Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population
In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a sin...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/108494 |
| _version_ | 1855541521875468288 |
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| author | Silva Pereira, G. da Gemenet, D. Mollinari, M. Olukolu, B.A. Wood, J.C. Díaz, F. Mosquera, V. Grüneberg, W.J. Buell, R. Yencho, George Craig Zeng, Z.B. |
| author_browse | Buell, R. Díaz, F. Gemenet, D. Grüneberg, W.J. Mollinari, M. Mosquera, V. Olukolu, B.A. Silva Pereira, G. da Wood, J.C. Yencho, George Craig Zeng, Z.B. |
| author_facet | Silva Pereira, G. da Gemenet, D. Mollinari, M. Olukolu, B.A. Wood, J.C. Díaz, F. Mosquera, V. Grüneberg, W.J. Buell, R. Yencho, George Craig Zeng, Z.B. |
| author_sort | Silva Pereira, G. da |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population ('Beauregard' × 'Tanzania') with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into the additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids. |
| format | Journal Article |
| id | CGSpace108494 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1084942025-11-29T05:22:24Z Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population Silva Pereira, G. da Gemenet, D. Mollinari, M. Olukolu, B.A. Wood, J.C. Díaz, F. Mosquera, V. Grüneberg, W.J. Buell, R. Yencho, George Craig Zeng, Z.B. sweet potatoes quantitative trait loci polyploidy hexaploidy yield components heritability In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population ('Beauregard' × 'Tanzania') with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into the additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids. 2020-07-01 2020-06-16T22:42:16Z 2020-06-16T22:42:16Z Journal Article https://hdl.handle.net/10568/108494 en Open Access Oxford University Press Da Silva Pereira, G.; Gemenet, D.; Mollinari, M.; Olukolu, B.A.; Wood, J.C.; Diaz, F.; Mosquera, V.; Gruneberg, W.J.; Khan, A.; Buell, R.; Yencho, G.C.; Zeng, Z.B. 2020. Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population Genetics. ISSN 1943-2631. Published online 05May2020 |
| spellingShingle | sweet potatoes quantitative trait loci polyploidy hexaploidy yield components heritability Silva Pereira, G. da Gemenet, D. Mollinari, M. Olukolu, B.A. Wood, J.C. Díaz, F. Mosquera, V. Grüneberg, W.J. Buell, R. Yencho, George Craig Zeng, Z.B. Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population |
| title | Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population |
| title_full | Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population |
| title_fullStr | Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population |
| title_full_unstemmed | Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population |
| title_short | Multiple QTL mapping in autopolyploids: A random-effect model approach with application in a hexaploid sweetpotato full-sib population |
| title_sort | multiple qtl mapping in autopolyploids a random effect model approach with application in a hexaploid sweetpotato full sib population |
| topic | sweet potatoes quantitative trait loci polyploidy hexaploidy yield components heritability |
| url | https://hdl.handle.net/10568/108494 |
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