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dc:title "HTML Summary of #11584 \n\nA sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction\n\n";
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bibo:abstract "Successful management and utilization of increasingly large genomic datasets is\r\nessential for breeding programs to accelerate cultivar development. To help with\r\nthis, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome\r\ndatabase that stores haplotypes and variant information. We developed two PHGs\r\nin sorghum that were used to identify genome-wide variants for 24 founders of the\r\nChibas sorghum breeding program from 0.01x sequence coverage. The PHG called\r\nsingle nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only\r\n3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally,\r\n207 progenies from the Chibas genomic selection (GS) training population\r\nwere sequenced and processed through the PHG. Missing genotypes were imputed\r\nfrom PHG parental haplotypes and used for genomic prediction. Mean prediction\r\naccuracies with PHG SNP calls range from .57–.73 and are similar to prediction\r\naccuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing\r\n(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\r\ngenotype calls across multiple sequencing platforms. By reducing input sequence\r\nrequirements, the PHG can decrease the cost of genotyping, make GS more feasible,\r\nand facilitate larger breeding populations. Our results demonstrate that the PHG is a\r\nuseful research and breeding tool that maintains variant information from a diverse\r\ngroup of taxa, stores sequence data in a condensed but readily accessible format, unifies\r\ngenotypes across genotyping platforms, and provides a cost-effective option for\r\ngenomic selection."^^xsd:string;
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dct:date "2020-03";
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