Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding
Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to expanding production areas by developing low-chilling cultivars better adapted to subtropi...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.676326/full |
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| author | Luís Felipe V. Ferrão Rodrigo R. Amadeu Juliana Benevenuto Ivone de Bem Oliveira Ivone de Bem Oliveira Patricio R. Munoz |
| author_facet | Luís Felipe V. Ferrão Rodrigo R. Amadeu Juliana Benevenuto Ivone de Bem Oliveira Ivone de Bem Oliveira Patricio R. Munoz |
| author_sort | Luís Felipe V. Ferrão |
| collection | DOAJ |
| description | Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to expanding production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on recurrent phenotypic selection. As an autopolyploid, outcrossing, perennial, long juvenile phase crop, blueberry breeding cycles are costly and time consuming, which results in low genetic gains per unit of time. Motivated by applying molecular markers for a more accurate selection in the early stages of breeding, we performed pioneering genomic selection studies and optimization for its implementation in the blueberry breeding program. We have also addressed some complexities of sequence-based genotyping and model parametrization for an autopolyploid crop, providing empirical contributions that can be extended to other polyploid species. We herein revisited some of our previous genomic selection studies and showed for the first time its application in an independent validation set. In this paper, our contribution is three-fold: (i) summarize previous results on the relevance of model parametrizations, such as diploid or polyploid methods, and inclusion of dominance effects; (ii) assess the importance of sequence depth of coverage and genotype dosage calling steps; (iii) demonstrate the real impact of genomic selection on leveraging breeding decisions by using an independent validation set. Altogether, we propose a strategy for using genomic selection in blueberry, with the potential to be applied to other polyploid species of a similar background. |
| first_indexed | 2024-12-17T05:33:28Z |
| format | Article |
| id | doaj.art-385f8fe1e6454959ba810e0079ac50f9 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-17T05:33:28Z |
| publishDate | 2021-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-385f8fe1e6454959ba810e0079ac50f92022-12-21T22:01:41ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-06-011210.3389/fpls.2021.676326676326Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry BreedingLuís Felipe V. Ferrão0Rodrigo R. Amadeu1Juliana Benevenuto2Ivone de Bem Oliveira3Ivone de Bem Oliveira4Patricio R. Munoz5Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United StatesBlueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United StatesBlueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United StatesBlueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United StatesHortifrut North America, Inc., Estero, FL, United StatesBlueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United StatesBlueberry (Vaccinium corymbosum and hybrids) is a specialty crop with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to expanding production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on recurrent phenotypic selection. As an autopolyploid, outcrossing, perennial, long juvenile phase crop, blueberry breeding cycles are costly and time consuming, which results in low genetic gains per unit of time. Motivated by applying molecular markers for a more accurate selection in the early stages of breeding, we performed pioneering genomic selection studies and optimization for its implementation in the blueberry breeding program. We have also addressed some complexities of sequence-based genotyping and model parametrization for an autopolyploid crop, providing empirical contributions that can be extended to other polyploid species. We herein revisited some of our previous genomic selection studies and showed for the first time its application in an independent validation set. In this paper, our contribution is three-fold: (i) summarize previous results on the relevance of model parametrizations, such as diploid or polyploid methods, and inclusion of dominance effects; (ii) assess the importance of sequence depth of coverage and genotype dosage calling steps; (iii) demonstrate the real impact of genomic selection on leveraging breeding decisions by using an independent validation set. Altogether, we propose a strategy for using genomic selection in blueberry, with the potential to be applied to other polyploid species of a similar background.https://www.frontiersin.org/articles/10.3389/fpls.2021.676326/fullgenotyping by sequencingsequencing depthallele dosageplant breedingmolecular markerfruit quality |
| spellingShingle | Luís Felipe V. Ferrão Rodrigo R. Amadeu Juliana Benevenuto Ivone de Bem Oliveira Ivone de Bem Oliveira Patricio R. Munoz Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding Frontiers in Plant Science genotyping by sequencing sequencing depth allele dosage plant breeding molecular marker fruit quality |
| title | Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding |
| title_full | Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding |
| title_fullStr | Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding |
| title_full_unstemmed | Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding |
| title_short | Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding |
| title_sort | genomic selection in an outcrossing autotetraploid fruit crop lessons from blueberry breeding |
| topic | genotyping by sequencing sequencing depth allele dosage plant breeding molecular marker fruit quality |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.676326/full |
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