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A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

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Relation http://oar.icrisat.org/11584/
https://doi.org/10.1002/tpg2.20009
doi:10.1002/tpg2.20009
 
Title A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction
 
Creator Jensen, S E
Charles, J R
Muleta, K
Bradbury, P J
Casstevens, T
Deshpande, S P
Gore, M A
Gupta, R
Ilut, D C
Johnson, L
Lozano, R
Miller, Z
Ramu, P
Rathore, A
Romay, M C
Upadhyaya, H D
Varshney, R K
Morris, G P
Pressoir, G
Buckler, E S
Ramstein, G P
 
Subject Plant Breeding
Sorghum
Genetics and Genomics
 
Description 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 Sorghum bicolor Practical Haplotype Graph (PHG) pangenome
database that stores haplotypes and variant information. We developed two PHGs
in sorghum that were used to identify genome-wide variants for 24 founders of the
Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called
single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only
3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally,
207 progenies from the Chibas genomic selection (GS) training population
were sequenced and processed through the PHG. Missing genotypes were imputed
from PHG parental haplotypes and used for genomic prediction. Mean prediction
accuracies with PHG SNP calls range from .57–.73 and are similar to prediction
accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing
(rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify
genotype calls across multiple sequencing platforms. By reducing input sequence
requirements, the PHG can decrease the cost of genotyping, make GS more feasible,
and facilitate larger breeding populations. Our results demonstrate that the PHG is a
useful research and breeding tool that maintains variant information from a diverse
group of taxa, stores sequence data in a condensed but readily accessible format, unifies
genotypes across genotyping platforms, and provides a cost-effective option for
genomic selection.
 
Publisher Crop Science Society of America
 
Date 2020-03
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11584/1/tpg2.20009.pdf
Jensen, S E and Charles, J R and Muleta, K and Bradbury, P J and Casstevens, T and Deshpande, S P and Gore, M A and Gupta, R and Ilut, D C and Johnson, L and Lozano, R and Miller, Z and Ramu, P and Rathore, A and Romay, M C and Upadhyaya, H D and Varshney, R K and Morris, G P and Pressoir, G and Buckler, E S and Ramstein, G P (2020) A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction. The Plant Genome (TSI), 13 (1). pp. 1-15. ISSN 1940-3372