Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification
Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL p...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2016-07-01
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| Series: | The Plant Genome |
| Online Access: | https://dl.sciencesocieties.org/publications/tpg/articles/9/2/plantgenome2015.10.0109 |
| _version_ | 1828386437577310208 |
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| author | Lijun Meng Longbiao Guo Kimberly Ponce Xiangqian Zhao Guoyou Ye |
| author_facet | Lijun Meng Longbiao Guo Kimberly Ponce Xiangqian Zhao Guoyou Ye |
| author_sort | Lijun Meng |
| collection | DOAJ |
| description | Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker–trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014. A population of 248 IRRI breeding lines and a population of 323 Chinese breeding lines were also included to compare genetic diversity and linkage disequilibrium (LD) pattern. Our study discovered that (i) the 8-way population had a higher gene diversity than the DC1, DC2, and IRRI populations; (ii) all three MAGIC populations showed no clear population structure; (iii) LD decayed to < 0.2 at about 2.5, 2.5, 1.25, 1.75, and 4.0 Mb for the DC1, DC2, 8-way, IRRI, and Chinese populations, respectively; and (iv) the 8-way population was more powerful than the DC1, DC2, and IRRI populations on QTL identification. The association analysis identified two and three QTL for PH and HD, respectively. Four of the five QTL had peak markers close to known genes. A novel QTL for PH was identified on chromosome 12 using the 8-way population. Therefore, our study suggests that the three new MAGIC populations are valuable resources for QTL identification. |
| first_indexed | 2024-12-10T05:37:17Z |
| format | Article |
| id | doaj.art-cb5558eb5e5244788967db7d007f645d |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-12-10T05:37:17Z |
| publishDate | 2016-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-cb5558eb5e5244788967db7d007f645d2022-12-22T02:00:22ZengWileyThe Plant Genome1940-33722016-07-019210.3835/plantgenome2015.10.0109plantgenome2015.10.0109Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci IdentificationLijun MengLongbiao GuoKimberly PonceXiangqian ZhaoGuoyou YeThree new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker–trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014. A population of 248 IRRI breeding lines and a population of 323 Chinese breeding lines were also included to compare genetic diversity and linkage disequilibrium (LD) pattern. Our study discovered that (i) the 8-way population had a higher gene diversity than the DC1, DC2, and IRRI populations; (ii) all three MAGIC populations showed no clear population structure; (iii) LD decayed to < 0.2 at about 2.5, 2.5, 1.25, 1.75, and 4.0 Mb for the DC1, DC2, 8-way, IRRI, and Chinese populations, respectively; and (iv) the 8-way population was more powerful than the DC1, DC2, and IRRI populations on QTL identification. The association analysis identified two and three QTL for PH and HD, respectively. Four of the five QTL had peak markers close to known genes. A novel QTL for PH was identified on chromosome 12 using the 8-way population. Therefore, our study suggests that the three new MAGIC populations are valuable resources for QTL identification.https://dl.sciencesocieties.org/publications/tpg/articles/9/2/plantgenome2015.10.0109 |
| spellingShingle | Lijun Meng Longbiao Guo Kimberly Ponce Xiangqian Zhao Guoyou Ye Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification The Plant Genome |
| title | Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification |
| title_full | Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification |
| title_fullStr | Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification |
| title_full_unstemmed | Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification |
| title_short | Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification |
| title_sort | characterization of three indica rice multiparent advanced generation intercross magic populations for quantitative trait loci identification |
| url | https://dl.sciencesocieties.org/publications/tpg/articles/9/2/plantgenome2015.10.0109 |
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