Journal ArticleDOI
Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation
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TLDR
A review of automated methods for the discovery of Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) can be found in this paper.Abstract:
Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in modern genetic analysis. The reducing cost of DNA sequencing has led to the availability of large sequence data sets derived from whole genome sequencing and large scale Expressed Sequence Tag (EST) discovery that enable the mining of SSRs and SNPs, which may then be applied to diversity analysis, genetic trait mapping, association studies, and marker assisted selection. These markers are inexpensive, require minimal labour to produce and can frequently be associated with annotated genes. Here we review automated methods for the discovery of SSRs and SNPs and provide an overview of the diverse applications of these markers.read more
Citations
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Journal ArticleDOI
Plant genome sequencing: applications for crop improvement
David Edwards,Jacqueline Batley +1 more
TL;DR: The increasing availability of DNA sequence information enables the discovery of genes and molecular markers associated with diverse agronomic traits creating new opportunities for crop improvement, however, the challenge remains to convert this mass of data into knowledge that can be applied in crop breeding programs.
Journal ArticleDOI
Accessing complex crop genomes with next-generation sequencing
TL;DR: This review describes next-generation sequencing and data analysis techniques that vastly improve the ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders.
Journal ArticleDOI
Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs
Vengaldas Rajaram,Vengaldas Rajaram,T. Nepolean,T. Nepolean,S. Senthilvel,Rajeev K. Varshney,Vincent Vadez,Rakesh K. Srivastava,Trushar Shah,Ambawat Supriya,Ambawat Supriya,Sushil Kumar,Sushil Kumar,Basava Ramana Kumari,Amindala BhanuPrakash,Mangamoori Lakshmi Narasu,Oscar Riera-Lizarazu,Oscar Riera-Lizarazu,Charles Thomas Hash +18 more
TL;DR: The consensus map developed in the present study contains the largest set of mapped SSRs reported to date for pearl millet, and represents a major consolidation of existing pearl millet genetic mapping information.
Journal ArticleDOI
Single nucleotide polymorphism discovery from wheat next‐generation sequence data
Kaitao Lai,Chris Duran,Paul J. Berkman,Paul J. Berkman,Michal T. Lorenc,Michal T. Lorenc,Jiri Stiller,Sahana Manoli,Matthew J. Hayden,Kerrie Forrest,Delphine Fleury,Ute Baumann,Manuel Zander,Manuel Zander,Annaliese S. Mason,Jacqueline Batley,David Edwards,David Edwards +17 more
TL;DR: In this article, a modified autoSNPdb method was used to identify SNPs in wheat transcriptome sequence data using 454 sequencing technology and applied this for SNP discovery using a modified autoencoder.
Journal ArticleDOI
Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection
TL;DR: Assessment of informativeness and efficiency of three different molecular markers for genetic diversity among 24 Citrus and its relative species provide basis for future efficient use of these molecular markers in the genetic analysis of Citrus.
References
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Journal ArticleDOI
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David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Tandem repeats finder: a program to analyze DNA sequences
TL;DR: A new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size is presented and its ability to detect tandem repeats that have undergone extensive mutational change is demonstrated.
Journal ArticleDOI
The International HapMap Project
John W. Belmont,Paul Hardenbol,Thomas D. Willis,Fuli Yu,Huanming Yang,Lan Yang Ch'Ang,Wei Huang,Bin Liu,Yan Shen,Paul K.H. Tam,Lap-Chee Tsui,Mary M.Y. Waye,Jeffrey Tze Fei Wong,Changqing Zeng,Qingrun Zhang,Mark S. Chee,Luana Galver,Semyon Kruglyak,Sarah S. Murray,Arnold Oliphant,Alexandre Montpetit,Fanny Chagnon,Vincent Ferretti,Martin Leboeuf,Michael S. Phillips,Andrei Verner,Shenghui Duan,Denise L. Lind,Raymond D. Miller,John P. Rice,Nancy L. Saccone,Patricia Taillon-Miller,Ming Xiao,Akihiro Sekine,Koki Sorimachi,Yoichi Tanaka,Tatsuhiko Tsunoda,Eiji Yoshino,David R. Bentley,Sarah E. Hunt,Don Powell,Houcan Zhang,Ichiro Matsuda,Yoshimitsu Fukushima,Darryl Macer,Eiko Suda,Charles N. Rotimi,Clement Adebamowo,Toyin Aniagwu,Patricia A. Marshall,Olayemi Matthew,Chibuzor Nkwodimmah,Charmaine D.M. Royal,Mark Leppert,Missy Dixon,Fiona Cunningham,Ardavan Kanani,Gudmundur A. Thorisson,Peter E. Chen,David J. Cutler,Carl S. Kashuk,Peter Donnelly,Jonathan Marchini,Gilean McVean,Simon Myers,Lon R. Cardon,Andrew P. Morris,Bruce S. Weir,James C. Mullikin,Michael Feolo,Mark J. Daly,Renzong Qiu,Alastair Kent,Georgia M. Dunston,Kazuto Kato,Norio Niikawa,Jessica Watkin,Richard A. Gibbs,Erica Sodergren,George M. Weinstock,Richard K. Wilson,Lucinda Fulton,Jane Rogers,Bruce W. Birren,Hua Han,Hongguang Wang,Martin Godbout,John C. Wallenburg,Paul L'Archevêque,Guy Bellemare,Kazuo Todani,Takashi Fujita,Satoshi Tanaka,Arthur L. Holden,Francis S. Collins,Lisa D. Brooks,Jean E. McEwen,Mark S. Guyer,Elke Jordan,Jane Peterson,Jack Spiegel,Lawrence M. Sung,Lynn F. Zacharia,Karen Kennedy,Michael Dunn,Richard Seabrook,Mark Shillito,Barbara Skene,John Stewart,David Valle,Ellen Wright Clayton,Lynn B. Jorde,Aravinda Chakravarti,Mildred K. Cho,Troy Duster,Troy Duster,Morris W. Foster,Maria Jasperse,Bartha Maria Knoppers,Pui-Yan Kwok,Julio Licinio,Jeffrey C. Long,Pilar N. Ossorio,Vivian Ota Wang,Charles N. Rotimi,Patricia Spallone,Patricia Spallone,Sharon F. Terry,Eric S. Lander,Eric H. Lai,Deborah A. Nickerson,Gonçalo R. Abecasis,David Altshuler,Michael Boehnke,Panos Deloukas,Julie A. Douglas,Stacey Gabriel,Richard R. Hudson,Thomas J. Hudson,Leonid Kruglyak,Yusuke Nakamura,Robert L. Nussbaum,Stephen F. Schaffner,Stephen T. Sherry,Lincoln Stein,Toshihiro Tanaka +145 more
TL;DR: The HapMap will allow the discovery of sequence variants that affect common disease, will facilitate development of diagnostic tools, and will enhance the ability to choose targets for therapeutic intervention.