Genetic dissection of grain nutritional traits and leaf blight resistance in rice
Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful i...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
MDPI
2019
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| Online Access: | https://hdl.handle.net/10568/164747 |
| _version_ | 1855527106035843072 |
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| author | Descalsota-Empleo, Gwen Iris Noraziyah, Abd Aziz Shamsudin Navea, Ian Paul Chung, Chongtae Dwiyanti, Maria Stefanie Labios, Reuben Jacob Dicen Ikmal, Asmuni Mohd Juanillas, Venice Margarette Inabangan-Asilo, Mary Ann Amparado, Amery Reinke, Russell Vera Cruz, Casiana M. Chin, Joong Hyoun Swamy, B.P. Mallikarjuna |
| author_browse | Amparado, Amery Chin, Joong Hyoun Chung, Chongtae Descalsota-Empleo, Gwen Iris Dwiyanti, Maria Stefanie Ikmal, Asmuni Mohd Inabangan-Asilo, Mary Ann Juanillas, Venice Margarette Labios, Reuben Jacob Dicen Navea, Ian Paul Noraziyah, Abd Aziz Shamsudin Reinke, Russell Swamy, B.P. Mallikarjuna Vera Cruz, Casiana M. |
| author_facet | Descalsota-Empleo, Gwen Iris Noraziyah, Abd Aziz Shamsudin Navea, Ian Paul Chung, Chongtae Dwiyanti, Maria Stefanie Labios, Reuben Jacob Dicen Ikmal, Asmuni Mohd Juanillas, Venice Margarette Inabangan-Asilo, Mary Ann Amparado, Amery Reinke, Russell Vera Cruz, Casiana M. Chin, Joong Hyoun Swamy, B.P. Mallikarjuna |
| author_sort | Descalsota-Empleo, Gwen Iris |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding. |
| format | Journal Article |
| id | CGSpace164747 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1647472025-12-08T09:54:28Z Genetic dissection of grain nutritional traits and leaf blight resistance in rice Descalsota-Empleo, Gwen Iris Noraziyah, Abd Aziz Shamsudin Navea, Ian Paul Chung, Chongtae Dwiyanti, Maria Stefanie Labios, Reuben Jacob Dicen Ikmal, Asmuni Mohd Juanillas, Venice Margarette Inabangan-Asilo, Mary Ann Amparado, Amery Reinke, Russell Vera Cruz, Casiana M. Chin, Joong Hyoun Swamy, B.P. Mallikarjuna Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding. 2019-01-08 2024-12-19T12:54:15Z 2024-12-19T12:54:15Z Journal Article https://hdl.handle.net/10568/164747 en Open Access MDPI Descalsota-Empleo, Gwen Iris; Noraziyah, Abd Aziz Shamsudin; Navea, Ian Paul; Chung, Chongtae; Dwiyanti, Maria Stefanie; Labios, Reuben Jacob Dicen; Ikmal, Asmuni Mohd; Juanillas, Venice Margarette; Inabangan-Asilo, Mary Ann; Amparado, Amery; Reinke, Russell; Cruz, Casiana M. Vera; Chin, Joong Hyoun and Swamy, B.P. Mallikarjuna. 2019. Genetic dissection of grain nutritional traits and leaf blight resistance in rice. Genes, Volume 10 no. 1 p. 30 |
| spellingShingle | Descalsota-Empleo, Gwen Iris Noraziyah, Abd Aziz Shamsudin Navea, Ian Paul Chung, Chongtae Dwiyanti, Maria Stefanie Labios, Reuben Jacob Dicen Ikmal, Asmuni Mohd Juanillas, Venice Margarette Inabangan-Asilo, Mary Ann Amparado, Amery Reinke, Russell Vera Cruz, Casiana M. Chin, Joong Hyoun Swamy, B.P. Mallikarjuna Genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| title | Genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| title_full | Genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| title_fullStr | Genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| title_full_unstemmed | Genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| title_short | Genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| title_sort | genetic dissection of grain nutritional traits and leaf blight resistance in rice |
| url | https://hdl.handle.net/10568/164747 |
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