When less can be better: How can we make genomic selection more cost-effective and accurate in barley?

When less can be better: How can we make genomic selection more cost-effective and accurate in... Key message We 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. Abstract 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 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png TAG Theoretical and Applied Genetics Springer Journals

When less can be better: How can we make genomic selection more cost-effective and accurate in barley?

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Publisher
Springer Berlin Heidelberg
Copyright
Copyright © 2018 by Springer-Verlag GmbH Germany, part of Springer Nature
Subject
Life Sciences; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Agriculture; Plant Biochemistry; Biochemistry, general; Biotechnology
ISSN
0040-5752
eISSN
1432-2242
D.O.I.
10.1007/s00122-018-3120-8
Publisher site
See Article on Publisher Site

Abstract

Key message We 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. Abstract 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

Journal

TAG Theoretical and Applied GeneticsSpringer Journals

Published: Jun 1, 2018

References

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