A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations
Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase pop...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.590012/full |
| _version_ | 1818717692488581120 |
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| author | Suhong Bu Suhong Bu Weiren Wu Yuan-Ming Zhang |
| author_facet | Suhong Bu Suhong Bu Weiren Wu Yuan-Ming Zhang |
| author_sort | Suhong Bu |
| collection | DOAJ |
| description | Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple families in the NAM population, which could discriminate the effects of QTLs in all subpopulations. A series of simulations with a real maize NAM genomic data were implemented. The results demonstrated that the new method improves the statistical power in QTL detection and the accuracy in QTL effect estimation. The new approach, along with single-family linkage mapping, was used to identify QTLs for three flowering time traits in the maize NAM population. As a result, most QTLs detected in single family linkage mapping were identified by the new method. In addition, the new method also mapped some new QTLs with small effects, although their functions need to be identified in the future. |
| first_indexed | 2024-12-17T19:39:12Z |
| format | Article |
| id | doaj.art-0ac3402ee59f4605b20af35679fc029c |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-17T19:39:12Z |
| publishDate | 2021-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0ac3402ee59f4605b20af35679fc029c2022-12-21T21:35:04ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.590012590012A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various SubpopulationsSuhong Bu0Suhong Bu1Weiren Wu2Yuan-Ming Zhang3College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, ChinaCrop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaNested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple families in the NAM population, which could discriminate the effects of QTLs in all subpopulations. A series of simulations with a real maize NAM genomic data were implemented. The results demonstrated that the new method improves the statistical power in QTL detection and the accuracy in QTL effect estimation. The new approach, along with single-family linkage mapping, was used to identify QTLs for three flowering time traits in the maize NAM population. As a result, most QTLs detected in single family linkage mapping were identified by the new method. In addition, the new method also mapped some new QTLs with small effects, although their functions need to be identified in the future.https://www.frontiersin.org/articles/10.3389/fgene.2020.590012/fullnested association mapping (NAM)multi-locus association modeljoint-familysubpopulationmaize |
| spellingShingle | Suhong Bu Suhong Bu Weiren Wu Yuan-Ming Zhang A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations Frontiers in Genetics nested association mapping (NAM) multi-locus association model joint-family subpopulation maize |
| title | A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations |
| title_full | A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations |
| title_fullStr | A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations |
| title_full_unstemmed | A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations |
| title_short | A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations |
| title_sort | multi locus association model framework for nested association mapping with discriminating qtl effects in various subpopulations |
| topic | nested association mapping (NAM) multi-locus association model joint-family subpopulation maize |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.590012/full |
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