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Simple Sequence Repeat (SSR) and GC Distribution in the Arabidopsis thaliana Genome
Mortimer Jennifer C,Batley Jacqueline,Love Christopher G,Logan Erica,Edwards David The Korean Society of Plant Biotechnology 2005 Plant molecular biology and biotechnology research Vol.7 No.1
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 genome and a strong association within and around transcribed sequences, while G/C density is associated specifically with the coding portions of transcribed sequences. SSR motif repeat number shows a high degree of variation for each SSR type and a high degree of motif sequence bias reflecting local genome sequence composition. PCR primers suitable for the amplification of identified SSRs have been designed where possible, and are available for further studies.
Applied Computational Tools for Crop Genome Research
Love Christopher G,Batley Jacqueline,Edwards David The Korean Society of Plant Biotechnology 2003 Plant molecular biology and biotechnology research Vol.5 No.4
A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.
Rapid divergence of repetitive DNAs in Brassica relatives
Koo, D.H.,Hong, C.P.,Batley, J.,Chung, Y.S.,Edwards, D.,Bang, J.W.,Hur, Y.,Lim, Y.P. Academic Press 2011 Genomics Vol.97 No.3
Centromeric, subtelomeric, and telomeric repetitive DNAs were characterized in Brassica species and the related Raphanus sativus and Arabidopsis thaliana. In general, rapid divergence of the repeats was found. The centromeric tandem satellite repeats were differentially distributed in the species studied, suggesting that centromeric repeats have diverged during the evolution of the A/C and B genome lineages. Sequence analysis of centromeric repeats suggested rapid evolution. Pericentromere-associated retrotransposons were identified and showed divergence during the evolution of the lineages as centromeric repeats. A novel subtelomeric tandem repeat from B. nigra was found to be conserved across the diploid Brassica genomes; however, this sequence was not identified in the related species. In contrast to previous studies, interstitial telomere-like repeats were identified in the pericentromeres of Brassica chromosomes, and these repeats may be associated with genomic stability. These results provide insight into genome evolution during polyploidization in Brassica and divergence within the Brassicaceae.
SNP discovery and applications in Brassica napus
Hayward, Alice,Mason, Annaliese S.,Dalton-Morgan, Jessica,Zander, Manuel,Edwards, David,Batley, Jacqueline The Korean Society of Plant Biotechnology 2012 식물생명공학회지 Vol.39 No.1
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 of genome sequencing, SNP discovery and analysis pipelines, and the associated challenges for this work in $B.$ $napus$, will be addressed. The biological applications of SNP technology for both evolutionary and molecular geneticists as well as plant breeders and industry are far-reaching, and will be invaluable to our understanding and advancement of the $Brassica$ crop species.
Genomic distribution of simple sequence repeats in Brassica rapa
Hong, Chang Pyo,Piao, Zhong Yun,Kang, Tae Wook,Batley, Jacqueline,Yang, Tae Jin,Hur, Yoon Kang,Bhak, Jong,Park, Beom Seok,Edwards, David,Lim, Yong Pyo Korean Society for Molecular and Cellular Biology 2007 Molecules and cells Vol.23 No.3
SNP discovery and applications in Brassica napus
Alice Hayward,Annaliese S. Mason,Jessica Dalton-Morgan,Manuel Zander,David Edwards,Jacqueline Batley 한국식물생명공학회 2012 식물생명공학회지 Vol.39 No.1
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 of genome sequencing, SNP discovery and analysis pipelines, and the associated challenges for this work in B. napus, will be addressed. The biological applications of SNP technology for both evolutionary and molecular geneticists as well as plant breeders and industry are far-reaching, and will be invaluable to our understanding and advancement of the Brassica crop species.