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Molecular Marker Discovery and Genetic Map Visualisation

Published on Jan 1, 2009
· DOI :10.1007/978-0-387-92738-1_8
Chris Duran15
Estimated H-index: 15
,
A. David Edwards DSc FMedSci94
Estimated H-index: 94
,
Jacqueline Batley43
Estimated H-index: 43
(University of Queensland)
Abstract
The bulk of variation at the nucleotide level is often not visible at the phenotypic level. However, this variation can be exploited using molecular genetic marker systems. Molecular genetic markers represent one of the most powerful tools for genome analysis and permit the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods and the availability of large amounts of sequence data for automated marker discovery. Two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) are the principal markers currently applied in modern genetic analysis. This are supplemented with anonymous marker systems such as Amplified Fragment Length Polymorphisms (AFLPs; Vos et al. 1995), and Diversity Array Technology (DArT; Jaccoud et al. 2001). The reducing cost of DNA sequencing has led to the availability of large sequence data sets that enable the mining of sequence based markers, such as SSRs and SNPs, which may then be applied to diversity analysis, genetic trait mapping, association studies, and marker assisted selection.
  • References (110)
  • Citations (15)
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References110
Newest
Published on Jan 1, 2009in Nucleic Acids Research 11.56
Chris Duran15
Estimated H-index: 15
(Australian Centre for Plant Functional Genomics),
Nikki Appleby5
Estimated H-index: 5
(Australian Centre for Plant Functional Genomics)
+ 4 AuthorsA. David Edwards DSc FMedSci94
Estimated H-index: 94
(Australian Centre for Plant Functional Genomics)
Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic marker as they represent the finest resolution of a DNA sequence (a single nucleotide), are generally abundant in populations and have a low mutation rate. Analysis of assembled EST sequence data provides a cost-effective means to identify large numbers of SNPs associated with functional genes. We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are ma...
64 Citations Source Cite
Published on Nov 1, 2008in Nature 41.58
David R. Bentley38
Estimated H-index: 38
,
Shankar Balasubramanian64
Estimated H-index: 64
+ 191 AuthorsHelen R. Bignell1
Estimated H-index: 1
DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of ...
2,580 Citations Source Cite
Published on May 1, 2008in Plant Molecular Biology 3.54
Gerardo Domingo Lucio Cervigni12
Estimated H-index: 12
(National Scientific and Technical Research Council),
Norma Paniego17
Estimated H-index: 17
(International Trademark Association)
+ 9 AuthorsSilvina Claudia Pessino17
Estimated H-index: 17
Eragrostis curvula (Schrad.) Nees is a forage grass native to the semiarid regions of Southern Africa, which reproduces mainly by pseudogamous diplosporous apomixis. A collection of ESTs was generated from four cDNA libraries, three of them obtained from panicles of near-isogenic lines with different ploidy levels and reproductive modes, and one obtained from 12 days-old plant leaves. A total of 12,295 high-quality ESTs were clustered and assembled, rendering 8,864 unigenes, including 1,490 cont...
27 Citations Source Cite
Published on Apr 17, 2008in Nature 41.58
D Altshuler177
Estimated H-index: 177
(Human Genome Sequencing Center),
Maithreyan Srinivasan5
Estimated H-index: 5
(Hoffmann-La Roche)
+ 24 AuthorsG. Thomas Roth1
Estimated H-index: 1
(Hoffmann-La Roche)
The DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels is reported.
1,470 Citations Source Cite
Published on Jan 1, 2008in Molecular Genetics and Genomics 2.73
Danilo Pumpernik5
Estimated H-index: 5
,
Borut Oblak1
Estimated H-index: 1
,
Branko Borštnik4
Estimated H-index: 4
Short tandem repeats (STRs) are subjected to two kinds of mutational modifications: point mutations and replication slippages. The latter is found to be the more frequent cause of STR modifications, but a satisfactory quantitative measure of the ratio of the two processes has yet to be determined. The comparison of entire genome sequences of closely enough related species enables one to obtain sufficient statistics by counting the differences in the STR regions. We analyzed human–chimpanzee DNA ...
31 Citations Source Cite
Published on Dec 23, 2007in Nucleic Acids Research 11.56
James C. Sullivan15
Estimated H-index: 15
(Boston University),
Adam M. Reitzel21
Estimated H-index: 21
(Boston University),
John R. Finnerty32
Estimated H-index: 32
(Boston University)
The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and...
19 Citations Source Cite
Published on Dec 23, 2007in Nucleic Acids Research 11.56
Jon Duvick2
Estimated H-index: 2
(University of South Dakota),
Ann Fu1
Estimated H-index: 1
(University of South Dakota)
+ 5 AuthorsVolker Brendel44
Estimated H-index: 44
(University of South Dakota)
PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and anno...
190 Citations Source Cite
Published on Dec 23, 2007in Nucleic Acids Research 11.56
Sook Jung22
Estimated H-index: 22
(Washington State University),
Margaret Staton12
Estimated H-index: 12
(Washington State University)
+ 4 AuthorsDoreen Main33
Estimated H-index: 33
(Washington State University)
The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the ent...
162 Citations Source Cite
Published on Nov 29, 2007in Brain 10.85
Ines Dierick13
Estimated H-index: 13
,
Jonathan Baets25
Estimated H-index: 25
+ 20 AuthorsWim Robberecht61
Estimated H-index: 61
Distal hereditary motor neuropathy (HMN) is a clinically and genetically heterogeneous group of disorders affecting spinal alpha-motor neurons. Since 2001, mutations in six different genes have been identified for autosomal dominant distal HMN; glycyl-tRNA synthetase (GARS), dynactin 1 (DCTN1), small heat shock 27 kDa protein 1 (HSPB1), small heat shock 22 kDa protein 8 (HSPB8), Berardinelli-Seip congenital lipodystrophy (BSCL2) and senataxin (SETX). In addition a mutation in the (VAMP)-associat...
83 Citations Source Cite
Published on Nov 1, 2007in Molecular Ecology Notes
Loretta M. Winton4
Estimated H-index: 4
(University of Alaska Fairbanks),
A. L. Krohn2
Estimated H-index: 2
(University of Alaska Fairbanks),
Roseann Hartke Leiner5
Estimated H-index: 5
(University of Alaska Fairbanks)
Eight polymorphic microsatellite loci were isolated from the ascomycete fungus Sclerotinia subarctica nom. prov. In Alaska, this pathogen causes white mold vegetable diseases sympatrically with the cosmopolitan and closely related Sclerotinia sclerotiorum. Eighteen alleles were observed across the 41 isolates tested and ranged from two to three alleles per locus. Together, the alleles from the eight polymorphic loci yielded only four haploid multilocus genotypes and exhibited significant linkage...
16 Citations Source Cite
Cited By15
Newest
Published on Jan 1, 2017
Zohra Aslam1
Estimated H-index: 1
(International Islamic University, Islamabad),
Jabar Zaman Khan Khattak5
Estimated H-index: 5
(International Islamic University, Islamabad)
+ 1 AuthorsMuhammad Asif3
Estimated H-index: 3
(Kansas State University)
Bioinformatics is an interdisciplinary science emerging from interaction of computer, statistics, biology and mathematics to analyze genome arrangement and contents, biological sequence data, predict the structure and function of macromolecules that use in interpreting and decoding plant genome. The broad amounts of data produced in life sciences resulted to the evolution and development of bioinformatics. Omics, bioinformatics and computational tools are very essential to understand genomics an...
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Published on Jan 1, 2015in Methods of Molecular Biology
A. C. Hayward33
Estimated H-index: 33
(University of Queensland),
Reece Tollenaere6
Estimated H-index: 6
(University of Queensland)
+ 1 AuthorsJacqueline Batley43
Estimated H-index: 43
(University of Queensland)
Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review th...
14 Citations Source Cite
Published on Jan 1, 2015in Methods of Molecular Biology
Kaitao Lai13
Estimated H-index: 13
(University of Queensland),
Michal T. Lorenc15
Estimated H-index: 15
(University of Queensland),
A. David Edwards DSc FMedSci94
Estimated H-index: 94
(University of Queensland)
The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range fr...
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Published on Jan 1, 2015in Methods of Molecular Biology
Agnieszka A. Golicz11
Estimated H-index: 11
(University of Queensland),
Philipp E. Bayer13
Estimated H-index: 13
(University of Queensland),
A. David Edwards DSc FMedSci94
Estimated H-index: 94
(University of Queensland)
Genotyping by sequencing (GBS) is a relatively new method used to determine the differences in the genetic makeup of individuals. Its novelty stems from a combination of two already available methods: genotyping and next-generation sequencing. Depending on the individual study design GBS protocols can take multiple forms, however most share a sequence of core steps that have to be undertaken. These include: sequencing of the DNA from the individuals of interest (usually two parents of a mapping ...
8 Citations Source Cite
Published on Jan 1, 2015in Methods of Molecular Biology
Pradeep Ruperao10
Estimated H-index: 10
(University of Queensland),
A. David Edwards DSc FMedSci94
Estimated H-index: 94
(University of Queensland)
With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization o...
6 Citations Source Cite
Published on Nov 25, 2013in Biology
Paul Visendi9
Estimated H-index: 9
,
Jacqueline Batley43
Estimated H-index: 43
,
A. David Edwards DSc FMedSci94
Estimated H-index: 94
Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on f...
7 Citations Source Cite
Published on Sep 1, 2013in Science & Engineering Faculty
Agnieszka A. Golicz11
Estimated H-index: 11
(University of Queensland),
Philipp E. Bayer13
Estimated H-index: 13
(University of Queensland)
+ 9 AuthorsA. David Edwards DSc FMedSci94
Estimated H-index: 94
(University of Queensland)
The genome sequence of an organism provides the basis for gene discovery, the analysis of genetic variation and the association of genomic variation with heritable traits. Genome sequence variation can vary from single nucleotide polymorphisms, insertions/deletions to presence/absence of large regions or rearrangements. Second generation sequencing technologies and applied bioinformatics tools can provide an unprecedented insight into genome structure and variation, with applications for underst...
1 Citations Source Cite
Published on Aug 27, 2012in Biology
Michal T. Lorenc15
Estimated H-index: 15
(University of Queensland),
Satomi Hayashi13
Estimated H-index: 13
+ 8 AuthorsJacqueline Batley43
Estimated H-index: 43
(Commonwealth Scientific and Industrial Research Organisation)
Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation ...
42 Citations Source Cite
Published on Aug 1, 2012in Plant Biotechnology Journal 6.30
A. David Edwards DSc FMedSci94
Estimated H-index: 94
(Australian Centre for Plant Functional Genomics),
Stephen Wilcox10
Estimated H-index: 10
(Walter and Eliza Hall Institute of Medical Research)
+ 15 AuthorsM. Bellgard31
Estimated H-index: 31
(Murdoch University)
The large and complex genome of wheat makes genetic and genomic analysis in this important species both expensive and resource intensive. The application of next-generation sequencing technologies is particularly resource intensive, with at least 17Gbp of sequence data required to obtain minimal (1×) coverage of the genome. A similar volume of data would represent almost 40× coverage of the rice genome. Progress can be made through the establishment of consortia to produce shared genomic resourc...
29 Citations Source Cite