Fig. 1: Construction and validation of the pan-tandem repeat loci dataset. | Nature Communications

Fig. 1: Construction and validation of the pan-tandem repeat loci dataset.

From: The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice

Fig. 1

a Schematic of the pan-TR polymorphism dataset. In a previous study, we assembled the genomes of 230 rice accessions with broad genetic diversity (including 202 O.sativa accessions and 28 O.rufipogon accessions) to construct a pan-genome graph34. In the present study, we conducted de novo whole-genome tandem repeat annotation for each accession and the Nipponbare genome. After integrating the TR annotations into the pan-genome graph to get TR variation loci, we obtained the pan-TR polymorphism dataset, which included TR loci absent from the reference genome. Known TR variations that are causal for rice phenotypes were validated in the pan-TR dataset. Alleles for TRs around OsSPL13 (b, c) and COLD11 (d, e) and their distribution among rice subpopulations.

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