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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

opulation-tailored mock genome enables genomic studies in species without a reference genom

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Author(s):
Sabadin, Felipe [1] ; Carvalho, Humberto Fanelli [1] ; Galli, Giovanni [1] ; Fritsche-Neto, Roberto [1]
Total Authors: 4
Affiliation:
[1] Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Genet, Piracicaba, SP - Brazil
Total Affiliations: 1
Document type: Journal article
Source: Molecular Genetics and Genomics; v. 297, n. 1 NOV 2021.
Web of Science Citations: 0
Abstract

Based on molecular markers, genomic prediction enables us to speed up breeding schemes and increase the response to selection. There are several high-throughput genotyping platforms able to deliver thousands of molecular markers for genomic study purposes. However, even though its widely applied in plant breeding, species without a reference genome cannot fully benefit from genomic tools and modern breeding schemes. We used a method to assemble a population-tailored mock genome to call single-nucleotide polymorphism (SNP) markers without an available reference genome, and for the first time, we compared the results with standard genotyping platforms (array and genotyping-by-sequencing (GBS) using a reference genome) for performance in genomic prediction models. Our results indicate that using a population-tailored mock genome to call SNP delivers reliable estimates for the genomic relationship between genotypes. Furthermore, genomic prediction estimates were comparable to standard approaches, especially when considering only additive effects. However, mock genomes were slightly worse than arrays at predicting traits influenced by dominance effects, but still performed as well as standard GBS methods that use a reference genome. Nevertheless, the array-based SNP markers methods achieved the best predictive ability and reliability to estimate variance components. Overall, the mock genomes can be a worthy alternative for genomic selection studies, especially for those species where the reference genome is not available. (AU)

FAPESP's process: 17/24327-0 - TCGA: an tropical corn germplasm assembly for genomic prediction and high-throughput phenotyping studies
Grantee:Roberto Fritsche Neto
Support Opportunities: Regular Research Grants