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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.
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Lijuan Wei,Meili Xiao,Annaliese S. Mason,Bi Ma,Kun Lu,Jia Na Li,Link Katrin,Donghui Fu 한국유전학회 2013 Genes & Genomics Vol.35 No.2
Brassica species, B. napus (canola), B. rapa and B. oleracea, are important sources of nutritionally valuable vegetable oil and protein-rich meal for animals and humans. Sequencing of the model plant Arabidopsis thaliana, has opened the way for investigations into the complex structure of the Brassica genomes, offering important insight into their evolution and composition. We use this sequence information for the characterization and functional analysis of SSR sequences that have diverged between the Brassica species. A total of 56 species-diverged sequences containing simple repeat units (SDS-SSR) of B. napus and its diploid progenitor species B. rapa and B. oleracea were isolated and characterized. Of these, 40 sequences showed homology with other Brassica sequences. Using the SSR Locator software, only 23 sequences were found to have SSRs,possibly due to the loss of SSR units in the process of species divergence. Sequence alignments with A. thaliana revealed that these species-diverged SSR sequences were responsible for Brassica divergence for differences between Brassica species in several genomic regions. Six active genes related to transferase, protein, transcription factor and retroelements were found in the SDS-SSRs. These results will further improve our understanding of the characteristics of species-diverged SSR fragments and their contribution to genome differentiation.
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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.
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Immobilization of Diatom Phaeodactylum tricornutum with Filamentous Fungi and Its Kinetics
Barzee Tyler J.,El-Mashad Hamed M.,Burch Andrew R.,Franz Annaliese K.,Zhang Ruihong 한국미생물·생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.2
Immobilizing microalgae cells in a hyphal matrix can simplify harvest while producing novel mycoalgae products with potential food, feed, biomaterial, and renewable energy applications; however, limited quantitative information to describe the process and its applicability under various conditions leads to difficulties in comparing across studies and scaling-up. Here, we demonstrate the immobilization of both active and heat-deactivated marine diatom Phaeodactylum tricornutum (UTEX 466) using different loadings of fungal pellets (Aspergillus sp.) and model the process through kinetics and equilibrium models. Active P. tricornutum cells were not required for the fungal-assisted immobilization process and the fungal isolate was able to immobilize more than its original mass of microalgae. The Freundlich isotherm model adequately described the equilibrium immobilization characteristics and indicated increased normalized algae immobilization (g algae removed/g fungi loaded) under low fungal pellet loadings. The kinetics of algae immobilization by the fungal pellets were found to be adequately modeled using both a pseudo-second order model and a model previously developed for fungal-assisted algae immobilization. These results provide new insights into the behavior and potential applications of fungal-assisted algae immobilization.
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Zou, Jun,Fu, Donghui,Gong, Huihui,Qian, Wei,Xia, Wei,Pires, J. Chris,Li, RuiYuan,Long, Yan,Mason, Annaliese S.,Yang, Tae‐,Jin,Lim, Yong P.,Park, Beom S.,Meng, Jinling Blackwell Publishing Ltd 2011 The Plant journal Vol.68 No.2
<P><B>Summary</B></P><P>Interspecific hybridization is a significant evolutionary force as well as a powerful method for crop breeding. Partial substitution of the AA subgenome in <I>Brassica napus</I> (A<SUP>n</SUP>A<SUP>n</SUP>C<SUP>n</SUP>C<SUP>n</SUP>) with the <I>Brassica rapa</I> (A<SUP>r</SUP>A<SUP>r</SUP>) genome by two rounds of interspecific hybridization resulted in a new introgressed type of <I>B.?napus</I> (A<SUP>r</SUP>A<SUP>r</SUP>C<SUP>n</SUP>C<SUP>n</SUP>). In this study, we construct a population of recombinant inbred lines of the new introgressed type of <I>B.?napus</I>. Microsatellite, intron‐based and retrotransposon markers were used to characterize this experimental population with genetic mapping, genetic map comparison and specific marker cloning analysis. Yield‐related traits were also recorded for identification of quantitative trait loci (QTLs). A remarkable range of novel genomic alterations was observed in the population, including simple sequence repeat (SSR) mutations, chromosomal rearrangements and retrotransposon activations. Most of these changes occurred immediately after interspecific hybridization, in the early stages of genome stabilization and derivation of experimental lines. These novel genomic alterations affected yield‐related traits in the introgressed <I>B.?napus</I> to an even greater extent than the alleles alone that were introgressed from the A<SUP>r</SUP> subgenome of <I>B.?rapa</I>, suggesting that genomic changes induced by interspecific hybridization are highly significant in both genome evolution and crop improvement.</P>
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