High-resolution association mapping with libraries of immortalized lines from ancestral landraces

KEY MESSAGE: Association mapping with immortalized lines of landraces offers several advantages including a high mapping resolution, as demonstrated here in maize by identifying the causal variants underlying QTL for oil content and the metabolite allantoin. ABSTRACT: Landraces are traditional varieties of crops that present a valuable yet largely untapped reservoir of genetic variation to meet future challenges of agriculture. Here, we performed association mapping in a panel comprising 358 immortalized maize lines from six European Flint landraces. Linkage disequilibrium decayed much faster in the landraces than in the elite lines included for comparison, permitting a high mapping resolution. We demonstrate this by fine-mapping a quantitative trait locus (QTL) for oil content down to the phenylalanine insertion F469 in DGAT1-2 as the causal variant. For the metabolite allantoin, related to abiotic stress response, we identified promoter polymorphisms and differential expression of an allantoinase as putative cause of variation. Our results demonstrate the power of this approach to dissect QTL potentially down to the causal variants, toward the utilization of natural or engineered alleles in breeding. Moreover, we provide guidelines for studies using ancestral landraces for crop genetic research and breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-021-03963-3.