Optimizing whole-genomic prediction for autotetraploid blueberry breeding
de Bem Oliveira, Ivone; Amadeu, Rodrigo R.; Ferrão, Luis Felipe; Munoz, Patricio R. (2020), Optimizing whole-genomic prediction for autotetraploid blueberry breeding, Dryad, Dataset, https://doi.org/10.5061/dryad.8pk0p2nk9
Blueberry (Vaccinium spp.) is an important autopolyploid crop with significant benefits for human health. Apart from its genetic complexity, the feasibility of genomic prediction has been proven for blueberry, enabling a reduction in the breeding cycle time and increasing genetic gain. However, as for other polyploid crops, sequencing costs still hinder the implementation of genome-based breeding methods for blueberry. This motivated us to evaluate the effect of training population sizes and composition, as well as the impact of marker density and sequencing depth on phenotype prediction for the species. For this, data from a large real breeding population of 1 804 individuals was used. Genotypic data from 86 930 markers and three traits with different genetic architecture (fruit firmness, fruit weight, and total yield) were evaluated. Herein, we suggested that marker density, sequencing depth, and training population size can be substantially reduced with no significant impact on model accuracy. Our results can help guide decisions towards resource allocation (e.g., genotyping and phenotyping) in order to maximize prediction accuracy. These findings have the potential to allow for a faster and more accurate release of varieties with a substantial reduction of resources for the application of genomic prediction in blueberry. We anticipate that the benefits and pipeline described in our study can be applied to optimize genomic prediction for other diploid and polyploid species.
Genotypes were obtained using capture-seq and processed as described by Benevenuto et al. (2019). In summary, 15,663 120-mer biotinylated probes designed based on the 2013 blueberry draft genome sequence were used (Bian et al. 2014; Gupta et al. 2015). Probes were aligned to a high-quality draft genome (Colle et al. 2019), using BLAST (Altschul et al. 1990). Probes that aligned uniquely and within homologous groups were selected, resulting in 9,390 probes used during single nucleotide polymorphisms (SNP) calling steps. A total of 276,212 SNPs were identified using FreeBayes v.1.0.1 (Garrison and Marth 2012), considering the tetraploid option. Only SNPs that met the following criteria were retained for further analysis: i) minimum mapping quality score of 20; ii) minimum SNP phred quality score of 10; iii) biallelic markers; iv) maximum genotype and marker missing data of 0.2; and v) minor population allele frequency of 0.05. In addition, markers were kept when presenting average sequencing depth per site across all individuals of 60X. To avoid the use of imputation methods, it was required that all data points presented a minimum sequencing depth of 2X. A total of 87,628 SNPs were obtained after filtering, and the sequencing depth data for the alternative and reference are presented here.