Re-Sequencing of Bi-Parental Recombinant Inbred Line Populations of Lotus japonicus Gifu x MG20 and Gifu x Lotus burtii Facilitates QTL Mapping and Genome Assembly

Recombinant inbred lines (RILs) derived from bi-parental populations are stable genetic resources, which are widely used for constructing genetic linkage maps. These genetic maps are essential for QTL mapping, and can greatly aid contig and scaffold anchoring in the final stages of genome assembly. In this study, two Lotus RIL populations, MG20 x  Gifu and Gifu x L. burtii,  were characterized by Illumina re-sequencing. Genotyping 187 MG20 x Gifu RILs at 88,874 informative marker positions and 96 Gifu x L. burtii RILs at 265,767 marker positions, allowed us to accurately identify 1,929 recombination breakpoints in the MG20 x Gifu RILs and 1,927 breakpoints in the Gifu x L. burtii population. The resulting high resolution genetic maps now facilitate high-accuracy QTL mapping and allow anchoring of a large fraction of the ~200 Mb scaffolds, which remained unanchored in the Lotus genome assembly version 3.0.