High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines

Niraj Shah; Hideki Hirakawa; Shohei Kusakabe; Niels Sandal; Jens Stougaard; Mikkel Heide Schierup; Shusei Sato; Stig Uggerhøj Andersen

doi:10.1093/dnares/dsw033

High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines

DNA Res. 2016 Oct 1;23(5):487-494. doi: 10.1093/dnares/dsw033.

Authors

Niraj Shah¹, Hideki Hirakawa², Shohei Kusakabe³, Niels Sandal¹, Jens Stougaard¹, Mikkel Heide Schierup⁴, Shusei Sato^{2

3}, Stig Uggerhøj Andersen¹

Affiliations

¹ Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark.
² Kazusa DNA Research Institute, Chiba 292-0818, Japan.
³ Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan.
⁴ Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C, Denmark.

Abstract

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 aid contig and scaffold anchoring in the final stages of genome assembly. In this study, two Lotus sp. RIL populations, Lotus japonicus MG-20 × Gifu and Gifu × L. burttii, were characterized by Illumina re-sequencing. Genotyping of 187 MG-20 × Gifu RILs at 87,140 marker positions and 96 Gifu × L. burttii RILs at 357,973 marker positions allowed us to accurately identify 1,929 recombination breakpoints in the MG-20 × Gifu RILs and 1,044 breakpoints in the Gifu × L. burttii population. The resulting high-density genetic maps now facilitate high-accuracy QTL mapping, identification of reference genome mis-assemblies, and characterization of structural variants.

Keywords: QTL mapping; assembly errors; chromosomal translocations; genetic map; recombinant inbred lines.