Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery

被引：86

作者：

Deschamps, Stephane ^{[1
]}

Campbell, Matthew A. ^{[2
]}

机构：

[1] DuPont Crop Genet, Expt Stn, Wilmington, DE 19880 USA

[2] Pioneer HiBred Int Inc, Johnston, IA 50131 USA

来源：

MOLECULAR BREEDING | 2010年 / 25卷 / 04期

关键词：

Plant genomics; SNP discovery; Genome; Transcriptome; Resequencing; Next generation sequencing; SHORT DNA-SEQUENCES; POLYMORPHISM SNP DISCOVERY; WHOLE-GENOME; LARGE-SCALE; DIFFERENTIAL METHYLATION; DRAFT SEQUENCE; BASE CALLER; SINGLE; IDENTIFICATION; ALIGNMENT;

D O I：

10.1007/s11032-009-9357-9

中图分类号：

S3 [农学（农艺学）];

学科分类号：

0901 ;

摘要：

Genome-wide variant detection within a species is the primary initial step towards linking genotypic variation and phenotypes. The conversion of these genetic variants (the most prevalent of these being single-nucleotide polymorphisms or SNPs) into genetic markers is particularly important in agronomically valuable crop species to allow for cost-effective marker-assisted selection strategies, whole-genome fingerprinting, association studies, map-based gene cloning and population-based analyses. Towards these goals, an increasing number of large-scale genetic variant discovery initiatives are being undertaken in conjunction with next-generation sequencing platforms, allowing for drastically quicker and cheaper variant discovery, and leading towards a far more comprehensive view of the genome or transcriptome. This review will summarize the current status of these initiatives and will discuss the expanding role of next-generation sequencing technologies in facilitating crop improvement.

引用

页码：553 / 570

页数：18

共 130 条

[61] HIGH-SPEED DNA SEQUENCING BY CAPILLARY ELECTROPHORESIS [J].

LUCKEY, JA ;

DROSSMAN, H ;

KOSTICHKA, AJ ;

MEAD, DA ;

DCUNHA, J ;

NORRIS, TB ;

SMITH, LM .

NUCLEIC ACIDS RESEARCH, 1990, 18 (15) :4417-4421

[62] Enhanced translocation of single DNA molecules through α-hemolysin nanopores by manipulation of internal charge [J].

Maglia, Giovanni ;

Restrepo, Marcela Rincon ;

Mikhailova, Ellina ;

Bayley, Hagan .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (50) :19720-19725

[63] Genome sequencing in microfabricated high-density picolitre reactors [J].

Margulies, M ;

Egholm, M ;

Altman, WE ;

Attiya, S ;

Bader, JS ;

Bemben, LA ;

Berka, J ;

Braverman, MS ;

Chen, YJ ;

Chen, ZT ;

Dewell, SB ;

Du, L ;

Fierro, JM ;

Gomes, XV ;

Godwin, BC ;

He, W ;

Helgesen, S ;

Ho, CH ;

Irzyk, GP ;

Jando, SC ;

Alenquer, MLI ;

Jarvie, TP ;

Jirage, KB ;

Kim, JB ;

Knight, JR ;

Lanza, JR ;

Leamon, JH ;

Lefkowitz, SM ;

Lei, M ;

Li, J ;

Lohman, KL ;

Lu, H ;

Makhijani, VB ;

McDade, KE ;

McKenna, MP ;

Myers, EW ;

Nickerson, E ;

Nobile, JR ;

Plant, R ;

Puc, BP ;

Ronan, MT ;

Roth, GT ;

Sarkis, GJ ;

Simons, JF ;

Simpson, JW ;

Srinivasan, M ;

Tartaro, KR ;

Tomasz, A ;

Vogt, KA ;

Volkmer, GA .

NATURE, 2005, 437 (7057) :376-380

[64] A general approach to single-nucleotide polymorphism discovery [J].

Marth, GT ;

Korf, I ;

Yandell, MD ;

Yeh, RT ;

Gu, ZJ ;

Zakeri, H ;

Stitziel, NO ;

Hillier, L ;

Kwok, PY ;

Gish, WR .

NATURE GENETICS, 1999, 23 (04) :452-456

[65] Transposons, DNA methylation and gene control [J].

Martienssen, R .

TRENDS IN GENETICS, 1998, 14 (07) :263-264

[66] The map-based sequence of the rice genome [J].

Matsumoto, T ;

Wu, JZ ;

Kanamori, H ;

Katayose, Y ;

Fujisawa, M ;

Namiki, N ;

Mizuno, H ;

Yamamoto, K ;

Antonio, BA ;

Baba, T ;

Sakata, K ;

Nagamura, Y ;

Aoki, H ;

Arikawa, K ;

Arita, K ;

Bito, T ;

Chiden, Y ;

Fujitsuka, N ;

Fukunaka, R ;

Hamada, M ;

Harada, C ;

Hayashi, A ;

Hijishita, S ;

Honda, M ;

Hosokawa, S ;

Ichikawa, Y ;

Idonuma, A ;

Iijima, M ;

Ikeda, M ;

Ikeno, M ;

Ito, K ;

Ito, S ;

Ito, T ;

Ito, Y ;

Iwabuchi, A ;

Kamiya, K ;

Karasawa, W ;

Kurita, K ;

Katagiri, S ;

Kikuta, A ;

Kobayashi, H ;

Kobayashi, N ;

Machita, K ;

Maehara, T ;

Masukawa, M ;

Mizubayashi, T ;

Mukai, Y ;

Nagasaki, H ;

Nagata, Y .

NATURE, 2005, 436 (7052) :793-800

[67] SNP Discovery via Genomic Reduction, Barcoding, and 454-Pyrosequencing in Amaranth [J].

Maughan, Peter J. ;

Yourstone, Scott M. ;

Jellen, Eric N. ;

Udall, Joshua A. .

PLANT GENOME, 2009, 2 (03) :260-270

[68] Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding [J].

McKernan, Kevin Judd ;

Peckham, Heather E. ;

Costa, Gina L. ;

McLaughlin, Stephen F. ;

Fu, Yutao ;

Tsung, Eric F. ;

Clouser, Christopher R. ;

Duncan, Cisyla ;

Ichikawa, Jeffrey K. ;

Lee, Clarence C. ;

Zhang, Zheng ;

Ranade, Swati S. ;

Dimalanta, Eileen T. ;

Hyland, Fiona C. ;

Sokolsky, Tanya D. ;

Zhang, Lei ;

Sheridan, Andrew ;

Fu, Haoning ;

Hendrickson, Cynthia L. ;

Li, Bin ;

Kotler, Lev ;

Stuart, Jeremy R. ;

Malek, Joel A. ;

Manning, Jonathan M. ;

Antipova, Alena A. ;

Perez, Damon S. ;

Moore, Michael P. ;

Hayashibara, Kathleen C. ;

Lyons, Michael R. ;

Beaudoin, Robert E. ;

Coleman, Brittany E. ;

Laptewicz, Michael W. ;

Sannicandro, Adam E. ;

Rhodes, Michael D. ;

Gottimukkala, Rajesh K. ;

Yang, Shan ;

Bafna, Vineet ;

Bashir, Ali ;

MacBride, Andrew ;

Alkan, Can ;

Kidd, Jeffrey M. ;

Eichler, Evan E. ;

Reese, Martin G. ;

De la Vega, Francisco M. ;

Blanchard, Alan P. .

GENOME RESEARCH, 2009, 19 (09) :1527-1541

[69] Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome [J].

Meyers, BC ;

Tingley, SV ;

Morgante, M .

GENOME RESEARCH, 2001, 11 (10) :1660-1676

[70] Mapping and quantifying mammalian transcriptomes by RNA-Seq [J].

Mortazavi, Ali ;

Williams, Brian A. ;

McCue, Kenneth ;

Schaeffer, Lorian ;

Wold, Barbara .

NATURE METHODS, 2008, 5 (07) :621-628

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