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RISS 인기검색어
- 검색키워드
- 저자 : Douglas R. Cook (검색결과 4 건)
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Bridging Comparative Genomics and DNA Marker-aided Molecular Breeding
Hong Kyu Choi,Douglas R. Cook 한국육종학회 2011 한국육종학회지 Vol.43 No.2
In recent years, genomic resources and information have accumulated at an ever increasing pace, in many plant species, through whole genome sequencing, large scale analysis of transcriptomes, DNA markers and functional studies of individual genes. Well-characterized species within key plant taxa, co-called "model systems", have played a pivotal role in nucleating the accumulation of genomic information and databases, thereby providing the basis for comparative genomic studies. In addition, recent advances to "Next Generation" sequencing technologies have propelled a new wave of genomics, enabling rapid, low cost analysis of numerous genomes, and the accumulation of genetic diversity data for large numbers of accessions within individual species. The resulting wealth of genomic information provides an opportunity to discern evolutionary processes that have impacted genome structure and the function of genes, using the tools of comparative analysis. Comparative genomics provides a platform to translate information from model species to crops, and to relate knowledge of genome function among crop species. Ultimately, the resulting knowledge will accelerate the development of more efficient breeding strategies through the identification of trait-associated orthologous genes and next generation functional gene-based markers.
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Choi, Hong-Kyu,Iandolino, Alberto,da Silva, Francisco Goes,Cook, Douglas R APS Press 2013 Molecular plant-microbe interactions Vol.26 No.6
<P>Pierce's disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grape, currently restricted to the Americas. To test the long-standing hypothesis that Pierce's disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a redirection of gene transcription involving 822 genes with a minimum twofold change (P < 0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis-related proteins, abscisic acid- and jasmonic acid-responsive biosynthesis, and downregulation of transcripts related to photosynthesis, growth, and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlate of the classical concept of the disease triangle in which environment impacts disease severity.</P>
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CSGM Designer: a convenient platform for designing cross-species intron-spanning genic markers
Jin-Hyun Kim,Chaeyoung Lee,Joo-Seok Park,Douglas R. Cook,Hong-Kyu Choi 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools that reliably access genes with orthology to the genomes of well-characterized reference species. Here we report an efficient platform for designing cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM designer is enhanced by graphical displays of query results, which we describe as “circular viewer” and “search-within-results” functions. CSGM platform provides a virtual PCR representation, called eHT-PCR, that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding.
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The CCAAT box-binding transcription factor NF-YA1 controls rhizobial infection
Laporte, Philippe,Lepage, Agnes,Fournier, Joë,lle,Catrice, Olivier,Moreau, Sandra,Jardinaud, Marie-Franç,oise,Mun, Jeong-Hwan,Larrainzar, Estibaliz,Cook, Douglas R.,Gamas, Pascal,Niebel, And Oxford University Press 2014 Journal of experimental botany Vol.65 No.2
<P>Symbiosis between legume plants and soil rhizobia culminates in the formation of a novel root organ, the ‘nodule’, containing bacteria differentiated as facultative nitrogen-fixing organelles. MtNF-YA1 is a <I>Medicago truncatula</I> CCAAT box-binding transcription factor (TF), formerly called HAP2-1, highly expressed in mature nodules and required for nodule meristem function and persistence. Here a role for MtNF-YA1 during early nodule development is demonstrated. Detailed expression analysis based on RNA sequencing, quantitiative real-time PCR (qRT-PCR), as well as promoter–β-glucuronidase (GUS) fusions reveal that <I>MtNF-YA1</I> is first induced at the onset of symbiotic development during preparation for, and initiation and progression of, symbiotic infection. Moreover, using a new knock-out mutant, <I>Mtnf-ya1-1</I>, it is shown that <I>MtNF-YA1</I> controls infection thread (IT) progression from initial root infection through colonization of nodule tissues. Extensive confocal and electronic microscopic observations suggest that the bulbous and erratic IT growth phenotypes observed in <I>Mtnf-ya1-1</I> could be a consequence of the fact that walls of ITs in this mutant are thinner and less coherent than in the wild type. It is proposed that <I>MtNF-YA1</I> controls rhizobial infection progression by regulating the formation and the wall of ITs.</P>
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