Trends Biotechnol. 2009 Sep;27(9):522-30. Epub 2009 Aug 11.

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

Varshney RK, Nayak SN, May GD, Jackson SA.

Source

Centre of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, A.P., India. r.k.varshney@cgiar.org

Abstract

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.

PMID:: 19679362; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms

Publication Types

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Related citations

Review Plant genome sequencing: applications for crop improvement. [Plant Biotechnol J. 2010]
Review Plant genome sequencing: applications for crop improvement.
Edwards D, Batley J. Plant Biotechnol J. 2010 Jan; 8(1):2-9. Epub 2009 Nov 9.
Review Sequencing crop genomes: approaches and applications. [New Phytol. 2011]
Review Sequencing crop genomes: approaches and applications.
Jackson SA, Iwata A, Lee SH, Schmutz J, Shoemaker R. New Phytol. 2011 Sep; 191(4):915-25. Epub 2011 Jun 27.
Review SNP identification in crop plants. [Curr Opin Plant Biol. 2009]
Review SNP identification in crop plants.
Ganal MW, Altmann T, Röder MS. Curr Opin Plant Biol. 2009 Apr; 12(2):211-7. Epub 2009 Jan 29.
Review Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. [Molecules. 2009]
Review Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops.
Park YJ, Lee JK, Kim NS. Molecules. 2009 Nov 10; 14(11):4546-69. Epub 2009 Nov 10.
Review Wheat functional genomics and engineering crop improvement. [Genome Biol. 2002]
Review Wheat functional genomics and engineering crop improvement.
Francki M, Appels R. Genome Biol. 2002; 3(5):reviews1013. Epub 2002 Apr 23.

See reviews... See all...

Cited by 16 PubMed Central articles

Pyrosequencing as a tool for better understanding of human microbiomes. [J Oral Microbiol. 2012]
Pyrosequencing as a tool for better understanding of human microbiomes.
Siqueira JF Jr, Fouad AF, Rôças IN. J Oral Microbiol. 2012; 4. Epub 2012 Jan 23.
Advances in omics and bioinformatics tools for systems analyses of plant functions. [Plant Cell Physiol. 2011]
Advances in omics and bioinformatics tools for systems analyses of plant functions.
Mochida K, Shinozaki K. Plant Cell Physiol. 2011 Dec; 52(12):2017-38.
Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum). [BMC Plant Biol. 2011]
Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum).
Russell JR, Bayer M, Booth C, Cardle L, Hackett CA, Hedley PE, Jorgensen L, Morris JA, Brennan RM. BMC Plant Biol. 2011 Oct 28; 11:147. Epub 2011 Oct 28.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Next-generation sequencing technologies and their implications for crop genetics...
Next-generation sequencing technologies and their implications for crop genetics and breeding.
Trends Biotechnol. 2009 Sep ;27(9):522-30. Epub 2009 Aug 11 .

PubMed
Reaching the depth of the Chinese hamster ovary cell transcriptome.
Reaching the depth of the Chinese hamster ovary cell transcriptome.
Biotechnol Bioeng. 2010 Apr 1 ;105(5):1002-9.

PubMed
Complete transcriptome of the soybean root hair cell, a single-cell model, and i...
Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection.
Plant Physiol. 2010 Feb ;152(2):541-52. Epub 2009 Nov 20 .

PubMed
Mammalian cell cytotoxicity and genotoxicity analysis of drinking water disinfec...
Mammalian cell cytotoxicity and genotoxicity analysis of drinking water disinfection by-products.
Environ Mol Mutagen. 2002 ;40(2):134-42.

PubMed
Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RN...
Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems.
PLoS Pathog. 2010 Feb 12 ;6(2):e1000764.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: