Literatura académica sobre el tema "Plant genome mapping"
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Artículos de revistas sobre el tema "Plant genome mapping"
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Chaney, Lindsay, Aaron R. Sharp, Carrie R. Evans y Joshua A. Udall. "Genome Mapping in Plant Comparative Genomics". Trends in Plant Science 21, n.º 9 (septiembre de 2016): 770–80. http://dx.doi.org/10.1016/j.tplants.2016.05.004.
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Doležel, Jaroslav, Marie Kubaláková, Jan Bartoš y Jiří Macas. "Flow cytogenetics and plant genome mapping". Chromosome Research 12, n.º 1 (2004): 77–91. http://dx.doi.org/10.1023/b:chro.0000009293.15189.e5.
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Lapitanz, Nora L. V. "Organization and evolution of higher plant nuclear genomes". Genome 35, n.º 2 (1 de abril de 1992): 171–81. http://dx.doi.org/10.1139/g92-028.
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The knowledge gained from studies on eukaryotic genome organization is important for understanding how genomes function and evolve, and it provides the basis for designing strategies for manipulating genomes. Hence, numerous studies on this subject have been conducted over the years, utilizing a variety of methods. In the recent decade, several techniques have been developed that allow the study of eukaryotic genome organization at different levels. Molecular techniques including molecular cloning, DNA sequencing, restriction fragment length polymorphism mapping, in situ hybridization, and pulsed field gel electrophoresis together provide a means of obtaining a comprehensive and detailed view of eukaryotic genomes. This paper summarizes recent findings on the organization and evolution of the nuclear genomes of higher plants, with emphasis on representative species with varying genome sizes, including Arabidopsis thaliana, tomato, maize, and wheat. Common, as well as unique, features in the organization of repeated DNA sequences and low copy sequences in these genomes are described and their evolutionary significance discussed.Key words: genome organization, evolution, higher plants, repeated DNA sequences, low copy number sequences.
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Ovesná, J., K. Poláková y L. Leišová. "DNA analyses and their applications in plant breeding". Czech Journal of Genetics and Plant Breeding 38, No. 1 (30 de julio de 2012): 29–40. http://dx.doi.org/10.17221/6108-cjgpb.
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In recent years, molecular markers have been developed based on the more detailed knowledge of genome structure. Considerable emphasis has been laid on the use of molecular markers in practical breeding and genotype identification. This review attempts to give an account of different molecular markers currently available for genome mapping and for tagging different traits – restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs) and microsatellites. Other markers, expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also mentioned. The importance of structural, functional genomic and comparative mapping is also discussed.
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Staňková, Helena, Alex R. Hastie, Saki Chan, Jan Vrána, Zuzana Tulpová, Marie Kubaláková, Paul Visendi et al. "BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes". Plant Biotechnology Journal 14, n.º 7 (23 de enero de 2016): 1523–31. http://dx.doi.org/10.1111/pbi.12513.
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Hou, Yuze, Li Wang y Weihua Pan. "Comparison of Hi-C-Based Scaffolding Tools on Plant Genomes". Genes 14, n.º 12 (27 de noviembre de 2023): 2147. http://dx.doi.org/10.3390/genes14122147.
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De novo genome assembly holds paramount significance in the field of genomics. Scaffolding, as a pivotal component within the genome assembly process, is instrumental in determining the orientation and arrangement of contigs, ultimately facilitating the generation of a chromosome-level assembly. Scaffolding is contingent on supplementary linkage information, including paired-end reads, bionano, physical mapping, genetic mapping, and Hi-C (an abbreviation for High-throughput Chromosome Conformation Capture). In recent years, Hi-C has emerged as the predominant source of linkage information in scaffolding, attributed to its capacity to offer long-range signals, leading to the development of numerous Hi-C-based scaffolding tools. However, to the best of our knowledge, there has been a paucity of comprehensive studies assessing and comparing the efficacy of these tools. In order to address this gap, we meticulously selected six tools, namely LACHESIS, pin_hic, YaHS, SALSA2, 3d-DNA, and ALLHiC, and conducted a comparative analysis of their performance across haploid, diploid, and polyploid genomes. This endeavor has yielded valuable insights in advancing the field of genome scaffolding research.
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Vlk, D. y J. Řepková. "Application of next-generation sequencing in plant breeding". Czech Journal of Genetics and Plant Breeding 53, No. 3 (13 de septiembre de 2017): 89–96. http://dx.doi.org/10.17221/192/2016-cjgpb.
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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.
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Wu, Xing, Wei Jiang, Christopher Fragoso, Jing Huang, Geyu Zhou, Hongyu Zhao y Stephen Dellaporta. "Prioritized candidate causal haplotype blocks in plant genome-wide association studies". PLOS Genetics 18, n.º 10 (17 de octubre de 2022): e1010437. http://dx.doi.org/10.1371/journal.pgen.1010437.
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Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects in many GWAS. In plant, the relatively small population size in GWAS and the high genetic diversity found in many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to prioritize the candidate causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, GMMAT, and BLINK in both simulated and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in high polygenicity simulation setting. Moreover, it resulted in smaller mapping intervals, especially in regions of high LD, achieved by prioritizing small candidate causal blocks in the larger haplotype blocks. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA’s results, and the average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved on mapping resolution to facilitate crop improvement.
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Lindeberg, Magdalen, Christopher R. Myers, Alan Collmer y David J. Schneider. "Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization". Molecular Plant-Microbe Interactions® 21, n.º 6 (junio de 2008): 685–700. http://dx.doi.org/10.1094/mpmi-21-6-0685.
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Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacteria. Among these are genes linked to epiphytic fitness, plant- and insect-active toxins, secretion pathways, and virulence regulators, all reflected in the recently updated DC3000 genome annotation. Distribution of virulence genes in relation to P. syringae genome organization was analyzed to distinguish patterns of conservation among genomes and association between genes and mobile genetic elements. Variable regions were identified on the basis of deviation in sequence composition and gaps in syntenic alignment among the three genomes. Mapping gene location relative to the genome structure revealed strong segregation of the HrpL regulon with variable genome regions (VR), divergent distribution patterns for toxin genes depending on association with plant or insect pathogenesis, and patterns of distribution for other virulence genes that highlight potential sources of strain-to-strain differences in host interaction. Distribution of VR among other sequenced bacterial genomes was analyzed and future plans for characterization of this potential reservoir of virulence genes are discussed.
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Foolad, Majid R. "Genome Mapping and Molecular Breeding of Tomato". International Journal of Plant Genomics 2007 (22 de agosto de 2007): 1–52. http://dx.doi.org/10.1155/2007/64358.
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The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum×L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes ∼214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs.
Tesis sobre el tema "Plant genome mapping"
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Fisk, Dianna G. "CRP1 : founding member of a novel protein family that functions in organellar gene expression /". view abstract of download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9987422.
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Islam, Mohammad Sayedul. "Genetic mapping of rooting in rice : exploiting a high throughput phenotyping in plants". Thesis, University of Aberdeen, 2016. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=229720.
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Meeting future demands of food security will require enhanced rice production that is more environmentally sustainable. To achieve this it is important to know the genetic and molecular mechanism controlling the root traits. High throughput phenotyping which can keep pace with genotyping is needed, but for many researchers this needs to be cheap as well as meaningful. Here a very simple, low cost and reliable method of assessing root depth of seedling using a layer of diuron-soaked filter paper buried 25 cm deep in a soil-filled box has been developed which is suitable for screening of hundreds of accessions. The assumption is that deep-rooting plants die quicker. This method was then used to screen five established rice panels. Deep rooted cultivars were screened from a panel of an aus panel from IRRI and a panel of Brazilian and Japanese cultivars by using this method. Root QTLs were detected by using bi-parental mapping population and GWA study was performed in two panels, the rice diversity panel (RDP-1) and Bengal Assam Association Population. Assessing 139 RILs from Bala x Azucena bi-parental population revealed heritability of 55% for herbicide symptoms where eleven QTLs were detected, many of which were co-localised with previously reported root QTLs in this population. A GWA study was performed using RDP1) of 356 accessions with 44k SNP markers. Analysis revealed 17% of phenotypic variation of herbicide score was attributable to rice sub-population where the aus showed the deepest rooting systems. A number of QTLs have been identified and a number of positional candidate gene lists were produced. A further 298 cultivars from Bengal and Assam were screened and GWA was performed using 2 M SNP database available from sequencing. ANOVA revealed 37% variation for herbicide score explained by genotype. Soil-filled rhizotron were used to assess 12 of these cultivars, revealing strong xx correlations between deep root traits and herbicide score, confirming the reliability of this method. GWA revealed a number of significant SNPs associated with the traits in this population. Finally a set of mutant gene (LOC_Os09g31478, LOC_Os05g40330, LOC_Os11g34140) which are functional candidate gene for root growth QTLs were studied. Here hydroponic phenotypic screening approach were used to identify the T-DNA mutant lines. However, no convincing mutants were revealed. The herbicide screening method has been shown to be a quick and robust system for the assessment of deep rooting rice plants in soil. This method can now be used for screening large number of cultivars and the identification of QTLs and candidate genes.
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Smith, Gavin James. "A molecular systematic study of the xylariales (ascomycota)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B30110841.
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Song, Weining. "Genome studies of cereals /". Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phs6984.pdf.
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Lonergan, Paul Francis. "Genetic characterisation and QTL mapping of zinc nutrition in barley (Hordeum vulgare)". Title page, contents and abstract only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phl847.pdf.
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Dimkpa, Stanley Obumneke Nyebuhi. "Genome wide association mapping and assessment of allelic variation in strigolactone synthesis genes involved in rice plant parasite interactions". Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=220456.
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Donald, Tamzin. "Organisation and expression of plant B chromosomes /". Title page, table of contents and abstract only, 1999. http://web4.library.adelaide.edu.au/theses/09PH/09phd6758.pdf.
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Hanson, Christopher Jon. "Exploration of the Gossypium raimondii Genome Using Bionano Genomics Physical Mapping Technology". BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/6854.
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Cotton is a crop with a large global economic impact as well as a large, complex genome. Most industrial cotton production is from two tetraploid species (Gossypium hirsutum L. and Gossypium barbadense L.) which contain two subgenomes, specifically the AT and DT subgenomes. The DT subgenome is nearly half the size of the AT subgenome in tetraploid cotton and is closely related to an extant D-genome Gossypium species, G. raimondii Ulbr. Characterization of the structural variants present in diploid D-genome should provide greater insight into the evolution of the DT subgenome in the tetraploid cotton. Bionano (BNG) optical mapping uses patterns of fluorescent labels inserted at specific endonuclease sites to create physical maps of the genomes which can then be examined for structural variation. To develop optical maps in G. raimondii, we first developed a de novo PacBio long read sequence assembly of G. raimondii. This sequence assembly consisted of 2,379 contigs, an average contig length of 413 Kb and a contig N50 of 4.9 Mb. Using BNG technology, we developed two optical maps of the diploid D genome of G. raimondii. One was created using the Nt.BssSI endonuclease and one with the Nt.BspQI endonuclease. Using the BNG optical maps, the PacBio assembly was hybrid scaffolded into 100 scaffolds (+ 5 unscaffolded contigs) with an average scaffold length of 7.5 Mb and a scaffold N50 of 13.1 Mb. A comparison between the Nt. BssSI BNG optical map and the two sequence assemblies identified 3,195 structural variants. These were used to validate the accuracy of the reference sequence of G. raimondii and structural variants were used to create a new phylogeny of nine major cotton species.
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Jean, Martine. "Genetic mapping of restorer genes for cytoplasmic male sterility in Brassica napus using DNA markers". Thesis, McGill University, 1995. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40147.
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DNA markers tightly-linked to nuclear fertility restorer genes for cytoplasmic male sterility (CMS) are valuable tools for breeders and researchers working with these genes. Two different targeting approaches were used to identify markers linked to the Rfp1 restorer gene for the pol CMS of canola (Brassica napus L.): nearly isogenic line (NIL) comparison and bulked segregant analysis. These methods were equally efficient in identifying markers linked to Rfp1; combining them allowed a targeting efficiency of 100% to be achieved. The efficiency of bulked segregant analysis was found to be limited by the inadvertent occurrence of shared homozygosity at specific chromosomal regions in the bulks, in contrast with the efficiency of NIL comparison which was limited by the occurrence of residual DNA from the donor cultivar at scattered sites around the genome of the NILs. Eleven DNA markers linked to the Rfp1 gene were identified, one of which perfectly co-segregates with Rfp1. The linkage group on which Rfp1 is localized contains 17 DNA markers. Two restorer genes of the pol CMS, Rfp1 and Rfp2, and a Rfn restorer gene of the nap CMS were found to be at least tightly linked to one another and may all reside at the same locus. A fourth restorer gene, the Rfo restorer for the ogu CMS, was, however, found to be unlinked to the other restorer genes. Different restorer genes for the nap CMS were found in the lines 'Westar-Rf and 'Karat'. A linkage map of the B. napus genome containing 146 markers organized into 23 linkage groups covering a total length of 850.2 cM was constructed from a BC$ sb1$ population. This map contains 63 loci previously localized on the B. napus genome through analysis of an F$ sb2$ population. Comparative analysis indicates that the total length of the BC$ sb1$-derived map is smaller than that of the F$ sb2$-derived map, which suggests that a reduction in recombination frequency is occurring in male gametes. The preferential use of two or three probe-
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Surber, Lisa Marie McKinley. "Is there a genetic basis for forage quality of barley for beef cattle?" Diss., Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/surber/SurberL0806.pdf.
Texto completoLibros sobre el tema "Plant genome mapping"
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1948-, Gresshoff Peter M., ed. Plant genome analysis. Boca Raton, Fla: CRC Press, 1994.
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USDA Plant Genome Research Program. USDA Plant Genome Research Program. [Washington, D.C.]: U.S. Dept. of Agriculture, Agricultural Research Service, 1991.
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P, Jauhar Prem, ed. Methods of genome analysis in plants. Boca Raton: CRC Press, 1996.
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Karłowski, Wojciech M. Genomy roślinne: Wybrane metody poznania i analizy. Poznań: Wydawnictwo Naukowe Uniwerystetu im. Adama Mickiewicza, 2006.
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Khalid, Meksem y Kahl Günter, eds. The Handbook of plant genome mapping: Genetic and physical mapping. Weinheim: Wiley-VCH, 2005.
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J, Henry Robert, ed. Plant genotyping II: SNP technology. Wallingford, UK: CABI, 2008.
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Sharma, Arun Kumar y Archana Sharma. Plant genome: Biodiversity and evolution : Phanerogams - Angiosperm. Editado por ebrary Inc. Enfield, NH: Science Publishers, 2008.
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Miyao, Akio, Kyōzō Eguchi y Masato Kawabata. Inegenomu enki hairetsu kaidoku no ayumi: Kanzen kaidoku o oete. Tōkyō: Nōrin Suisanshō Nōrin Suisan Gijutsu Kaigi Jimukyoku, 2004.
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de, Vienne D., ed. Molecular markers in plant genetics and biotechnology. Enfield, NH: Science Publishers, 2003.
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United States. Agricultural Research Service., ed. The USDA-ARS Plant Genome Research Program. [Washington, D.C.?]: U.S. Dept. of Agriculture, Agricultural Research Service, 1994.
Buscar texto completoCapítulos de libros sobre el tema "Plant genome mapping"
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Kole, C. y P. K. Gupta. "Genome Mapping and Map Based Cloning". En Plant Breeding, 257–99. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-94-007-1040-5_11.
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Schneider, Katharina. "Mapping Populations and Principles of Genetic Mapping". En The Handbook of Plant Genome Mapping, 1–21. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603514.ch1.
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Hass-Jacobus, Barbara y Scott A. Jackson. "Physical Mapping of Plant Chromosomes". En The Handbook of Plant Genome Mapping, 131–49. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603514.ch6.
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Gardiner, Susan E., Ji Mei Zhu, Heather C. M. Whitehead y Charlotte Madie. "The New Zealand apple genome mapping project". En Developments in Plant Breeding, 275–79. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0467-8_56.
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Rasheed, Awais, Humaira Qayyum y Rudi Appels. "Genome-Informed Discovery of Genes and Framework of Functional Genes in Wheat". En Compendium of Plant Genomes, 165–86. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-38294-9_9.
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AbstractThe complete reference genome of wheat was released in 2018 (IWGSC in Science 361:eaar7191, 2018), and since then many wheats genomic resources have been developed in a short period of time. These resources include resequencing of several hundred wheat varieties, exome capture from thousands of wheat germplasm lines, large-scale RNAseq studies, and complete genome sequences with de novo assemblies of 17 important cultivars. These genomic resources provide impetus for accelerated gene discovery and manipulation of genes for genetic improvement in wheat. The groundwork for this prospect includes the discovery of more than 200 genes using classical gene mapping techniques and comparative genomics approaches to explain moderate to major phenotypic variations in wheat. Similarly, QTL repositories are available in wheat which are frequently used by wheat genetics researchers and breeding communities for reference. The current wheat genome annotation is currently lagging in pinpointing the already discovered genes and QTL, and annotation of such information on the wheat genome sequence can significantly improve its value as a reference document to be used in wheat breeding. We aligned the currently discovered genes to the reference genome, provide their position and TraesIDs, and present a framework to annotate such genes in future.
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Gresshoff, Peter M. "Positional Cloning of Plant Developmental Genes". En The Handbook of Plant Genome Mapping, 233–56. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603514.ch10.
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Atwell, Susanna y Daniel J. Kliebenstein. "Conducting Genome-Wide Association Mapping of Metabolites". En The Handbook of Plant Metabolomics, 255–71. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2013. http://dx.doi.org/10.1002/9783527669882.ch14.
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Nguyen, Henry T. y Xiaolei Wu. "Molecular Marker Systems for Genetic Mapping". En The Handbook of Plant Genome Mapping, 23–52. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603514.ch2.
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Nelson, James C. "Methods and Software for Genetic Mapping". En The Handbook of Plant Genome Mapping, 53–74. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603514.ch3.
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Doležel, Jaroslav, Marie Kubaláková, Jan Bartoš y Jiří Macas. "Chromosome Flow Sorting and Physical Mapping". En The Handbook of Plant Genome Mapping, 151–71. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603514.ch7.
Texto completoActas de conferencias sobre el tema "Plant genome mapping"
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"Genome-Wide Association Mapping of diverse set of spring wheat germplasm in Western Siberia". En Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-165.
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Woody, Scott. "GameteMaker: An Online Resource to Enhance Student Understanding of Genetic and Gemic Sciences Through Gene Mapping Experiments". En ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.531631.
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"Association mapping of the gene controlling melanin synthesis in barley grain using plant genetic resources collections". En Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-066.
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Liu, Y., L. Deng, A. Augustine, H. Thar, A. Al Ali, A. K. Anurag, A. Alkatheeri, A. Soliman, E. Elabsy y M. Atia. "Maximize Sweep Efficiency Using Proactive Tar Boundary Detection to Effectively Place a Water Injector Well Using Multiple Workflows of Distance-To-Boundary Inversion Techniques". En ADIPEC. SPE, 2023. http://dx.doi.org/10.2118/216017-ms.
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Abstract In most field developments, the major objectives of placing water injectors are to minimize oil column below the well trajectory, maximize the sweep efficiency and avoid drilling below tar which acts as permeability barrier reducing the effectiveness of the injectors. The case study showcases integration of two conceptual tar models in the well planning phase & implementation of multiple inversion workflows for deep azimuthal resistivity (DAR) tool to enable a successful detection & mapping of tar surface. Two tar models were generated from seismic inversion and a petroleum system study. They highlight the depth and areal extension uncertainties for tar presence to be incorporated in well planning stages. A detailed Reservoir Navigation feasibility model constructed in pre-drilling stage showed that the tar surface shows characteristic high resistivity in offset wells. This could be used for early detection and avoidance of tar by using a DAR tool, NMR-Density-Neutron, and mud logging which were selected to effectively characterize and map the tar. While drilling, Azimuthal resistivity data based multiple inversion workflows were utilized in real-time to accurately assess several possible scenarios. More guidance was applied along sections with moderate change of environment, while open models allowed to check the global equivalency or find solutions in regions where changes in resistivity were substantial. The integrated work from planning to execution stage not only saved a pilot hole, sidetrack cost but also maximized value for injector placement & subsurface characterization. The well was successfully landed above the modelled shallower tar surface. The tar presence was evaluated using joint analysis of resistivity inversion, NMR-Density-Neutron data and cutting samples. It was key to have both conceptual models to provide a much smoother well profile for accessibility and to avoid any possible sidetrack. For the subject well, inversion workflows with optimized parameter inputs provided good mapping of the tar mat. Linear uncertainty analysis of the resistivity data inversion results confirmed high accuracy of the distance to boundary estimation. The multiple inversion workflows allowed to adjust the variables based on the environment and provide an interpretation output, that mapped the tar surface with high confidence & Geosteering decisions were made timely. The resistive top tar layer was tagged for final confirmation and interpretation from cuttings & NMR-Density / Neutron tool before TD. Proactive Geosteering recommendations allowed a gentle incident angle relative to the resistive tar layer below. The well was placed around 5 ft. TVD above the tar surface, thus minimizing oil column above the tar & below the wellbore thus increasing sweep efficiency. The DAR tool enabled 5000 ft. lateral mapping of tar surface for the first time in the field and enhanced the subsurface understanding for future field development plan. Utilization of resistivity data based multiple workflow inversion in real-time provided a higher confidence level & improved proactive Geosteering decision making that enabled the best well placement for this injector well while avoiding the shallower tar.
Informes sobre el tema "Plant genome mapping"
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Katzir, Nurit, Rafael Perl-Treves y Jack E. Staub. Map Merging and Homology Studies in Cucumis Species. United States Department of Agriculture, septiembre de 2000. http://dx.doi.org/10.32747/2000.7575276.bard.
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List of original objectives (1) Construct a saturated map of melon, using RFLP, SSR, RAPD and Inter-SSR genetic markers. (2) Study the homology between the genomes of cucumber and melon. (3) Add to the Cucumis map, biologically important genes that had been cloned in other plant systems. Background Cucumber and melon are important vegetable crops in Israel and the US. Genome analysis of these crops has lagged behind the major plant crops, but in the last few years genetic maps with molecular markers have been developed. The groups that participated in this program were all involved in initial mapping of cucurbit crops. This grant was meant to contribute to this trend and promote some of the more advanced applications of genome analysis, i.e., map saturation and comparative mapping between cucurbit species. Major achievements The main achievements of the research were (a) the construction of melon maps that include important horticultural traits and Resistance Gene Homologues, (b) the development of approximately 200 SSR markers of melon and cucumber, (c) the preliminary map merging of melon maps and of comparative mapping between melon and cucumber. Implications As a result of this program, we have a good estimate of the applicability of different types or markers developed in one cucurbit species to genetic mapping in other species. Since the linkage groups of melon and cucumber can now be related to each other, future identification of important genes in the two crops will be facilitated. Moreover, the further saturation of the maps with additional markers will now allow us to target several disease resistance loci, horticultural traits for marker-assisted selection, fine mapping and positional cloning.
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Zhang, Hongbin B., David J. Bonfil y Shahal Abbo. Genomics Tools for Legume Agronomic Gene Mapping and Cloning, and Genome Analysis: Chickpea as a Model. United States Department of Agriculture, marzo de 2003. http://dx.doi.org/10.32747/2003.7586464.bard.
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The goals of this project were to develop essential genomic tools for modern chickpea genetics and genomics research, map the genes and quantitative traits of importance to chickpea production and generate DNA markers that are well-suited for enhanced chickpea germplasm analysis and breeding. To achieve these research goals, we proposed the following research objectives in this period of the project: 1) Develop an ordered BAC library with an average insert size of 150 - 200 kb (USA); 2) Develop 300 simple sequence repeat (SSR) markers with an aid of the BAC library (USA); 3) Develop SSR marker tags for Ascochyta response, flowering date and grain weight (USA); 4) Develop a molecular genetic map consisting of at least 200 SSR markers (Israel and USA); 5) Map genes and QTLs most important to chickpea production in the U.S. and Israel: Ascochyta response, flowering and seed set date, grain weight, and grain yield under extreme dryland conditions (Israel); and 6) Determine the genetic correlation between the above four traits (Israel). Chickpea is the third most important pulse crop in the world and ranks the first in the Middle East. Chickpea seeds are a good source of plant protein (12.4-31.5%) and carbohydrates (52.4-70.9%). Although it has been demonstrated in other major crops that the modern genetics and genomics research is essential to enhance our capacity for crop genetic improvement and breeding, little work was pursued in these research areas for chickpea. It was absent in resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. For instance, there were no large-insert BAC and BIBAC libraries, no sufficient and user- friendly DNA markers, and no intraspecific genetic map. Grain sizes, flowering time and Ascochyta response are three main constraints to chickpea production in drylands. Combination of large seeds, early flowering time and Ascochyta blight resistance is desirable and of significance for further genetic improvement of chickpea. However, it was unknown how many genes and/or loci contribute to each of the traits and what correlations occur among them, making breeders difficult to combine these desirable traits. In this period of the project, we developed the resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. In particular, we constructed the proposed large-insert BAC library and an additional plant-transformation-competent BIBAC library from an Israeli advanced chickpea cultivar, Hadas. The BAC library contains 30,720 clones and has an average insert size of 151 kb, equivalent to 6.3 x chickpea haploid genomes. The BIBAC library contains 18,432 clones and has an average insert size of 135 kb, equivalent to 3.4 x chickpea haploid genomes. The combined libraries contain 49,152 clones, equivalent to 10.7 x chickpea haploid genomes. We identified all SSR loci-containing clones from the chickpea BAC library, generated sequences for 536 SSR loci from a part of the SSR-containing BACs and developed 310 new SSR markers. From the new SSR markers and selected existing SSR markers, we developed a SSR marker-based molecular genetic map of the chickpea genome. The BAC and BIBAC libraries, SSR markers and the molecular genetic map have provided essential resources and tools for modern genetic and genomic analyses of the chickpea genome. Using the SSR markers and genetic map, we mapped the genes and loci for flowering time and Ascochyta responses; one major QTL and a few minor QTLs have been identified for Ascochyta response and one major QTL has been identified for flowering time. The genetic correlations between flowering time, grain weight and Ascochyta response have been established. These results have provided essential tools and knowledge for effective manipulation and enhanced breeding of the traits in chickpea.
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Moore, Gloria A., Gozal Ben-Hayyim, Charles L. Guy y Doron Holland. Mapping Quantitative Trait Loci in the Woody Perennial Plant Genus Citrus. United States Department of Agriculture, mayo de 1995. http://dx.doi.org/10.32747/1995.7570565.bard.
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As is true for all crops, production of Citrus fruit is limited by traits whose characteristics are the products of many genes (i.e. cold hardiness). In order to modify these traits by marker aided selection or molecular genetic techniques, it is first necessary to map the relevant genes. Mapping of quantitative trait loci (QTLs) in perennial plants has been extremely difficult, requiring large numbers of mature plants. Production of suitable mapping populations has been inhibited by aspects of reproductive biology (e.g. incompatibility, apomixis) and delayed by juvenility. New approaches promise to overcome some of these obstacles. The overall objective of this project was to determine whether QTLs for environmental stress tolerance could be effectively mapped in the perennial crop Citrus, using an extensive linkage map consisting of various types of molecular markers. Specific objectives were to: 1) Produce a highly saturated genetic linkage map of Citrus by continuing to place molecular markers of several types on the map. 2) Exploiting recently developed technology and already characterized parental types, determine whether QTLs governing cold acclimation can be mapped using very young seedling populations. 3) Determine whether the same strategy can be transferred to a different situation by mapping QTLs influencing Na+ and C1- exclusion (likely components of salinity tolerance) in the already characterized cross and in new alternative crosses. 4) Construct a YAC library of the citrus genome for future mapping and cloning.
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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir y Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, diciembre de 2013. http://dx.doi.org/10.32747/2013.7594399.bard.
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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.
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Fridman, Eyal, Jianming Yu y Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, enero de 2012. http://dx.doi.org/10.32747/2012.7597925.bard.
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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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Savaldi-Goldstein, Sigal y Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, diciembre de 2012. http://dx.doi.org/10.32747/2012.7699849.bard.
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Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is apparent that hormones are acting in selected cells of the plant body to regulate organ growth, and furthermore, that local cell-cell communication is an important mechanism. In this proposal our goals were to identify the global profile of translated genes in response to BR stimulation and depletion in specific tissues in Arabidopsis; determine the spatio-temporal dependency of BR response on auxin transport and signaling and construct an interactive public website that will provide an integrated analysis of the data set. Our technology incorporated cell-specific polysome isolation and sequencing using the Solexa technology. In the first aim, we generated and confirmed the specificity of novel transgenic lines expressing tagged ribosomal protein in various cell types in the Arabidopsis primary root. We next crossed these lines to lines with targeted expression of BRI1 in the bri1 background. All lines were treated with BRs for two time points. The RNA-seq of their corresponding immunopurified polysomal RNA is nearly completed and the bioinformatic analysis of the data set will be completed this year. Followed, we will construct an interactive public website (our third aim). In the second aim we started revealing how spatio-temporalBR activity impinges on auxin transport in the Arabidopsis primary root. We discovered the unexpected role of BRs in controlling the expression of specific auxin efflux carriers, post-transcriptionally (Hacham et al, 2012). We also showed that this regulation depends on the specific expression of BRI1 in the epidermis. This complex and long term effect of BRs on auxin transport led us to focus on high resolution analysis of the BR signaling per se. Taking together, our ongoing collaboration and synergistic expertise (hormone action and plant development (IL) and whole-genome scale data analysis (US)) enabled the establishment of a powerful system that will tell us how distinct cell types respond to local and systemic BR signal. BR research is of special agriculture importance since BR application and BR genetic modification have been shown to significantly increase crop yield and to play an important role in plant thermotolerance. Hence, our integrated dataset is valuable for improving crop traits without unwanted impairment of unrelated pathways, for example, establishing semi-dwarf stature to allow increased yield in high planting density, inducing erect leaves for better light capture and consequent biomass increase and plant resistance to abiotic stresses.
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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor y Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, enero de 2016. http://dx.doi.org/10.32747/2016.7600047.bard.
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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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Breiman, Adina, Jan Dvorak, Abraham Korol y Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, diciembre de 2011. http://dx.doi.org/10.32747/2011.7697121.bard.
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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Sela, Hanan, Eduard Akhunov y Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, enero de 2014. http://dx.doi.org/10.32747/2014.7598170.bard.
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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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Fridman, Eyal y Eran Pichersky. Tomato Natural Insecticides: Elucidation of the Complex Pathway of Methylketone Biosynthesis. United States Department of Agriculture, diciembre de 2009. http://dx.doi.org/10.32747/2009.7696543.bard.
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Plant species synthesize a multitude of specialized compounds 10 help ward off pests. and these in turn may well serve as an alternative to synthetic pesticides to reduce environmental damage and health risks to humans. The general goal of this research was to perform a genetic and biochemical dissection of the natural-insecticides methylketone pathway that is specific to the glandular trichomes of the wild species of tomato, Solanumhabrochaites f. glabratum (accession PI126449). Previous study conducted by us have demonstrated that these compounds are synthesized de novo as a derivate pathway of the fatty acid biosynthesis, and that a key enzyme. designated MethylketoneSynthase 1 (MKS 1). catalyzes conversion of the intermediate B-ketoacyl- ACPs to the corresponding Cn-1 methylketones. The approach taken in this proposed project was to use an interspecific F2 population. derived from the cross between the cultivated lV182 and the wild species PIl26449. for three objectives: (i) Analyze the association between allelic status of candidate genes from the fatty acid biosynthesis pathway with the methylketone content in the leaves (ii) Perform bulk segregant analysis of genetic markers along the tomato genome for identifying genomic regions that harbor QTLs for 2TD content (iii) Apply differential gene expression analysis using the isolated glands of bulk segregant for identifying new genes that are involved in the pathway. The genetic mapping in the interspecific F2 population included app. 60 genetic markers, including the candidate genes from the FAS pathway and SSR markers spread evenly across the genome. This initial; screening identified 5 loci associated with MK content including the candidate genes MKS1, ACC and MaCoA:ACP trans. Interesting observation in this genetic analysis was the connection between shape and content of the glands, i.e. the globularity of the four cells, typical to the wild species. was associated with increased MK in the segregating population. In the next step of the research transcriptomic analysis of trichomes from high- and 10w-MK plants was conducted. This analysis identified a new gene, Methy1ketone synthase 2 (MKS2), whose protein product share sequence similarity to the thioesterase super family of hot-dog enzymes. Genetic analysis in the segregating population confirmed its association with MK content, as well as its overexpression in E. coli that led to formation of MK in the media. There are several conclusions drawn from this research project: (i) the genetic control of MK accumulation in the trichomes is composed of biochemical components in the FAS pathway and its vicinity (MKS 1 and MKS2). as well as genetic factors that mediate the morphology of these specialized cells. (ii) the biochemical pathway is now realized different from what was hypothesized before with MKS2 working upstream to I\1KS 1 and serves as the interface between primary (fatty acids) and secondary (MK) metabolism. We are currently testing the possible physical interactions between these two proteins in vitro after the genetic analysis showed clear epistatic interactions. (iii) the regulation of the pathway that lead to specialized metabolism in the wild species is largely mediated by transcription and one of the achievements of this project is that we were able to isolate and verify the specificity of the MKS1 promoter to the trichomes which allows manipulation of the pathways in these cells (currently in progress). The scientific implications of this research project is the advancement in our knowledge of hitherto unknown biochemical pathway in plants and new leads for studying a new family in plants (hot dog thioesterase). The agricultural and biotechnological implication are : (i) generation of new genetic markers that could assist in importing this pathway to cultivated tomato hence enhancing its natural resistance to insecticides, (ii) the discovery of MKS2 adds a new gene for genetic engineering of plants for making new fatty acid derived compounds. This could be assisted with the use of the isolated and verified MKS1 promoter. The results of this research were summarized to a manuscript that was published in Plant Physiology (cover paper). to a chapter in a proceeding book. and one patent was submitted in the US.