Journal article
A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction
The Plant Genome, Vol.13(1), Art. e20009
2020
Abstract
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.
Details
- Title
- A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction
- Authors/Creators
- S.E. Jensen (Author/Creator) - Cornell UniversityJ.R. Charles (Author/Creator) - Quisqueya UniversityK. Muleta (Author/Creator) - Kansas State UniversityP. J. Bradbury (Author/Creator) - Cornell UniversityT. Casstevens (Author/Creator) - Cornell UniversityS.P. Deshpande (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM.A. Gore (Author/Creator) - Cornell UniversityR. Gupta (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsD.C. Ilut (Author/Creator) - Cornell UniversityL. Johnson (Author/Creator) - Cornell UniversityR. Lozano (Author/Creator) - Cornell UniversityZ. Miller (Author/Creator) - Cornell UniversityP. Ramu (Author/Creator) - Cornell UniversityA. Rathore (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM.C. Romay (Author/Creator) - Cornell UniversityH.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsG.P. Morris (Author/Creator) - Kansas State UniversityG. Pressoir (Author/Creator) - Quisqueya UniversityE.S. Buckler (Author/Creator) - Cornell UniversityG.P. Ramstein (Author/Creator) - Cornell University
- Publication Details
- The Plant Genome, Vol.13(1), Art. e20009
- Publisher
- Wiley Periodicals, Inc. on behalf of Crop Science Society of America
- Identifiers
- 991005541557207891
- Copyright
- © 2020 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites
Metrics
36 File views/ downloads
112 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Genetics & Heredity
- Plant Sciences
- ESI research areas
- Plant & Animal Science