Abstract
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.The 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 biparental F1 population 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.
Highlights
Phenotyping under recurrent selection has been an important approach for variety development in plant breeding, with substantial success to date
Cornell GBS in potato resulted in 295,401 biallelic single nucleotide polymorphisms (SNPs) at the variant calling step that were hard-filtered to 3262 high confidence SNPs by setting minimum allele frequency (MAF) ≥ 3%, call rate ≥ 70% and average read depth (DP) ≥ 16 (Online Resource 4)
The 3262 SNP profiles are shown in Fig. 1C, D showing MAF ranging from 0.03 (3%) to 0.5 (50%), with a mean of 0.15 (15%) and polymorphic information content (PIC) ranging from 0.0 to 0.5, with a mean of 0.23
Summary
Phenotyping under recurrent selection has been an important approach for variety development in plant breeding, with substantial success to date This process may take a long time for most crops, for clonally propagated crops (Slater et al 2016). In potato, it typically takes an entire year to develop enough tubers from botanical seed obtained from crossing nurseries, for experimental trial purposes. This is followed by at least 2 years of field evaluation for qualitative traits, with evaluation for most quantitative traits in replicated multi-environment trials beginning in around year four (Endelman et al 2018). This represents a stark contrast with what can be achieved in cereal and legume crops, where up
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