An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies
Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selec...
| Autores principales: | , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Public Library of Science
2020
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164507 |
| _version_ | 1855541587260473344 |
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| author | Morales, Karina Y. Singh, Namrata Perez, Francisco Agosto Ignacio, John Carlos Thapa, Ranjita Arbelaez, Juan D. Tabien, Rodante E. Famoso, Adam Wang, Diane R. Septiningsih, Endang M. Shi, Yuxin Kretzschmar, Tobias McCouch, Susan R. Thomson, Michael J. |
| author_browse | Arbelaez, Juan D. Famoso, Adam Ignacio, John Carlos Kretzschmar, Tobias McCouch, Susan R. Morales, Karina Y. Perez, Francisco Agosto Septiningsih, Endang M. Shi, Yuxin Singh, Namrata Tabien, Rodante E. Thapa, Ranjita Thomson, Michael J. Wang, Diane R. |
| author_facet | Morales, Karina Y. Singh, Namrata Perez, Francisco Agosto Ignacio, John Carlos Thapa, Ranjita Arbelaez, Juan D. Tabien, Rodante E. Famoso, Adam Wang, Diane R. Septiningsih, Endang M. Shi, Yuxin Kretzschmar, Tobias McCouch, Susan R. Thomson, Michael J. |
| author_sort | Morales, Karina Y. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding. |
| format | Journal Article |
| id | CGSpace164507 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1645072025-01-24T14:20:55Z An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies Morales, Karina Y. Singh, Namrata Perez, Francisco Agosto Ignacio, John Carlos Thapa, Ranjita Arbelaez, Juan D. Tabien, Rodante E. Famoso, Adam Wang, Diane R. Septiningsih, Endang M. Shi, Yuxin Kretzschmar, Tobias McCouch, Susan R. Thomson, Michael J. general agricultural and biological sciences general biochemistry genetics and molecular biology general medicine Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding. 2020-05-14 2024-12-19T12:53:59Z 2024-12-19T12:53:59Z Journal Article https://hdl.handle.net/10568/164507 en Open Access Public Library of Science Morales, Karina Y.; Singh, Namrata; Perez, Francisco Agosto; Ignacio, John Carlos; Thapa, Ranjita; Arbelaez, Juan D.; Tabien, Rodante E.; Famoso, Adam; Wang, Diane R.; Septiningsih, Endang M.; Shi, Yuxin; Kretzschmar, Tobias; McCouch, Susan R. and Thomson, Michael J. 2020. An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies. PLoS ONE, Volume 15 no. 5 p. e0232479 |
| spellingShingle | general agricultural and biological sciences general biochemistry genetics and molecular biology general medicine Morales, Karina Y. Singh, Namrata Perez, Francisco Agosto Ignacio, John Carlos Thapa, Ranjita Arbelaez, Juan D. Tabien, Rodante E. Famoso, Adam Wang, Diane R. Septiningsih, Endang M. Shi, Yuxin Kretzschmar, Tobias McCouch, Susan R. Thomson, Michael J. An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies |
| title | An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies |
| title_full | An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies |
| title_fullStr | An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies |
| title_full_unstemmed | An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies |
| title_short | An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies |
| title_sort | improved 7k snp array the c7air provides a wealth of validated snp markers for rice breeding and genetics studies |
| topic | general agricultural and biological sciences general biochemistry genetics and molecular biology general medicine |
| url | https://hdl.handle.net/10568/164507 |
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