http://oar.icrisat.org/id/eprint/11584 2020-09-04T12:45:08Z info:eu-repo/semantics/descriptiveMetadata http://oar.icrisat.org/11584/ A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction 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 Plant Breeding Sorghum Genetics and Genomics 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. Crop Science Society of America 2020-03 Article PeerReviewed application/pdf en 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 https://doi.org/10.1002/tpg2.20009 doi:10.1002/tpg2.20009 info:eu-repo/semantics/objectFile info:eu-repo/semantics/humanStartPage