Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles
The University of Florida strawberry (Fragaria × ananassa) breeding program has implemented genomic prediction (GP) as a tool for choosing outstanding parents for crosses over the last five seasons. This has allowed the use of some parents 1 year earlier than with traditional methods, thus reducing...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-01-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.596258/full |
| _version_ | 1818394369830420480 |
|---|---|
| author | Luis F. Osorio Salvador A. Gezan Sujeet Verma Vance M. Whitaker |
| author_facet | Luis F. Osorio Salvador A. Gezan Sujeet Verma Vance M. Whitaker |
| author_sort | Luis F. Osorio |
| collection | DOAJ |
| description | The University of Florida strawberry (Fragaria × ananassa) breeding program has implemented genomic prediction (GP) as a tool for choosing outstanding parents for crosses over the last five seasons. This has allowed the use of some parents 1 year earlier than with traditional methods, thus reducing the duration of the breeding cycle. However, as the number of breeding cycles increases over time, greater knowledge is needed on how multiple cycles can be used in the practical implementation of GP in strawberry breeding. Advanced selections and cultivars totaling 1,558 unique individuals were tested in field trials for yield and fruit quality traits over five consecutive years and genotyped for 9,908 SNP markers. Prediction of breeding values was carried out using Bayes B models. Independent validation was carried out using separate trials/years as training (TRN) and testing (TST) populations. Single-trial predictive abilities for five polygenic traits averaged 0.35, which was reduced to 0.24 when individuals common across trials were excluded, emphasizing the importance of relatedness among training and testing populations. Training populations including up to four previous breeding cycles increased predictive abilities, likely due to increases in both training population size and relatedness. Predictive ability was also strongly influenced by heritability, but less so by changes in linkage disequilibrium and effective population size. Genotype by year interactions were minimal. A strategy for practical implementation of GP in strawberry breeding is outlined that uses multiple cycles to predict parental performance and accounts for traits not included in GP models when constructing crosses. Given the importance of relatedness to the success of GP in strawberry, future work could focus on the optimization of relatedness in the design of TRN and TST populations to increase predictive ability in the short-term without compromising long-term genetic gains. |
| first_indexed | 2024-12-14T06:00:07Z |
| format | Article |
| id | doaj.art-1d5e4b5e85134330bd7b5f46443cb92b |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T06:00:07Z |
| publishDate | 2021-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-1d5e4b5e85134330bd7b5f46443cb92b2022-12-21T23:14:27ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.596258596258Independent Validation of Genomic Prediction in Strawberry Over Multiple CyclesLuis F. Osorio0Salvador A. Gezan1Sujeet Verma2Vance M. Whitaker3Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United StatesSchool of Forest Resources and Conservation, University of Florida, Gainesville, FL, United StatesGulf Coast Research and Education Center, University of Florida, Wimauma, FL, United StatesGulf Coast Research and Education Center, University of Florida, Wimauma, FL, United StatesThe University of Florida strawberry (Fragaria × ananassa) breeding program has implemented genomic prediction (GP) as a tool for choosing outstanding parents for crosses over the last five seasons. This has allowed the use of some parents 1 year earlier than with traditional methods, thus reducing the duration of the breeding cycle. However, as the number of breeding cycles increases over time, greater knowledge is needed on how multiple cycles can be used in the practical implementation of GP in strawberry breeding. Advanced selections and cultivars totaling 1,558 unique individuals were tested in field trials for yield and fruit quality traits over five consecutive years and genotyped for 9,908 SNP markers. Prediction of breeding values was carried out using Bayes B models. Independent validation was carried out using separate trials/years as training (TRN) and testing (TST) populations. Single-trial predictive abilities for five polygenic traits averaged 0.35, which was reduced to 0.24 when individuals common across trials were excluded, emphasizing the importance of relatedness among training and testing populations. Training populations including up to four previous breeding cycles increased predictive abilities, likely due to increases in both training population size and relatedness. Predictive ability was also strongly influenced by heritability, but less so by changes in linkage disequilibrium and effective population size. Genotype by year interactions were minimal. A strategy for practical implementation of GP in strawberry breeding is outlined that uses multiple cycles to predict parental performance and accounts for traits not included in GP models when constructing crosses. Given the importance of relatedness to the success of GP in strawberry, future work could focus on the optimization of relatedness in the design of TRN and TST populations to increase predictive ability in the short-term without compromising long-term genetic gains.https://www.frontiersin.org/articles/10.3389/fgene.2020.596258/fulltraining populationFragariabreedingBayes Bgenome-wide predictiontest population |
| spellingShingle | Luis F. Osorio Salvador A. Gezan Sujeet Verma Vance M. Whitaker Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles Frontiers in Genetics training population Fragaria breeding Bayes B genome-wide prediction test population |
| title | Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles |
| title_full | Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles |
| title_fullStr | Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles |
| title_full_unstemmed | Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles |
| title_short | Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles |
| title_sort | independent validation of genomic prediction in strawberry over multiple cycles |
| topic | training population Fragaria breeding Bayes B genome-wide prediction test population |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.596258/full |
| work_keys_str_mv | AT luisfosorio independentvalidationofgenomicpredictioninstrawberryovermultiplecycles AT salvadoragezan independentvalidationofgenomicpredictioninstrawberryovermultiplecycles AT sujeetverma independentvalidationofgenomicpredictioninstrawberryovermultiplecycles AT vancemwhitaker independentvalidationofgenomicpredictioninstrawberryovermultiplecycles |