TY - JOUR
T1 - High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines
AU - Shah, Niraj
AU - Hirakawa, Hideki
AU - Kusakabe, Shohei
AU - Sandal, Niels
AU - Stougaard, Jens
AU - Schierup, Mikkel Heide
AU - Sato, Shusei
AU - Andersen, Stig Uggerhøj
N1 - Funding Information:
This work was supported by the Genome Information Upgrading Program of the National BioResource Project in 2014 (SS), the Danish National Research Foundation grant no. DNRF79 (JS), the ERC Advanced Grant 268523 (JS), grant no. 10-081677 from The Danish Council for Independent ResearchjTechnology and Production Sciences (SUA).
Publisher Copyright:
© The Author 2016.
PY - 2016/10
Y1 - 2016/10
N2 - 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.
AB - 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.
KW - Assembly errors
KW - Chromosomal translocations
KW - Genetic map
KW - QTL mapping
KW - Recombinant inbred lines
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U2 - 10.1093/dnares/dsw033
DO - 10.1093/dnares/dsw033
M3 - Article
AN - SCOPUS:84991794939
SN - 1340-2838
VL - 23
SP - 487
EP - 494
JO - DNA Research
JF - DNA Research
IS - 5
ER -