Next-generation sequencing technologies and their implications for crop genetics and breeding

被引：599

作者：

Varshney, Rajeev K. ^{[1
,2
]}

Nayak, Spurthi N. ^{[1
]}

May, Gregory D. ^{[3
]}

Jackson, Scott A. ^{[4
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, CEG, Patancheru 502324, Andhra Pradesh, India

[2] CIMMYT, Genom Gene Discovery Subprogramme, GCP, Int APDO, Mexico City 06600, DF, Mexico

[3] NCGR, Santa Fe, NM 87505 USA

[4] Purdue Univ, Dept Agron, W Lafayette, IN 47907 USA

来源：

TRENDS IN BIOTECHNOLOGY | 2009年 / 27卷 / 09期

基金：

美国国家科学基金会;

关键词：

GENOME SEQUENCE; DRAFT SEQUENCE; SNP DISCOVERY; DNA; TRANSCRIPTOME; ACCURACY; QUALITY; TAGS;

D O I：

10.1016/j.tibtech.2009.05.006

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Using next-generation sequencing technologies it is possible to resequence entire plant genomes or sample entire transcriptomes more efficiently and economically and in greater depth than ever before. Rather than sequencing individual genomes, we envision the sequencing of hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identification and tracking of genetic variation are now so efficient and precise that thousands of variants can be tracked within large populations. In this review, we outline some important areas such as the large-scale development of molecular markers for linkage mapping, association mapping, wide crosses and alien introgression, epigenetic modifications, transcript profiling, population genetics and de novo genome/organellar genome assembly for which these technologies are expected to advance crop genetics and breeding, leading to crop improvement.

引用

页码：522 / 530

页数：9

共 83 条

[31] Genome-wide mapping of in vivo protein-DNA interactions [J].

Johnson, David S. ;

Mortazavi, Ali ;

Myers, Richard M. ;

Wold, Barbara .

SCIENCE, 2007, 316 (5830) :1497-1502

[32] The search for a sequencing thoroughbred [J].

Kling, J .

NATURE BIOTECHNOLOGY, 2005, 23 (11) :1333-1335

[33]

KOFIER R, 2009, BMC BIOINFORMATICS, V10, P143

[34] Archaea predominate among ammonia-oxidizing prokaryotes in soils [J].

Leininger, S. ;

Urich, T. ;

Schloter, M. ;

Schwark, L. ;

Qi, J. ;

Nicol, G. W. ;

Prosser, J. I. ;

Schuster, S. C. ;

Schleper, C. .

NATURE, 2006, 442 (7104) :806-809

[35] Mapping short DNA sequencing reads and calling variants using mapping quality scores [J].

Li, Heng ;

Ruan, Jue ;

Durbin, Richard .

GENOME RESEARCH, 2008, 18 (11) :1851-1858

[36] SOAP: short oligonucleotide alignment program [J].

Li, Ruiqiang ;

Li, Yingrui ;

Kristiansen, Karsten ;

Wang, Jun .

BIOINFORMATICS, 2008, 24 (05) :713-714

[37] ZOOM! Zillions of oligos mapped [J].

Lin, Hao ;

Zhang, Zefeng ;

Zhang, Michael Q. ;

Ma, Bin ;

Li, Ming .

BIOINFORMATICS, 2008, 24 (21) :2431-2437

[38] Highly integrated single-base resolution maps of the epigenome in Arabidopsis [J].

Lister, Ryan ;

O'Malley, Ronan C. ;

Tonti-Filippini, Julian ;

Gregory, Brian D. ;

Berry, Charles C. ;

Millar, A. Harvey ;

Ecker, Joseph R. .

CELL, 2008, 133 (03) :523-536

[39]

Madabhushi RS, 1998, ELECTROPHORESIS, V19, P224

[40] ChIP-seq: welcome to the new frontier [J].

Mardis, Elaine R. .

NATURE METHODS, 2007, 4 (08) :613-614

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