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

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

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

5 Citations (Scopus)

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.

Original language	English
Journal	D N A Research
Volume	23
Issue	5
Pages (from-to)	487-495
Number of pages	9
ISSN	1340-2838
DOIs	https://doi.org/10.1093/dnares/dsw033
Publication status	Published - Oct 2016

Keywords

Assembly errors
Chromosomal translocations
Genetic map
QTL mapping
Recombinant inbred lines

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10.1093/dnares/dsw033

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

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 = "Assembly errors, Chromosomal translocations, Genetic map, QTL mapping, Recombinant inbred lines",

author = "Niraj Shah and Hideki Hirakawa and Shohei Kusakabe and Niels Sandal and Jens Stougaard and Schierup, {Mikkel Heide} and Shusei Sato and Andersen, {Stig Uggerh{\o}j}",

note = "{\textcopyright} The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.",

year = "2016",

month = oct,

doi = "10.1093/dnares/dsw033",

language = "English",

volume = "23",

pages = "487--495",

journal = "D N A Research",

issn = "1340-2838",

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High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. / Shah, Niraj; Hirakawa, Hideki; Kusakabe, Shohei et al.
In: D N A Research, Vol. 23, No. 5, 10.2016, p. 487-495.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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 - © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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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DO - 10.1093/dnares/dsw033

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SN - 1340-2838

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

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Keywords

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