Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
| Autor: | Neal W. Tilhou, Michael D. Casler |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
education.field_of_study
Population Pooling Plant culture Plant Science Computational biology Perennial crop DNA Genomics Sequence Analysis DNA QH426-470 Biology biology.organism_classification Panicum SB1-1110 Plant Breeding Genetic gain Genetics Panicum virgatum Dna pooling education Agronomy and Crop Science Genomic selection Genome Plant |
| Zdroj: | The Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021) |
| ISSN: | 1940-3372 |
| Popis: | Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of 80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence‐based GS when sequencing resources were restricted (2,000 DNA samples per 5‐yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5‐yr cycle). This study highlights multiple routes for reduced sequencing costs in GS. |
| Databáze: | OpenAIRE |
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