ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2018
When less can be better: How can we make genomic selection more cost-effective and accurate in barley?
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 67 citations in OpenAlex.
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- Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals.Genes · 2023Review
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- 3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes.Plant methods · 2023Article
- A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple.Journal of advanced research · 2022Article
- Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs.The plant genome · 2022Article
- Genomic Selection: A Tool for Accelerating the Efficiency of Molecular Breeding for Development of Climate-Resilient Crops.Frontiers in genetics · 2022Review
- Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects.Frontiers in plant science · 2022Review
- Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL-based genomics-assisted prediction.Plant biotechnology journal · 2021Article
- Genotyping crossing parents and family bulks can facilitate cost-efficient genomic prediction strategies in small-scale line breeding programs.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection.The plant genome · 2021Article
- GPTransformer: A Transformer-Based Deep Learning Method for Predicting Fusarium Related Traits in Barley.Frontiers in plant science · 2021Article
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- Quantitative trait loci-based genomics-assisted prediction for the degree of apple fruit cover color.The plant genome · 2020Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageWe were able to obtain good prediction accuracy in genomic selection with ~ 2000 GBS-derived SNPs. SNPs in genic regions did not improve prediction accuracy compared to SNPs in intergenic regions. Since genotyping can represent an important cost in genomic selection, it is important to minimize it without compromising the accuracy of predictions. The objectives of the present study were to explore how a decrease in the unit cost of genotyping impacted: (1) the number of single nucleotide polymorphism (SNP) markers; (2) the accuracy of the resulting genotypic data; (3) the extent of coverage on both physical and genetic maps; and (4) the prediction accuracy (PA) for six important traits in barley. Variations on the genotyping by sequencing protocol were used to generate 16 SNP sets ranging from ~ 500 to ~ 35,000 SNPs. The accuracy of SNP genotypes fluctuated between 95 and 99%. Marker distribution on the physical map was highly skewed toward the terminal regions, whereas a fairly uniform coverage of the genetic map was achieved with all but the smallest set of SNPs. We estimated the PA using three statistical models capturing (or not) the epistatic effect; the one modeling both additivity and epistasis was selected as the best model. The PA obtained with the different SNP sets was measured and found to remain stable, except with the smallest set, where a significant decrease was observed. Finally, we examined if the localization of SNP loci (genic vs. intergenic) affected the PA. No gain in PA was observed using SNPs located in genic regions. In summary, we found that there is considerable scope for decreasing the cost of genotyping in barley (to capture ~ 2000 SNPs) without loss of PA.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.