Fig. 1.

Accuracy determination of three linked SNP markers for a bacterial leaf blight resistance gene (xa5) among resequenced lines in the IRRI Irrigated breeding program. a The haplotype of the validated donor line indicates the known resistant haplotype. b IRBB 60, IRBB 61 and IRBB 64 as validated trait donors for the resistant xa5 allele. c A breeding line with a negative marker score for trait marker 1, but harboring the QTL[+] haplotype (i.e., a false negative for marker 1). d A breeding line with a positive marker score for trait marker 2, but possessing a QTL[−] haplotype (i.e., a false positive for trait marker 2). e Line exhibiting a favorable phenotypic response from another unlinked locus or phenotyping error. f Seed source variation (error) between the phenotyped source and the sequenced source showing susceptible phenotypes among the QTL[+] haplotype group