Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications
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ORIGINAL ARTICLE
Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops Dorcus C. Gemenet1,4 · Hannele Lindqvist‑Kreuze2 · Bert De Boeck2 · Guilherme da Silva Pereira3,5 · Marcelo Mollinari3 · Zhao‑Bang Zeng3 · G. Craig Yencho3 · Hugo Campos2 Received: 1 March 2020 / Accepted: 21 August 2020 © The Author(s) 2020
Key message Polypoid 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. Abstract 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.
Introduction Communicated by Herman J. van Eck. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03673-2) contains supplementary material, which is available to authorized users. * Dorcus C. Gemenet [email protected] 1
International Potato Center, ILRI Campus, P.O. Box 25171‑00603, Nairobi, Kenya
2
International Potato Center, Av. La Molina 1895, Lima, Peru
3
North Carolina State University, Raleigh, NC 27695, USA
4
Present Address: CGIAR Excellence in Breeding Platform, International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, 1041‑00621 Nairobi, Kenya
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Present Address: International Potato Center, Nairobi, Kenya
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