Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops
The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a...
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2020
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/109198 |
| _version_ | 1855543338146463744 |
|---|---|
| author | Gemenet, D. Lindqvist-Kreuze, H. Boeck, B. de Silva Pereira, G. da Mollinari, M. Zeng, Z.B. Yencho, George Craig Campos, Hugo |
| author_browse | Boeck, B. de Campos, Hugo Gemenet, D. Lindqvist-Kreuze, H. Mollinari, M. Silva Pereira, G. da Yencho, George Craig Zeng, Z.B. |
| author_facet | Gemenet, D. Lindqvist-Kreuze, H. Boeck, B. de Silva Pereira, G. da Mollinari, M. Zeng, Z.B. Yencho, George Craig Campos, Hugo |
| author_sort | Gemenet, D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations. |
| format | Journal Article |
| id | CGSpace109198 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1091982025-11-29T05:22:25Z Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops Gemenet, D. Lindqvist-Kreuze, H. Boeck, B. de Silva Pereira, G. da Mollinari, M. Zeng, Z.B. Yencho, George Craig Campos, Hugo potatoes sweet potatoes marker-assisted selection polyploidy The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations. 2020-12 2020-09-03T21:23:56Z 2020-09-03T21:23:56Z Journal Article https://hdl.handle.net/10568/109198 en Open Access Springer Gemenet, D.C.; Lindqvist-Kreuze, H.; De Boeck, B.; da Silva Pereira, G.; Mollinari, M.; Zeng, Z.B.; Yencho, G.C.; Campos, H. (2020). Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops. Theoretical and Applied Genetics. Published Online 02Sep2020. |
| spellingShingle | potatoes sweet potatoes marker-assisted selection polyploidy Gemenet, D. Lindqvist-Kreuze, H. Boeck, B. de Silva Pereira, G. da Mollinari, M. Zeng, Z.B. Yencho, George Craig Campos, Hugo Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| title | Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| title_full | Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| title_fullStr | Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| title_full_unstemmed | Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| title_short | Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| title_sort | sequencing depth and genotype quality accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops |
| topic | potatoes sweet potatoes marker-assisted selection polyploidy |
| url | https://hdl.handle.net/10568/109198 |
| work_keys_str_mv | AT gemenetd sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT lindqvistkreuzeh sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT boeckbde sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT silvapereiragda sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT mollinarim sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT zengzb sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT yenchogeorgecraig sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops AT camposhugo sequencingdepthandgenotypequalityaccuracyandbreedingoperationconsiderationsforgenomicselectionapplicationsinautopolyploidcrops |