Whole genome sequencing to identify genes and QTL in rice

Ryohei Terauchi; Akira Abe; Hiroki Takagi; Muluneh Tamiru; Rym Fekih; Satoshi Natsume; Hiroki Yaegashi; Shunichi Kosugi; Hiroyuki Kanzaki; Hideo Matsumura; Hiromasa Saitoh; Kentaro Yoshida; Liliana Cano; Sophien Kamoun

doi:10.1007/978-3-319-17157-9_3

Whole genome sequencing to identify genes and QTL in rice

Ryohei Terauchi, Akira Abe, Hiroki Takagi, Muluneh Tamiru, Rym Fekih, Satoshi Natsume, Hiroki Yaegashi, Shunichi Kosugi, Hiroyuki Kanzaki, Hideo Matsumura, Hiromasa Saitoh, Kentaro Yoshida, Liliana Cano, Sophien Kamoun

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8 Citations (Scopus)

Abstract

The recent accumulation of whole genome sequences (WGS) in a large number of plant species creates new opportunities to use this information for identifying genes/quantitative trait loci (QTL) and to accelerate crop improvement. To this end, we recently developed the MutMap method (Abe et al., Nat Biotechnol 30:174-178, 2012) and its derivatives MutMap+ (Fekih et al., PLoS One 8(7):e68529, 2013) and MutMap-Gap (Takagi et al., New Phytol 200(1):276–283, 2013a), which take full advantage of WGS to efficiently identify mutant genes from EMS mutagenized plant populations. We also reported QTL-seq (Takagi et al., Plant J 74:174-183, 2013b), a WGS-based method for identification of QTL. We applied these methods to rice for rapid identification and discovery of genes of agronomic importance. In this chapter, we introduce these WGS-based methods, MutMap family and QTL-seq, and provide an overview of the genetic analyses that we expect to accelerate crop improvement in rice and other crop species of economic importance

Original language	English
Title of host publication	Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches
Publisher	Springer
Pages	33-42
Number of pages	10
ISBN (Print)	9783319171579, 9783319171562
DOIs	https://doi.org/10.1007/978-3-319-17157-9_3
Publication status	Published - 1 Jan 2015

Keywords

Crop
Mutation
Mutmap
Ngs
Qtl
Qtl-seq
Rice
Snp-index
Wgs

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10.1007/978-3-319-17157-9_3

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Terauchi, R., Abe, A., Takagi, H., Tamiru, M., Fekih, R., Natsume, S., Yaegashi, H., Kosugi, S., Kanzaki, H., Matsumura, H., Saitoh, H., Yoshida, K., Cano, L., & Kamoun, S. (2015). Whole genome sequencing to identify genes and QTL in rice. In Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches (pp. 33-42). Springer. https://doi.org/10.1007/978-3-319-17157-9_3

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title = "Whole genome sequencing to identify genes and QTL in rice",

abstract = "The recent accumulation of whole genome sequences (WGS) in a large number of plant species creates new opportunities to use this information for identifying genes/quantitative trait loci (QTL) and to accelerate crop improvement. To this end, we recently developed the MutMap method (Abe et al., Nat Biotechnol 30:174-178, 2012) and its derivatives MutMap+ (Fekih et al., PLoS One 8(7):e68529, 2013) and MutMap-Gap (Takagi et al., New Phytol 200(1):276–283, 2013a), which take full advantage of WGS to efficiently identify mutant genes from EMS mutagenized plant populations. We also reported QTL-seq (Takagi et al., Plant J 74:174-183, 2013b), a WGS-based method for identification of QTL. We applied these methods to rice for rapid identification and discovery of genes of agronomic importance. In this chapter, we introduce these WGS-based methods, MutMap family and QTL-seq, and provide an overview of the genetic analyses that we expect to accelerate crop improvement in rice and other crop species of economic importance",

keywords = "Crop, Mutation, Mutmap, Ngs, Qtl, Qtl-seq, Rice, Snp-index, Wgs",

author = "Ryohei Terauchi and Akira Abe and Hiroki Takagi and Muluneh Tamiru and Rym Fekih and Satoshi Natsume and Hiroki Yaegashi and Shunichi Kosugi and Hiroyuki Kanzaki and Hideo Matsumura and Hiromasa Saitoh and Kentaro Yoshida and Liliana Cano and Sophien Kamoun",

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doi = "10.1007/978-3-319-17157-9_3",

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Terauchi, R, Abe, A, Takagi, H, Tamiru, M, Fekih, R, Natsume, S, Yaegashi, H, Kosugi, S, Kanzaki, H, Matsumura, H, Saitoh, H, Yoshida, K, Cano, L & Kamoun, S 2015, Whole genome sequencing to identify genes and QTL in rice. in Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches. Springer, pp. 33-42. https://doi.org/10.1007/978-3-319-17157-9_3

TY - CHAP

T1 - Whole genome sequencing to identify genes and QTL in rice

AU - Terauchi, Ryohei

AU - Abe, Akira

AU - Takagi, Hiroki

AU - Tamiru, Muluneh

AU - Fekih, Rym

AU - Natsume, Satoshi

AU - Yaegashi, Hiroki

AU - Kosugi, Shunichi

AU - Kanzaki, Hiroyuki

AU - Matsumura, Hideo

AU - Saitoh, Hiromasa

AU - Yoshida, Kentaro

AU - Cano, Liliana

AU - Kamoun, Sophien

PY - 2015/1/1

Y1 - 2015/1/1

N2 - The recent accumulation of whole genome sequences (WGS) in a large number of plant species creates new opportunities to use this information for identifying genes/quantitative trait loci (QTL) and to accelerate crop improvement. To this end, we recently developed the MutMap method (Abe et al., Nat Biotechnol 30:174-178, 2012) and its derivatives MutMap+ (Fekih et al., PLoS One 8(7):e68529, 2013) and MutMap-Gap (Takagi et al., New Phytol 200(1):276–283, 2013a), which take full advantage of WGS to efficiently identify mutant genes from EMS mutagenized plant populations. We also reported QTL-seq (Takagi et al., Plant J 74:174-183, 2013b), a WGS-based method for identification of QTL. We applied these methods to rice for rapid identification and discovery of genes of agronomic importance. In this chapter, we introduce these WGS-based methods, MutMap family and QTL-seq, and provide an overview of the genetic analyses that we expect to accelerate crop improvement in rice and other crop species of economic importance

AB - The recent accumulation of whole genome sequences (WGS) in a large number of plant species creates new opportunities to use this information for identifying genes/quantitative trait loci (QTL) and to accelerate crop improvement. To this end, we recently developed the MutMap method (Abe et al., Nat Biotechnol 30:174-178, 2012) and its derivatives MutMap+ (Fekih et al., PLoS One 8(7):e68529, 2013) and MutMap-Gap (Takagi et al., New Phytol 200(1):276–283, 2013a), which take full advantage of WGS to efficiently identify mutant genes from EMS mutagenized plant populations. We also reported QTL-seq (Takagi et al., Plant J 74:174-183, 2013b), a WGS-based method for identification of QTL. We applied these methods to rice for rapid identification and discovery of genes of agronomic importance. In this chapter, we introduce these WGS-based methods, MutMap family and QTL-seq, and provide an overview of the genetic analyses that we expect to accelerate crop improvement in rice and other crop species of economic importance

KW - Crop

KW - Mutation

KW - Mutmap

KW - Ngs

KW - Qtl

KW - Qtl-seq

KW - Rice

KW - Snp-index

KW - Wgs

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U2 - 10.1007/978-3-319-17157-9_3

DO - 10.1007/978-3-319-17157-9_3

M3 - Chapter

AN - SCOPUS:84945137226

SN - 9783319171579

SN - 9783319171562

SP - 33

EP - 42

BT - Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

PB - Springer

ER -

Whole genome sequencing to identify genes and QTL in rice

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Keywords

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Sophien Kamoun

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