Novel methods to optimize genotypic imputation for low‐coverage, next‐generation sequence data in crop plants
Next‐generation sequencing technology such as genotyping‐by‐sequencing (GBS) made
low‐cost, but often low‐coverage, whole‐genome sequencing widely available. Extensive …
low‐cost, but often low‐coverage, whole‐genome sequencing widely available. Extensive …
[HTML][HTML] Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references
Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged
as a popular technology for genetic and breeding applications in bread wheat (Triticum …
as a popular technology for genetic and breeding applications in bread wheat (Triticum …
[HTML][HTML] Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding
N Wang, Y Yuan, H Wang, D Yu, Y Liu, A Zhang… - Scientific reports, 2020 - nature.com
Abstract Genotyping-by-Sequencing (GBS) is a low-cost, high-throughput genotyping
method that relies on restriction enzymes to reduce genome complexity. GBS is being widely …
method that relies on restriction enzymes to reduce genome complexity. GBS is being widely …
Efficient genome-wide genotyping strategies and data integration in crop plants
Key message Next-generation sequencing (NGS) has revolutionized plant and animal
research by providing powerful genotyping methods. This review describes and discusses …
research by providing powerful genotyping methods. This review describes and discusses …
Factors affecting the accuracy of genotype imputation in populations from several maize breeding programs
Genomic selection and association mapping offer great potential to increase rates of genetic
progress in plants. The prediction of genomic breeding values usually requires that missing …
progress in plants. The prediction of genomic breeding values usually requires that missing …
LinkImpute: fast and accurate genotype imputation for nonmodel organisms
Obtaining genome-wide genotype data from a set of individuals is the first step in many
genomic studies, including genome-wide association and genomic selection. All genotyping …
genomic studies, including genome-wide association and genomic selection. All genotyping …
A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction
SE Jensen, JR Charles, K Muleta… - The Plant …, 2020 - Wiley Online Library
Successful management and utilization of increasingly large genomic datasets is essential
for breeding programs to accelerate cultivar development. To help with this, we developed a …
for breeding programs to accelerate cultivar development. To help with this, we developed a …
[HTML][HTML] Fast imputation using medium or low-coverage sequence data
PM VanRaden, C Sun, JR O'Connell - BMC genetics, 2015 - Springer
Background Accurate genotype imputation can greatly reduce costs and increase benefits
by combining whole-genome sequence data of varying read depth and array genotypes of …
by combining whole-genome sequence data of varying read depth and array genotypes of …
Potential of low‐coverage genotyping‐by‐sequencing and imputation for cost‐effective genomic selection in biparental segregating populations
Genotyping‐by‐sequencing (GBS) is an alternative genotyping method to single‐nucleotide
polymorphism (SNP) arrays that has received considerable attention in the plant breeding …
polymorphism (SNP) arrays that has received considerable attention in the plant breeding …
[HTML][HTML] Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum
Abstract Background Eight diverse sorghum (Sorghum bicolor L. Moench) accessions were
subjected to short-read genome sequencing to characterize the distribution of single …
subjected to short-read genome sequencing to characterize the distribution of single …