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

التفاصيل البيبلوغرافية
العنوان: Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops.
المؤلفون: Gemenet DC; International Potato Center, ILRI Campus, P.O. Box 25171-00603, Nairobi, Kenya. d.gemenet@cgiar.org.; CGIAR Excellence in Breeding Platform, International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, 1041-00621, Nairobi, Kenya. d.gemenet@cgiar.org., Lindqvist-Kreuze H; International Potato Center, Av. La Molina 1895, Lima, Peru., De Boeck B; International Potato Center, Av. La Molina 1895, Lima, Peru., da Silva Pereira G; North Carolina State University, Raleigh, NC, 27695, USA.; International Potato Center, Nairobi, Kenya., Mollinari M; North Carolina State University, Raleigh, NC, 27695, USA., Zeng ZB; North Carolina State University, Raleigh, NC, 27695, USA., Craig Yencho G; North Carolina State University, Raleigh, NC, 27695, USA., Campos H; International Potato Center, Av. La Molina 1895, Lima, Peru.
المصدر: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik [Theor Appl Genet] 2020 Dec; Vol. 133 (12), pp. 3345-3363. Date of Electronic Publication: 2020 Sep 02.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Springer Country of Publication: Germany NLM ID: 0145600 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-2242 (Electronic) Linking ISSN: 00405752 NLM ISO Abbreviation: Theor Appl Genet Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Berlin, New York, Springer
مواضيع طبية MeSH: Genotype* , Plant Breeding* , Polymorphism, Single Nucleotide* , Polyploidy* , Selection, Genetic*, Crops, Agricultural/*genetics , Ipomoea batatas/*genetics, Crops, Agricultural/growth & development ; Ipomoea batatas/growth & development ; Phenotype ; Quantitative Trait Loci ; Sequence Analysis, DNA
مستخلص: 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. 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 F 1 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.
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معلومات مُعتمدة: OPP1052983 Bill and Melinda Gates Foundation
تواريخ الأحداث: Date Created: 20200903 Date Completed: 20210528 Latest Revision: 20240329
رمز التحديث: 20240329
مُعرف محوري في PubMed: PMC7567692
DOI: 10.1007/s00122-020-03673-2
PMID: 32876753
قاعدة البيانات: MEDLINE
الوصف
تدمد:1432-2242
DOI:10.1007/s00122-020-03673-2