Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

• DOI: 10.1007/s00122-020-03673-2
• Publication Date: 2020-09-02T10:02:59Z
• Authors: Dorcus C. Gemenet; Hannele Lindqvist...; Bert De Boeck; Guilherme da Silv...; Marcelo Mollinari; Zhao-Bang Zeng; G. Craig Yencho; Hugo Campos
• Keywords: Deep sequencing; Trait; Plant Science; Gene; marker-assisted selection; Agricultural and Biological Sciences; Computational biology; Selection (genetic algorithm); Cultivar Evaluation and Mega-Environment Investigation; Sociology; sweet potatoes; Ipomoea batatas; polyploidy; Single-nucleotide polymorphism; 2. Zero hunger; 0303 health sciences; Genome; Life Sciences; Genomics; FOS: Sociology; Programming language; Rice Genomics; Genetic Mapping; Phenotype; Genetic Architecture of Quantitative Traits; Genetic gain; Genomic Selection in Plant and Animal Breeding; Original Article; Biotechnology; Crops, Agricultural; Quantitative trait locus; Genotype; Quantitative Trait Loci; Population; Polyploid; Polymorphism, Single Nucleotide; Quantitative Genetics; Polyploidy; 03 medical and health sciences; Genetic Value Prediction; Biochemistry, Genetics and Molecular Biology; Machine learning; Genetics; Genetic architecture; potatoes; Genetic variation; Selection, Genetic; Biology; Demography; Sequence Analysis, DNA; Computer science; Plant Breeding; FOS: Biological sciences

Key messagePolypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture.AbstractThe 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 biparentalF1population 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.