Projects per year
Description
Abstract
Two barley populations were genotyped for use in studies of genomewide selection: a training population of 183 individuals and a selection candidate population of 1200 individuals.
Description
1383 (1200 + 183) barley individuals were genotyped using genotyping-by-sequencing (GBS). 100 - 150 bp single-end reads were generated from the USDA-ARS Small Grains Genotyping Lab in Fargo, ND. SNPs were called using a custom pipeline (https://github.com/neyhartj/GBarleyS) and were filtered for mapping quality, genotype quality, and read depth (see README). Markers and entries were further processed and filtered on minor allele frequency and missingness using the relevant R script (see README). Missing marker genotypes were imputed using 3 different methods using the relevant R script (see README). Both the unimputed ("discrete") and imputed ("imputed") marker genotypes are available in this repository.
Funding information
Sponsorship: U.S. Wheat and Barley Scab Initiative; Minnesota Department of Agriculture; Rahr Malting Company; the Brewers Association; American Malting Barley Association; USDA-NIFA Grant #2018-67011-28075
Two barley populations were genotyped for use in studies of genomewide selection: a training population of 183 individuals and a selection candidate population of 1200 individuals.
Description
1383 (1200 + 183) barley individuals were genotyped using genotyping-by-sequencing (GBS). 100 - 150 bp single-end reads were generated from the USDA-ARS Small Grains Genotyping Lab in Fargo, ND. SNPs were called using a custom pipeline (https://github.com/neyhartj/GBarleyS) and were filtered for mapping quality, genotype quality, and read depth (see README). Markers and entries were further processed and filtered on minor allele frequency and missingness using the relevant R script (see README). Missing marker genotypes were imputed using 3 different methods using the relevant R script (see README). Both the unimputed ("discrete") and imputed ("imputed") marker genotypes are available in this repository.
Funding information
Sponsorship: U.S. Wheat and Barley Scab Initiative; Minnesota Department of Agriculture; Rahr Malting Company; the Brewers Association; American Malting Barley Association; USDA-NIFA Grant #2018-67011-28075
| Date made available | 2019 |
|---|---|
| Publisher | Data Repository for the University of Minnesota |
| Date of data production | Sep 1 2014 - Sep 1 2015 |
Projects
- 1 Finished
-
Building and deploying a nationwide dataset to support g
Neyhart, J. (PI) & Smith, K. P. (CoI)
UNITED STATES DEPARTMENT OF AGRICULTURE
3/15/18 → 3/14/20
Project: Research project
Research output
- 3 Article
-
Multi-trait Improvement by Predicting Genetic Correlations in Breeding Crosses
Neyhart, J. L., Lorenz, A. J. & Smith, K. P., Oct 1 2019, In: G3: Genes, Genomes, Genetics. 9, 10, p. 3153-3165 13 p.Research output: Contribution to journal › Article › peer-review
Open Access49 Scopus citations -
Registration of the S2MET barley mapping population for multi-environment genomewide selection
Neyhart, J. L., Sweeney, D., Sorrells, M., Kapp, C., Kephart, K. D., Sherman, J., Stockinger, E. J., Fisk, S., Hayes, P., Daba, S., Mohammadi, M., Hughes, N., Lukens, L., Barrios, P. G., Gutiérrez, L. & Smith, K. P., May 2019, In: Journal of Plant Registrations. 13, 2, p. 270-280 11 p.Research output: Contribution to journal › Article › peer-review
10 Scopus citations -
Validating genomewide predictions of genetic variance in a contemporary breeding program
Neyhart, J. L. & Smith, K. P., May 1 2019, In: Crop Science. 59, 3, p. 1062-1072 11 p.Research output: Contribution to journal › Article › peer-review
21 Scopus citations