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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 Duran14
Estimated H-index: 14
,
David Edwards59
Estimated H-index: 59
,
Jacqueline Batley41
Estimated H-index: 41
(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 (109)
  • Cited By (15)
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References109
Published on Mar 1, 2005in Journal of Plant Biotechnology
Jennifer C Mortimer1
Estimated H-index: 1
,
Jacqueline Batley41
Estimated H-index: 41
+ 2 AuthorsDavid Edwards59
Estimated H-index: 59
We have mined each of the five A. thaliana chromosomes for the presence of simple sequence repeats (SSRs) and developed custom perl scripts to examine their distribution and abundance in relation to genomic position, local G/C content and location within and around transcribed sequences. The distribution of repeats and G/C content with respect to genomic regions (exons, UTRs, introns, intergenic regions and proximity to expressed genes) are shown. SSRs show a non-random distribution across the g...
14 Citations
Published on Jan 1, 1990
J.-L. Weber1
Estimated H-index: 1
208 Citations
Published on Sep 1, 2007in Chinese Medical Journal 1.60
Weilin Wang21
Estimated H-index: 21
(Zhejiang University),
Zhang Gl1
Estimated H-index: 1
+ 7 AuthorsZheng Ss1
Estimated H-index: 1
Background Although the use of hepatitis B immunoglobulin (HBIG) may lead to a significant reduction in recurrent hepatitis B virus (HBV) infection and improve the survival of patients who have undergone liver transplantation (LT) for hepatitis B-related diseases, the recurrence of the disease still remains at a lower level. Different clinical curative effects were observed in patients with the same HBV-related diseases and the same therapy. This study was undertaken to investigate whether the e...
5 Citations Source Cite
Published on Feb 25, 2001
Pushpendra Kumar Gupta31
Estimated H-index: 31
,
Joy Roy5
Estimated H-index: 5
,
Manoj Prasad58
Estimated H-index: 58
Molecular markers are useful for a variety of purposes relevant to crop improvement. The most important of these uses is the indirect marker­ assisted selection (MAS) exercised during plant breeding. For this purpose, molecular markers need to be amenable to automation and high throughput approaches. However, the gel-based assays that are needed for most molecular markers are time con­ suming and expensive, limiting their utility. The new generation molecular markers, called single nucleo­ tide ...
242 Citations
Published on Dec 1, 2006in BMC Bioinformatics 2.21
Arun M Jesubatham1
Estimated H-index: 1
(Texas Tech University),
Mark D. Burow26
Estimated H-index: 26
(Texas Tech University)
Background Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics. However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut.
9 Citations Source Cite
Published on Dec 1, 1999in Nature Genetics 27.13
Gabor T. Marth35
Estimated H-index: 35
(Washington University in St. Louis),
Ian Korf38
Estimated H-index: 38
(Washington University in St. Louis)
+ 7 AuthorsWarren Gish8
Estimated H-index: 8
(Washington University in St. Louis)
Single-nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and a resource for mapping complex genetic traits 1 . The large volume of data produced by high-throughput sequencing projects is a rich and largely untapped source of SNPs (refs 2‐5). We present here a unified approach to the discovery of variations in genetic sequence data of arbitrary DNA sources. We propose to use the rapidly emerging genomic sequence6,7 as a template on which to layer often unmapped...
444 Citations Source Cite
Published on Feb 1, 2003in Theoretical and Applied Genetics 3.93
Thomas Thiel15
Estimated H-index: 15
,
Wolfgang Michalek7
Estimated H-index: 7
+ 1 AuthorsAndreas Graner54
Estimated H-index: 54
A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived...
1,275 Citations Source Cite
Published on May 1, 1996in BioTechniques 2.10
Keith J. Edwards54
Estimated H-index: 54
(University of Bristol),
J. H. A. Barker8
Estimated H-index: 8
(University of Bristol)
+ 2 AuthorsA. Karp42
Estimated H-index: 42
(University of Bristol)
493 Citations Source Cite
Published on Aug 1, 2001in Genome Biology 13.21
Natalia Volfovsky15
Estimated H-index: 15
,
Brian J. Haas64
Estimated H-index: 64
,
Steven L. Salzberg118
Estimated H-index: 118
Background A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.
118 Citations Source Cite
Published on Jan 1, 2007
Nnadozie Oraguzie13
Estimated H-index: 13
,
Erik H. A. Rikkerink25
Estimated H-index: 25
+ 1 AuthorsH. N. de Silva1
Estimated H-index: 1
An Overview of Association Mapping.- Linkage Disequilibrium.- What Are SNPs?.- Single Nucleotide Polymorphism Discovery.- Single Nucleotide Polymorphism Genotyping in Plants.- SNP Applications in Plants.- Linkage Disequilibrium Mapping Concepts.- Statistical Analysis and Experimental Design.- Linkage Disequilibrium-Based Association Mapping in Forage Species.- Gene-Assisted Selection Applications of Association Genetics for Forest Tree Breeding.- Prospects of Association Mapping in Perennial Hor...
125 Citations Source Cite
Cited By15
Published on Sep 1, 2013in Science & Engineering Faculty
Agnieszka A. Golicz10
Estimated H-index: 10
(University of Queensland),
Philipp E. Bayer13
Estimated H-index: 13
(University of Queensland)
+ 9 AuthorsDavid Edwards59
Estimated H-index: 59
(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 Jan 1, 2015in Methods of Molecular Biology
Pradeep Ruperao10
Estimated H-index: 10
(University of Queensland),
David Edwards59
Estimated H-index: 59
(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...
5 Citations Source Cite
Published on Nov 1, 2010in Genome 1.89
Wallace Cowling23
Estimated H-index: 23
,
E. Balazs2
Estimated H-index: 2
(Hungarian Academy of Sciences)
were submitted forpublication following the conference ‘‘Exploiting Genome-wide Association in Oilseed Brassicas: a model for geneticimprovement of major OECD crops for sustainable futurefarming’’, held at The University of Western Australia, 9–12 November 2009, which was sponsored by the OECDCo-operative Research Programme on Biological ResourceManagement for Sustainable Agricultural Systems
14 Citations Source Cite
Published on Nov 1, 2010in Genome 1.89
Chris Duran14
Estimated H-index: 14
,
Dominic EalesD. Eales2
Estimated H-index: 2
+ 9 AuthorsJacqueline Batley41
Estimated H-index: 41
Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb fo...
41 Citations Source Cite
Published on Mar 31, 2012in Journal of Plant Biotechnology
A. C. Hayward24
Estimated H-index: 24
,
Annaliese S. Mason19
Estimated H-index: 19
+ 3 AuthorsJacqueline Batley41
Estimated H-index: 41
(University of Queensland)
This review summarises the biology, discovery and applications of single nucleotide polymorphisms in complex polyploid crop genomes, with a focus on the important oilseed crop Brassica napus. Brassica napus is an allotetraploid species, and along with soybean and oil palm is one of the top three most important oilseed crops globally. Current efforts are well underway to de novo assemble the B. napus genome, following the release of the related B. rapa ``A`` genome last year. The next generation ...
30 Citations Source Cite
Published on Aug 27, 2012in Biology
Michal T. Lorenc13
Estimated H-index: 13
(University of Queensland),
Satomi Hayashi12
Estimated H-index: 12
+ 8 AuthorsJacqueline Batley41
Estimated H-index: 41
(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 ...
41 Citations Source Cite
Published on Nov 25, 2013in Biology
Paul Visendi8
Estimated H-index: 8
,
Jacqueline Batley41
Estimated H-index: 41
,
David Edwards59
Estimated H-index: 59
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...
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Published on Aug 1, 2012in Plant Biotechnology Journal 6.30
David Edwards59
Estimated H-index: 59
(Australian Centre for Plant Functional Genomics),
Stephen Wilcox7
Estimated H-index: 7
(Walter and Eliza Hall Institute of Medical Research)
+ 15 AuthorsM. Bellgard30
Estimated H-index: 30
(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...
26 Citations Source Cite
Published on Mar 20, 2012in Agronomy
Kaitao Lai12
Estimated H-index: 12
(University of Queensland),
T. Lorenc1
Estimated H-index: 1
(University of Queensland),
David Edwards59
Estimated H-index: 59
(University of Queensland)
Genomics is playing an increasing role in plant breeding and this is accelerating with the rapid advances in genome technology. Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases. These range from large generic databases which hold specific data types for a broad range of species, to carefully integrated and curated databases which act as a resource for the improvement of specific crops. In t...
26 Citations Source Cite
Published on Feb 1, 2012in Plant and Cell Physiology 4.06
Kaitao Lai12
Estimated H-index: 12
(Australian Centre for Plant Functional Genomics),
Paul J. Berkman15
Estimated H-index: 15
(Australian Centre for Plant Functional Genomics)
+ 5 AuthorsDavid Edwards59
Estimated H-index: 59
(Australian Centre for Plant Functional Genomics)
34 Citations Source Cite
View next paperDiscovering genetic polymorphisms in next-generation sequencing data.