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i> International Journal of Molecular Sciences <i>Oryza sativa</i> L. grain length re-sequencing fine mapping P450 protein |
| title | Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i> |
| title_full | Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i> |
| title_fullStr | Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i> |
| title_full_unstemmed | Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i> |
| title_short | Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL <i>qGL9.1</i> |
| title_sort | fine mapping and candidate gene analysis of rice grain length qtl i qgl9 1 i |
| topic | <i>Oryza sativa</i> L. grain length re-sequencing fine mapping P450 protein |
| url | https://www.mdpi.com/1422-0067/24/14/11447 |
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