Relevant bibliographies by topics / Clonal and genetic diversity

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Academic literature on the topic 'Clonal and genetic diversity'

Author: Grafiati
Published: 19 December 2024

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Journal articles on the topic "Clonal and genetic diversity"

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Rozenfeld, Alejandro F., Sophie Arnaud-Haond, Emilio Hernández-García, Víctor M. Eguíluz, Manuel A. Matías, Ester Serrão, and Carlos M. Duarte. "Spectrum of genetic diversity and networks of clonal organisms." Journal of The Royal Society Interface 4, no. 17 (May 2007): 1093–102. http://dx.doi.org/10.1098/rsif.2007.0230.

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Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations were examined using a combination of new tools to analyse microsatellite data in the marine angiosperm Posidonia oceanica . These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of immigration seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed a ‘small-world’ topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in subfamilies of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intra-population genetic structure of the clonal organism investigated; these therefore represent promising analytical tools in population genetics.
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Black, James R. M., and Nicholas McGranahan. "Genetic and non-genetic clonal diversity in cancer evolution." Nature Reviews Cancer 21, no. 6 (March 16, 2021): 379–92. http://dx.doi.org/10.1038/s41568-021-00336-2.

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Stelzer, H. E. "Evaluating genetic diversity concerns in clonal deployments." Canadian Journal of Forest Research 27, no. 3 (March 1, 1997): 438–41. http://dx.doi.org/10.1139/x96-201.

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Reisch, Christoph, Stefanie Meier, Christoph Schmid, and Maik Bartelheimer. "Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients." PeerJ 8 (June 3, 2020): e8887. http://dx.doi.org/10.7717/peerj.8887.

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In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge Carex nigra in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot. Clonal diversity and genetic variation of C. nigra were assessed with nuclear microsatellites using leaf material collected in 20 subplots along a diagonal cross within each study plot. The influence of water regime and soil mineral nutrients on clonal diversity and genetic variation was estimated by Bayesian multiple regression. Our study revealed a clear impact of soil nutrient conditions on clonal diversity and genetic variation of C. nigra, which increased with the concentration of phosphorous and decreased with the concentration of potassium. Key background to these findings seems to be the relative offspring success from generative as compared to clonal propagation. Phosphorous acquisition is essential during seedling establishment. Clonal diversity and genetic variation increase, therefore, at sites with higher phosphorous contents due to more successful recruitment. High levels of clonal diversity and genetic variation at sites of low potassium availability may in contrast be mainly caused by increased plant susceptibility to abiotic stress under conditions of potassium deficiency, which brings about more gaps in C. nigra stands and favors the ingrowth from other clones or recruitment from seeds.
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Balloux, François, Laurent Lehmann, and Thierry de Meeûs. "The Population Genetics of Clonal and Partially Clonal Diploids." Genetics 164, no. 4 (August 1, 2003): 1635–44. http://dx.doi.org/10.1093/genetics/164.4.1635.

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Abstract The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as FST value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).
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Duchmann, Matthieu, Lucie Laplane, and Raphael Itzykson. "Clonal Architecture and Evolutionary Dynamics in Acute Myeloid Leukemias." Cancers 13, no. 19 (September 29, 2021): 4887. http://dx.doi.org/10.3390/cancers13194887.

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Acute myeloid leukemias (AML) results from the accumulation of genetic and epigenetic alterations, often in the context of an aging hematopoietic environment. The development of high-throughput sequencing—and more recently, of single-cell technologies—has shed light on the intratumoral diversity of leukemic cells. Taking AML as a model disease, we review the multiple sources of genetic, epigenetic, and functional heterogeneity of leukemic cells and discuss the definition of a leukemic clone extending its definition beyond genetics. After introducing the two dimensions contributing to clonal diversity, namely, richness (number of leukemic clones) and evenness (distribution of clone sizes), we discuss the mechanisms at the origin of clonal emergence (mutation rate, number of generations, and effective size of the leukemic population) and the causes of clonal dynamics. We discuss the possible role of neutral drift, but also of cell-intrinsic and -extrinsic influences on clonal fitness. After reviewing available data on the prognostic role of genetic and epigenetic diversity of leukemic cells on patients’ outcome, we discuss how a better understanding of AML as an evolutionary process could lead to the design of novel therapeutic strategies in this disease.
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Maley, Carlo C., Patricia C. Galipeau, Jennifer C. Finley, V. Jon Wongsurawat, Xiaohong Li, Carissa A. Sanchez, Thomas G. Paulson, et al. "Genetic clonal diversity predicts progression to esophageal adenocarcinoma." Nature Genetics 38, no. 4 (March 26, 2006): 468–73. http://dx.doi.org/10.1038/ng1768.

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Nakajima, Yuichi, Yu Matsuki, Miguel D. Fortes, Wilfredo H. Uy, Wilfredo L. Campos, Kazuo Nadaoka, and Chunlan Lian. "Strong Genetic Structure and Limited Gene Flow among Populations of the Tropical Seagrass Thalassia hemprichii in the Philippines." Journal of Marine Science and Engineering 11, no. 2 (February 5, 2023): 356. http://dx.doi.org/10.3390/jmse11020356.

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Seagrasses are marine angiosperms, and seagrass beds maintain the species diversity of tropical and subtropical coastal ecosystems. For proper understanding, management and conservation of coastal ecosystems, it is essential to understand seagrass population dynamics. Population genetic studies can cover large geographic scales and contribute to a comprehensive understanding of reproductive dynamics and potential dispersal among locations. The clonal and genetic diversity and genetic connectivity of Thalassia hemprichii in the Philippines were estimated by a population genetics approach. The geographic scale of this study has a direct distance of approximately 1600 km. Although high clonal diversity was found in some sites (R = 0.07–1.00), both sexual and asexual reproduction generally maintains separate populations. Genetic diversity is not definitely correlated with latitude, and genetic differentiation is significant in all pairs of sites (FST = 0.026–0.744). Complex genetic structure was found in some regions, even at a fine geographic scale. The migration of fruits and seedlings was elucidated as an infrequent and stochastic event. These results suggest the necessity for the conservation of this species due to a deficiency in migrants from external regions.
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Ebert, Benjamin L. "Clonal Diversity and Mutated Genes in Myelodysplastic Syndromes." Blood 126, no. 23 (December 3, 2015): SCI—3—SCI—3. http://dx.doi.org/10.1182/blood.v126.23.sci-3.sci-3.

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Myelodysplastic syndromes (MDS) are driven by somatic genetic mutations that drive clonal explansion of neoplastic cells. The identification of these lesions has enabled large-scale studies to assess the association of genetic lesions with clinical and biological phenotype. Single mutations in driver genes in isolation, without concurrent mutations in additional driver genes, commonly do not cause overt disease, but rather cause an expanded population of blood cells without cytopenias, a condition that we have termed clonal hematopoiesis of indeterminate potential (CHIP). CHIP is common in the general population and is associated with age, risk of hematologic malignancy, and overall mortality. In contrast, patients with MDS generally have mutations in multiple genes as well as the disease-defining morphologic dysplastia and peripheral blood cytopenias. The particular mutations that drive MDS in an individual patient are powerfully associated with clinical phenotype, including cytopenias, specific morphologic abnormalities, blast percentage, overall survival, and response to therapy. Clonal architecture adds an additional layer of complexity as disease progression or response to therapy may be associated with shifts in the dominant genetic clone in the bone marrow. As the availability of genetic testing for panels of genes becomes widespread as a clinical assay, current endeavors are to move validated research findings into routine clinical use and to employ deep genetic analyses to evaluate response to investigational therapies in clinical trials. Disclosures Ebert: Genoptix: Consultancy, Patents & Royalties; H3 Biomedicine: Consultancy; Celgene: Consultancy.
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Lusasi, Justin. "Cyperus papyrus in Lake Victoria: Genetic Information, Utilisation and Resource Sustainability." JOURNAL OF THE GEOGRAPHICAL ASSOCIATION OF TANZANIA 36, no. 2 (July 10, 2021): 73–118. http://dx.doi.org/10.56279/jgat.v36i2.152.

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Many wetlands in the Lake Victoria basin are dominated by Cyperus papyrus, which are very productive and, therefore, have an important role both ecologically and socially. The increasing harvesting pressure of papyrus threatens its future. Thus, a conservation approach was employed to determine the intensity of the pressure and threat to the papyrus diversity at clonal level. Eight microsatellite loci were used for analysing the clonal diversity and genetic diversity of Cyperus papyrus in 6 swamps of Mwanza bay (Tanzania) and 5 swamps of Nyanza bay (Kenya). From 304 individuals, we observed a total of 49 alleles in Mwanza bay and 44 alleles in Nyanza bay, a high clonal diversity (R = 0.64 to 1 Mwanza bay and R=0.70 to 1 in Nyanza bay), and a high genetic diversity (HE) with an average of 0.558 and 0.493 for Mwanza and Nyanza bay, respectively. The analysis of molecular variance showed that most of the allelic variances were within individuals. This resulted in a moderate differentiation (FST, 0.126 and Nm, 1.7) from all studied population in Lake Victoria. Gene flow was high between populations within each bay of the Lake (Nm > 4). The observed disturbance in the swamps showed no effects on any of the papyrus diversity variables. The clonal diversity (R) was even higher in the disturbed swamps than in pristine ones, with values ranging from 0.78 to 1 for disturbed, and 0.64 to 1 for pristine swamps. This explains that, although it is a clonal plant, papyrus maintains sexual reproduction and successful seed dispersal, making them resilient to even strong environmental and anthropogenic disturbance.
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Dissertations / Theses on the topic "Clonal and genetic diversity"

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Weidow, Elliot D. "Genetic Diversity in an Invasive Clonal Plant? A Historical and Contemporary Perspective." ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/td/2522.

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Introduced populations of Eichhornia crassipes (Pontederiaceae) possess extremely low levels of genetic diversity due to severe bottleneck events and clonal reproduction. While populations elsewhere have been well studied, North American populations of E. crassipes remain understudied. We used Amplified Fragment Length Polymorphism markers to assess genetic diversity and population structure in North American E. crassipes populations. Patterns of diversity over the past fifty years were analyzed using herbarium specimens. Furthermore, we sampled populations across the Gulf Coast of the United States throughout a year to determine contemporary genetic diversity and assess potential seasonal effects. Genetic diversity was found to be scant in the United States without population structure, agreeing with previous studies from other regions. Genetic diversity has remained consistently low over the past fifty years despite significant changes in selection pressure. However, evidence for and against population structure between seasons was found and the consequences of this are discussed.
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Bullock, James Michael. "The maintenance of genotypic diversity in a clonal plant." Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279711.

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McClintock, Katherine. "Genetic variability, clonal diversity and taxonomic comparisons of Carex lasiocarpa Ehrh. and Carex lanuginosa Michx. (Cyperaceae)." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=61192.

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Enzyme electrophoresis, chromosome counts and self-incompatibility trials were used to compare genetic and clonal diversity in Carex lasiocarpa and C. lanuginosa, two closely-related wetland sedge species of north-temperate distribution. Genetic variation was similar in the two species, but C. lanuginosa was somewhat less diverse and had a higher coefficient of genetic differentiation among populations than C. lasiocarpa. Wright's fixation index indicated that both species are primarily outcrossing, although crossing experiments suggested that C. lanuginosa may be self-fertile. The haploid chromosome numbers were n = 38 for C. lasiocarpa and n = 40 or 41 for C. lanuginosa. Cluster analysis using genetic identities and principal components analysis of allele frequencies clearly grouped the two species, but the separation was less clear for morphological data. Clonal diversity was higher and clone size smaller in C. lasiocarpa than in C. lanuginosa, but C. lasiocarpa showed less clonal and genetic diversity at dry than at wet sites.
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Metzger, Genevieve. "CLONALITY AND GENETIC DIVERSITY IN POLYGONELLA MYRIOPHYLLA, A LAKE WALES RIDGE ENDEMIC PLANT." Master's thesis, University of Central Florida, 2010. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2103.

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Although capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I use microsatellite markers to investigate questions about clonal structure and genetic diversity in five populations of P. myriophylla and address some of the implications of my findings for conservation of this species: Overall, I find that 57% of sampled clusters of P. myriophylla are composed of a single genet (genetic individual) with multiple physiological units (ramets) while the remainder are made up of two or more genets. I found differences in both clonal reproduction and genetic diversity among populations. I also found evidence of limited gene flow even over small spatial scales (less than 10 km) and for at least 4 genetic clusters occurring within the species range. Despite high levels of genetic diversity overall, there is evidence of reduced genetic diversity in two populations My results suggest that high levels of clonality may be important in maintaining genetic diversity in P. myriophylla. I also provide evidence that dirt roadsides may not represent a refuge for this species.
M.S.
Department of Biology
Sciences
Biology MS
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Stokes, Richard L. "Pollination Ecology, Self-incompatibility and Genetic Diversity in the Herbaceous Eastern North American Spring Ephemeral, Erythronium americanum." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1353089025.

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Solé, Magali. "Factors affecting the genotypic and genetic diversity of the dioecious clonal plant Cirsium arvense at the metapopulation level." [S.l.] : [s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=971596697.

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Maciel, Kelly de Jesus Silva. "Análise da diversidade e divergência genética em clones de Eucalyptus spp. potencialmente importantes para Goiás." Universidade Federal de Goiás, 2014. http://repositorio.bc.ufg.br/tede/handle/tede/6247.

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Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG
The success of the Brazilian forestry is due largely to the excellent adaptability of the Eucalyptus genus to our climate and soil conditions. The recent expansion of eucalypts to the North and Midwest regions of Brazil presents challenges such as the need for clones adapted to drought, high temperatures and nutrient deficient soils of Cerrado. Three clonal trials were installed in different regions of Goiás State to evaluate the adaptability and growth of 113 elite clones of Eucalyptus spp. The objective of this study was to estimate the genetic diversity and divergence among 90 of the clones used in three clonal trials installed in different regions of Goiás State. The clones were genotyped with nine microsatellite loci organized into four "multiplex" systems for PCR. The amplified fragments were separated on the ABI–3100 platform (Applied Biosystems). The genotyping was performed using the GeneMapper software (Applied Biosystems). Genetic diversity parameters were estimated using the GDA and Fstat programs. The parameters number of alleles (A), expected heterozygosity (He), observed heterozygosity (Ho), intrapopulation fixation index (f) and allelic richness were estimated for each microsatellite locus. The results showed that all loci used in this study were highly polymorphic, with an average of 16.78 alleles per locus. The EMBRA28 and EMBRA3 loci showed the highest number of alleles (24 and 22). In general, for most markers, the observed heterozygosity had similar estimates when compared to the expected heterozigosity under Hardy-Weinberg Equilibrium. As a result, the fixation index (f) did not differ significantly from zero. Analyses of genetic structure of the clones was performed using the software Structure (version 2.3.4), with K values ranging from 1 to 10, with 10 interactions each. Results indicated presence of three distinct genetic groups (K = 3). However, there was no clear relationship between the populations obtained and the different species of Eucalyptus used in the study. This result can be explained by the clone sample is originated from breeding programs where crosses may have admixed populations, disrupting some genetic structures. Most importantly, the molecular analyses indicate extraordinary genetic diversity within the clonal trials installed in Goiás. This genetic diversity can be exploited for breeding new genetic material adapted to the Cerrado conditions.
O sucesso do setor florestal brasileiro deve-se em grande parte à excelente adaptabilidade do gênero Eucalyptus ao nosso clima e condições do solo. A recente expansão do eucalipto para as regiões norte e central do Brasil requer pesquisas para que os clones se adaptem à seca, elevadas temperaturas e escassez de nutrientes nos solos do Cerrado. O objetivo deste estudo foi estimar a diversidade e divergência genética entre 90 dos clones utilizados em uma rede de testes clonais no estado de Goiás. Os clones foram genotipados com nove locos microssatélites organizados em quatro sistemas “multiplex” para PCR. Os fragmentos amplificados foram separados na plataforma ABI-3100 (Applied Biosystems). A genotipagem foi realizada utilizando o programa GeneMapper (Applied Biosystems). Os parâmetros de diversidade genética foram estimados usando os programas GDA e Fstat. Os parâmetros número de alelos (A), heterozigosidade esperada (He), heterozigosidade observada (Ho), índice de fixação intrapopulacional (f) e riqueza alélica foram estimados para cada loco microssatélite. Os resultados mostraram que todos os locos utilizados neste estudo foram altamente polimórficos, com média de 16,78 alelos por loco. A genotipagem dos locos EMBRA28 e EMBRA3 mostrou o maior número de alelos (24 e 22). De maneira geral, para a maioria dos locos estudados, a heterozigosidade observada apresentou estimativas semelhantes à heterozigosidade esperada dentro das condições do Equilíbrio de Hardy-Weimberg. Como resultado, o índice de fixação (f) não diferiu significativamente de zero. A análise da estrutura genética dos clones foi realizada utilizando o programa Structure (versão 2.3.4), com valores de K variando de 1 a 10, com 10 iterações cada. Os resultados indicaram a presença de três grupos genéticos distintos (K = 3). Entretanto, não foi observada uma clara relação entre as populações obtidas e as diferentes espécies de Eucalyptus utilizadas no estudo. Esse resultado pode ser explicado pelo fato da amostra de clone ser originada de programas de melhoramento, onde os cruzamentos recombinam o material genético das populações, desfazendo algumas estruturas genéticas. De forma mais importante, as análises moleculares indicaram grande diversidade genética dentre os clones que estão sendo avaliados em Goiás. Esta diversidade genética pode ser explorada em um programa de melhoramento para obtenção de novos materiais genéticos adaptados às condições do Cerrado.
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Starnes, John H. "CHARACTERIZATION AND DISTRIBUTION OF NOVEL NON-LTR RETROELEMENTS DRIVING HIGH TELOMERE RFLP DIVERSITY IN CLONAL LINES OF MAGNAPORTHE ORYZAE." UKnowledge, 2013. http://uknowledge.uky.edu/plantpath_etds/6.

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The filamentous ascomycete fungus Magnaporthe oryzae is a pathogen of over 50 genera of grasses. Two important diseases it can cause are gray leaf spot in Lolium perenne (perennial ryegrass) and blast in Oryza sativa (rice). The telomeres of M. oryzae isolates causing gray leaf spot are highly variable, and can spontaneously change during fungal culture. In this dissertation, it is shown that a rice-infecting isolate is much more stable at the telomeres than an isolate from gray leaf spot. To determine the molecular basis of telomere instability several gray leaf spot isolates telomeres were cloned, which revealed two non-LTR retrotransposons inserted into the telomere repeats. The elements have been termed Magnaporthe oryzae Telomeric Retrotransposons (MoTeRs). These elements do not have poly-A tails common to many other non-LTR retrotransposons, but instead have telomere like sequences at their 5’ end that allow them to insert into telomeres. Intact copies of MoTeRs were restricted to the telomeres of isolates causing gray leaf spot. Surveys for the presence of these elements in M. oryzae showed they were present in several host-specialized forms including gray leaf spot isolates, but were largely absent in the rice blast isolates. The absence of MoTeRs in rice blast isolates, which are relatively stable by comparison, suggested that the telomere instability in gray leaf spot isolates could be due to MoTeRs. Analyzing spontaneous alterations in telomere restriction fragment profiles of asexual progeny revealed that MoTeRs were involved. Expansion and contraction of MoTeR arrays were observed and account for some telomere restriction profile changes. New telomere formation in asexual progeny followed by MoTeR addition was also observed. Based on this evidence, MoTeRs are largely responsible for the high variability of telomere restriction profiles observed in GLS isolates.
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鳥丸, 猛., and Takeshi TORIMARU. "クローンを形成する雌雄異株低木ヒメモチにおけるクローン多様性と遺伝的変異." 名古屋大学農学部付属演習林, 2005. http://hdl.handle.net/2237/8623.

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Gu, Hongcang. "GENETIC DIVERSITY AND SYMPTOM SEVERITY DETERMINANTS OF BEAN POD MOTTLE VIRUS." UKnowledge, 2004. http://uknowledge.uky.edu/gradschool_diss/441.

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Bean pod mottle virus (BPMV), a member of the genus Comovirus in the family Comoviridae, is widespread in the major soybean-growing areas in the United States. Soybean yield losses of 10-40% have been reported as a consequence of BPMV infection. The complete nucleotide sequences of two strains, K-Ha1 and K-Ho1, were determined. Field isolates of BPMV were classified into two distinct subgroups (I and II) based on slot blot hybridization and sequence analyses. Full-length cDNA clones from which infectious transcripts can be produced were constructed for strains K-G7, K-Ho1 and K-Ha1. Whereas strains K-Ha1 and K-G7 induced mild or moderate symptoms in infected soybean plants, strain K-Ho1 produced very severe symptoms. Symptom severity was mapped to RNA1. Chimeric RNA1 constructs were generated by exchanging full or partial coding regions of the five RNA1-encoded mature proteins between the full-length cDNA clones of the three RNA1s and the resultant transcripts were inoculated onto soybean. The results showed that the coding regions of the protease co-factor (Co-pro) and the putative helicase (Hel) are determinants of symptom severity. Although symptom severity correlated well with accumulation of viral RNA, neither the Co-pro nor Hel protein could be demonstrated as a suppressor of RNA silencing. Furthermore, separate expression of the Co-pro or Hel proteins from a PVX vector induced necrosis on the inoculated leaves of Nicotiana benthamiana. Characterization of BPMV K-Ho1 indicated that it is a diploid reassortant, containing two distinct types of RNA1s and one type of RNA2. Examination of field isolates from various locations in the United States and Canada revealed that diploid reassortants are of frequent occurrence in natural populations of BPMV. The vary severe symptoms induced by BPMV K-Ho1 can be mimicked by inoculation of plants with a mixture of RNA1 transcripts from two distinct strain subgroups and RNA2 transcript from either subgroup. Plants inoculated with a mixture of transcripts containing two types of RNA1 from the same strain subgroup did not produce very severe symptoms. These are due to interactions between two distinct types of RNA1s. At present, no soybean cultivars with resistance to BPMV are commercially available. Therefore, the feasibility of cross protection as an alternative disease management strategy was studied. Two mild strains of BPMV (K-Da1 and K-Ha1), belonging to subgroup II, were tested for their ability to protect infected plants against a severe strain (K-Ho1). Inoculation of the soybean cultivar Essex on the primary leaves with either of the two mild strains conferred complete protection against challenge inoculation with the severe strain K-Ho1, regardless of the timing of challenge inoculation. Cross-protection was evident regardless of whether virions or BPMV-RNA were used as inocula. Cross protection was independent of the soybean cultivar used and method of virus inoculation, sap-inoculation or by the bean leaf beetle, vector of BPMV. Protection was complete and durable.
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Books on the topic "Clonal and genetic diversity"

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Barnes, Jennifer L. Genetic diversity, gene flow and clonal structure of the Salmon River populations of MacFarlane's Four O'Clock Mirabilis Macfarlanei (Nyctaginaceae). Boise, Idaho: Bureau of Land Management, Idaho State Office, 1997.

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Steele, E. J. Lamarck's signature: How retrogenes are changing Darwin's natural selection paradigm. Reading, Mass: Perseus Books, 1998.

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L, Mahoney Conner, and Springer Douglas A, eds. Genetic diversity. Hauppauge, NY: Nova Science Publishers, 2009.

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Caliskan, Mahmut. Genetic diversity in microorganisms. Rijeka, Croatia: InTech, 2012.

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Amaya, Julian A. Cervantes, and Miguel M. Franco Jimenez. Genetic diversity: New research. Hauppauge, N.Y: Nova Science Publisher's, Inc., 2011.

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Çalişkan, Mahmut. Genetic diversity in plants. Rijeka, Croatia: InTech, 2012.

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National Research Council (U.S.). Committee on Human Genome Diversity. and National Research Council (U.S.). Commission on Life Sciences., eds. Evaluating human genetic diversity. Washington, D.C: National Academy Press, 1997.

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Project, California Agricultural Lands, ed. Biotechnology and genetic diversity. San Francisco, CA: California Agricultural Lands Project, 1985.

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Jan, Engels, ed. Managing plant genetic diversity. New York: CABI Pub., 2002.

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Holland, John J., ed. Genetic Diversity of RNA Viruses. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-77011-1.

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Book chapters on the topic "Clonal and genetic diversity"

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Roux, Nicolas, Rachel Chase, Ines van den Houwe, Chih-Ping Chao, Xavier Perrier, Jean-Pierre Jacquemoud-Collet, Julie Sardos, and Mathieu Rouard. "Somaclonal variation in clonal crops: containing the bad, exploring the good." In Mutation breeding, genetic diversity and crop adaptation to climate change, 355–65. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0037.

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Abstract Somaclonal variation describes random cellular changes in plants regenerated through tissue culture. It occurs in certain crops that undergo micropropagation and has been recorded in different explant sources, from leaves and shoots to meristems and embryos. In banana (Musa spp.), a clonal crop conserved in vitro, somaclonal variation has been observed after prolonged periods in tissue culture, resulting from an increase in subcultures performed on a given clone. According to scientific literature, variants, or off-types, often show characteristics such as abnormal growth and flower or fruit defects in frequencies ranging from 1% to 32%. This variation poses a problem for gene bank managers, whose mandate is to maintain the genetic integrity of their collections for research and breeding. In the case of the Bioversity International Musa Germplasm Transit Centre (ITC), stress during the in vitro process is minimized by various techniques and plants are regenerated after 10 years, making it a long and costly process. Identifying somaclonal variation at an early stage would be an ideal solution; however, this requires suitable molecular markers. Recent studies revealed that techniques such as direct DNA sequencing and single nucleotide polymorphisms (SNPs) are able to detect the underlying factors of somaclonal variation and are becoming more accessible. On the other hand, somaclonal variation can be beneficial as it allows the natural development of new varieties and supplies genetic stocks used for future genetic studies. Harnessing the diversity of somaclones is easier, faster and cheaper compared with other methods of crop improvement, although it is also less predictable. So far, variants of crops such as apple, strawberry, potato and banana have been successfully adopted into global markets. In this chapter, we will discuss how to minimize the adverse effects of somaclonal variation while maximizing its benefits for greater crop diversity, with a particular focus on banana.
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Jankowicz-Cieslak, Joanna, Florian Goessnitzer, Sneha Datta, Altus Viljoen, Ivan Ingelbrecht, and Bradley J. Till. "Induced mutations for generating bananas resistant to Fusarium wilt tropical race 4." In Mutation breeding, genetic diversity and crop adaptation to climate change, 366–78. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0038.

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Abstract Bananas are a staple for more than 400 million people. Additionally, more than 16.5 million tonnes are exported, making it both an important food security and a cash crop. Productivity of Cavendish-type bananas is threatened by both abiotic and biotic stresses. The fact that triploid bananas are sterile, parthenocarpic and obligate vegetatively propagated makes them particularly susceptible to diseases, including Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (Foc TR4). This is because continual clonal propagation has led to loss of genetic diversity. Additionally, lack of meiosis limits methods for breeding. Foc TR4 has been devastating Cavendish bananas in South-east Asia but has recently also been reported from Queensland in Australia, the Middle East and Mozambique, thus threatening global banana production. To address this, we are performing mutagenesis of in vitro propagated bananas to broaden the genetic diversity in order to find new alleles conferring disease resistance. We have developed methods for efficient induction of mutations in isolated apical meristems from shoot tips using chemical mutagens and ionizing radiation. Mutation discovery methods have been adapted to recover mutations including single point mutations and large deletions spanning millions of base pairs. We have created approximately 5000 mutated lines for forward-genetic screens to identify TR4 resistance in greenhouse- evaluated material. A subset of ca. 500 in vitro plantlets was subjected to glasshouse-based screening using a virulent F. oxysporum isolate. To date, 23 lines showing altered resistance responses to Foc TR4 have been identified.
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Reisch, Christoph, and Sebastian Scheitler. "Disturbance by mowing affects clonal diversity: the genetic structure of Ranunculus ficaria (Ranunculuaceae) in meadows and forests." In Herbaceous Plant Ecology, 335–43. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-90-481-2798-6_28.

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Konzen, Enéas Ricardo, Luciano Cesar Pozzobon, Denys Matheus Santana Costa Souza, Sérgio Bruno Fernandes, Wellington Ferreira Campos, Gilvano Ebling Brondani, Dulcinéia de Carvalho, and Siu Mui Tsai. "Molecular Markers in Bamboos: Understanding Reproductive Biology, Genetic Structure, Interspecies Diversity, and Clonal Fidelity for Conservation and Breeding." In Biotechnological Advances in Bamboo, 33–62. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-1310-4_2.

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Vanoverbeke, J., and L. De Meester. "Among-populational genetic differentiation in the cyclical parthenogen Daphnia magna (Crustacea, Anomopoda) and its relation to geographic distance and clonal diversity." In Cladocera: the Biology of Model Organisms, 135–42. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-4964-8_15.

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Bastianel, Marinês, Vera L. N. P. Barros, Augusto Tulmann Neto, Paulo S. Souza, Rose M. Pio, and Rodrigo R. Latado. "Induction and selection of mandarin mutants with fruits containing low number of seeds." In Mutation breeding, genetic diversity and crop adaptation to climate change, 379–85. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0039.

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Abstract The Brazilian citrus industry has a worldwide presence for production and export of sweet orange juice, but it has little contribution to the production of fruits for the fresh fruit market. One requirement of this market is the production of seedless fruits. The Fremont IAC 543 mandarin produces fruits with good commercial qualities, large numbers of seeds (10-12), and plants with resistance to Alternaria brown spot (ABS), an important disease present in several countries. The objective of this work was to induce and select mutants of Fremont IAC 543 mandarin with seedless fruits or fruits with a low number of seeds, using gamma-ray induced mutagenesis. In vivo buds were irradiated with doses of 20 and 30 Gy of gamma-rays. After irradiation and grafting of 2000 in vivo buds with each mutagenic dose, 4000 plants were produced and planted in an experimental field. During development of these plants, they were pruned several times allowing only the development of M1V4 branches or more advanced ones (without new grafting). A total of 32 branches were selected during the harvesting period because they produced seedless fruits and nine mutant clones were selected after another vegetative multiplication. Fruit and juice qualities, including seed number of the fruits, were evaluated in a further experiment including six mutants and a control. The results obtained showed that all mutants produced fruits with a lower number of seeds (between 3.7 and 9.1 seeds per fruit) in relation to the control (22.0 seeds per fruit), but without the existence of other alterations (fruit metric and chemical characteristics of the juice). All selected mutants (nine) are participating in advanced agronomic evaluation experiments, with a greater number of replicates and several local checks, in order to evaluate commercial yield, presence of chimeras, disease resistance and organoleptic quality of the fruits.
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Morales, Yonis, and Rolando Grajeda. "Virulence genes of new population of coffee rust (Hemileia vastatrix) affecting coffee variety 'Lempira', in Honduras; resistant and susceptible varieties." In Mutation breeding, genetic diversity and crop adaptation to climate change, 338–43. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0035.

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Abstract The coffee variety 'Lempira', released in Honduras in 1998, was classified 100% resistant to races I and II of coffee rust identified by Portugal's Centre for Research into Coffee Rusts (Centro de Investigação das Ferrugens do Cafeeiro) (CIFC) in 1997. However, since 2007, the disease has been reported in seed foundation plots and producer farms, the most recent epidemic report being in April 2016 in Vegas de Jalan, Juticalpa Olancho, affecting 210 ha. Since this variety constitutes 45% of the cultivated area under coffee in the country, there is a need to identify the virulence genes of the new strain and to determine the resistance and susceptibility of other cultivated varieties. For these purposes, mass samples of rust were inoculated on leaf discs of the differential clones 1343/269, 110/5, 147/1, 152/3, 33/1, 419/20, 832/1 and 832/2, together with 87/1, 1006/10, 420/10 and 420/2 from the Federal University of Vicosa, as well as on the two main cultivated resistant varieties ('Parainema' and 'IHCAFE- 90'), and seven promising genotypes, under controlled temperature conditions and relative humidity. After 20-60 days of inoculation, seven virulence genes were identified (v1, v2, v4, v5, v6, v7, v9), of which v1, v4, v6, v7 and v9 had not been reported in Honduras previously. It is inferred that this rust population arose by recombination of race v5 with v6, v7 or v9. Races with 3, 4, 5, 6 or 7 virulence determinants were identified as the most complex and aggressive strains described but they lacked the v3 and v8 determinants. In addition, it was found that 'Parainema', 'H27', 'T5296-170', 'Central American', 'Pacamara yellow' and 'Anacafe-14' are resistant because they possess the SH8 gene, absent from 'Lempira'. 'IHCAFE-90' and 'Obatá' showed 20% susceptibility, and 'Ruiru 11' was susceptible. The results reveal the diversity of rust virulence genes in Honduras and emphasize the importance of the SH3 and SH8 genes as sources of resistance.
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Thomas, Richard. "Genetic Diversity." In Global Biodiversity, 1–6. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2282-5_1.

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Ramírez, Fernando, and Thomas Lee Davenport. "Genetic Diversity." In Uchuva (Physalis peruviana L.) Reproductive Biology, 161–65. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-66552-4_11.

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Wellband, Kyle, Shauna M. Baillie, Paul Bentzen, and Louis Bernatchez. "Genetic Diversity." In The Lake Charr Salvelinus namaycush: Biology, Ecology, Distribution, and Management, 119–65. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-62259-6_5.

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Conference papers on the topic "Clonal and genetic diversity"

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Beutner, D., N. Abedpour, G. Bosco, V. Tischler, M. Bergwelt-Baildon, M. Pfeifer, and A. Lechner. "Clonal Evolution in head and neck squamous cell carcinoma? Temporal changes of genetic diversity." In Abstract- und Posterband – 89. Jahresversammlung der Deutschen Gesellschaft für HNO-Heilkunde, Kopf- und Hals-Chirurgie e.V., Bonn – Forschung heute – Zukunft morgen. Georg Thieme Verlag KG, 2018. http://dx.doi.org/10.1055/s-0038-1639982.

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Sholihin. "Genetic diversity, heritability and path analysis of sweet cassava promising clone." In INTERNATIONAL CONFERENCE ON ENVIRONMENTAL, MINING, AND SUSTAINABLE DEVELOPMENT 2022. AIP, 2024. http://dx.doi.org/10.1063/5.0198941.

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Uzan, G., A. Lajmanovich, M. H. Prandini, Ph Frachet, A. Duperray, and G. Marguerie. "MOLECULAR CLONING OF PLATELET GPIIb FROM HEL CELLS AND HUMAN MEGAKARYOCYTES." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643960.

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Platelet GP IIb-IIIa is an heterodimer which functions as a receptor for fibrinogen, fibronectin and Von Willebrand factor and is implicated in platelet adhesive reactions. To study the structure function relationship of this glycoprotein, a recombinant DNA approach was initiated. cDNA expression libraries were constructed in » gtll vector, from erythro-leukemia cells (HEL) and megakaryocytes mRNA. The human megakaryocytes were isolated from patients with chronic myeloid leukemia. The HEL library was initially screened with polyclonal antibodies anti GPIIb IIIa. One clone, λIIbI, containing a 1.65 kbp insert reacted with a panel of different polyclonal antibodies anti GPIIb IIIa and a monoclonal antibody anti GPIIb. To further characterize this clone the synthesis of the fusion protein was induced by IPTG. The bacterial protein was then blotted onto nitro cellulose and incubated with antisera anti GPIIb-IIIa. Antibodies that specifically bound with the fusion protein were eluted and tested on platelet membrane extracts. The selected antibodies produced a positive signal at the GPIIb position similar to the signal produced by the monoclonal antibody anti GPIIb on the same membrane extract. Finally on western blotting, a protein of Mr= 170kD reacted with the monoclonal antibody anti GPIIb. λIIbI insert was used to screen the megakaryocyte library and 3 clones, λIIb2,λIIb3 and λIIb4 were isolated. The size of HEL cells and megakaryocytes GPIIb mRNA was estimated by northern blotting. Only one species of 3.9 kb was identified in both cells. The four different clones accounted for 50% of the coding sequence of this mRNA.Sequencing of these cDNAs indicated that the plasmatic domain of GPIIb contains a cystein rich region. The sequence of these clones will allow the study of the adhesines genetic diversity in different cellular systems.
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Ludwig, Simone A. "Clonal selection based fuzzy C-means algorithm for clustering." In GECCO '14: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2014. http://dx.doi.org/10.1145/2576768.2598270.

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Ludwig, Simone A. "Clonal selection based genetic algorithm for workflow service selection." In 2012 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2012. http://dx.doi.org/10.1109/cec.2012.6256465.

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Hu, Yubo, and Tiejun Chen. "Multi-objective Optimization Algorithm Based on Clonal Selection." In 2008 Second International Conference on Genetic and Evolutionary Computing (WGEC). IEEE, 2008. http://dx.doi.org/10.1109/wgec.2008.42.

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Bulanova, Nina, Arina Buzdalova, and Maxim Buzdalov. "Fitness-Dependent Hybridization of Clonal Selection Algorithm and Random Local Search." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2908996.

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WANG, WILLIAM S. Y. "HUMAN DIVERSITY AND LANGUAGE DIVERSITY." In Genetic, Linguistic and Archaeological Perspectives on Human Diversity in Southeast Asia. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812810847_0002.

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Xu, Xiaowen, and Weibin Chen. "Towards improved Clonal Selection Algorithm by increasing the diversity degree of antibody." In 2011 6th IEEE Joint International Information Technology and Artificial Intelligence Conference (ITAIC). IEEE, 2011. http://dx.doi.org/10.1109/itaic.2011.6030336.

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Pierrot, Thomas, Valentin Macé, Felix Chalumeau, Arthur Flajolet, Geoffrey Cideron, Karim Beguir, Antoine Cully, Olivier Sigaud, and Nicolas Perrin-Gilbert. "Diversity policy gradient for sample efficient quality-diversity optimization." In GECCO '22: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2022. http://dx.doi.org/10.1145/3512290.3528845.

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Reports on the topic "Clonal and genetic diversity"

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Michelmore, Richard, Eviatar Nevo, Abraham Korol, and Tzion Fahima. Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7573075.bard.

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Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.
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Sherman, A., D. N. Kuhn, Y. Cohen, R. Ophir, and R. Goenaga. Exploring the polyembryonic seed trait in mango as a basis for a biotechnology platform for fruit tree crops. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134176.bard.

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Mango is one of the most important fruit crops. However, the biology of this fruit tree is under studied. The lack of genetic and genomic resources has limited progress in mango research and breeding. Several research groups have recently started developing genomic tools for mango by creating transcriptome and genomic data. Sexual reproduction in plants is the main pathway for the creation of new genetic combinations. In modern agriculture, breeders exploit the genetic diversity generated through sexual reproduction to develop elite cultivars; however, these cultivars require genetic stabilization before they are suitable for mass propagation for uniform crop production. In heterozygous plants such as fruit trees, vegetative propagation (cloning) is the primary path for the propagation of genetically uniform plants. Another natural plant mechanism that can create genetically uniform plants (clones) is apomixes. Apomixis is defined as asexual reproduction through seeds that lead to the production of clonal progeny whose genotype is identical to that of the mother plant. In fruit crops like citrus and mango, sporophytic apomixes result in polyembryony, where seeds contain multiple embryos, one of which is sexually originated, and the others are clones of the mother tree. As part of this research, the reference genome of mango was established as a basic platform for mango breeding and research. It was used to map two important mango traits fruit size and polyembryony. The draft genome 'Tommy Atkins' sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins,' supplemented by 10X Genomics long read sequencing to improve the initial assembly. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango. The availability of a genome enables the genetic dissection of important traits. We demonstrated the utility of the genome assembly and the 'Tommy Atkins' x 'Kensington Pride' map by analyzing fruit weight phenotypic data and identifying two QTLs for this trait.
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Shannon Bayliss, Shannon Bayliss. Can genetic diversity preserve a friendship? Experiment, January 2014. http://dx.doi.org/10.18258/1855.

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Akbulut, Mustafa, Mehmet Polat, Sezai Ercisli, and Karim Sorkheh. Genetic Diversity of Prunus angustifolia Accessions. "Prof. Marin Drinov" Publishing House of Bulgarian Academy of Sciences, October 2019. http://dx.doi.org/10.7546/crabs.2019.10.07.

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Steffenson, B. J., I. Mayrose, Gary J. Muehlbauer, and A. Sharon. ing and comparative sequence analysis of powdery mildew and leaf rust resistance gene complements in wild barley. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134173.bard.

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Our overall, long-term goal is to exploit the genetic diversity present in cereal wild relatives for the development of cultivars with durable disease resistance. Our specific objectives for this proposal were to: 1) Utilize Association Genetics Resistance Gene Enrichment Sequencing (AgRenSeq) to identify and clone powdery mildew and leaf rust resistance gene complements in wild barley and 2) Conduct comparative sequence analyses of the cloned resistance genes to elucidate the basis of their specificity and evolution. The deployment of resistant cultivars is the most effective, economically efficient, and environmentally sound means of controlling plant diseases, especially in small grain cereals. The systems selected for study in this proposal are barley (Hordeum vulgare ssp. vulgare, Hvv), its wild progenitor (Hordeum vulgare ssp. spontaneum, Hvs) and the powdery mildew (Blumeria graminis f. sp. hordei, Bgs) and leaf rust (Puccinia hordei, Ph) pathogens. We compiled a diverse panel of Hvs accessions (the Wild Barley Diversity Collection or WBDC; N = 314) from across its native range and evaluated it to 40 isolates of Bgs and 12 isolates of Ph. We obtained genomic DNA sequences enriched for Nucleotide Binding Site-Leucine Rich Repeat (NLR) type resistance genes for 203 WBDC accessions, plus cultivar Morex for which the first reference genome sequence of barley was based. We assembled the 250 bp Illumina sequencing reads into contigs using CLC assembly cell. From this effort, we successfully assembled the sequences of 201 WBDC accessions plus Morex and used NLR Parser to identify contigs containing NLR genes. AgRenSeq was then used to identify k-mers (short oligonucleotide sequences of length k) that were associated with resistance to each isolate of the two pathogens. This analysis was performed individually for all WBDC accessions and each individual pathogen race (9,898 host accession x pathogen race combinations). We visualized the results from these analyses in Manhattan plots and identified 311 and 144 peaks for powdery mildew and leaf rust resistance, respectively. The next step in the analysis was to identify the contigs associated with the peaks in the Manhattan plots. BLAST (Basic Local Alignment Search Tool) searches were employed to identify closely related contigs in other WBDC accessions or in Morex. We identified two candidate R genes that were only present in resistant WBDC accessions. One of these was present in seven WBDC lines and was associated with resistance to four leaf rust isolates. BLAST analysis of this gene revealed that it was Rph15, one of the most widely effective leaf rust resistance genes reported in Hordeum. This gene was cloned and functionally validated in association with our Australian colleagues (Cheng et al., 2021). We are currently in the process of cloning six of other resistance genes: four for powdery mildew and two for leaf rust. As the contigs do not contain much of the promoter sequences, we have employed a genome walking approach to identify 2,500 bp of promoter sequence. To speed up and simplify the cloning of resistance genes from the WBDC, the PI established the International Wild Barley Sequencing Consortium (IWBSC; https://iwbsc.umn.edu/) comprised of over 60 researchers from 14 different countries and raised over $150,000 through crowdfunding to pay for 10X depth sequence coverage. Genome-wide association study (GWAS) of whole genome sequencing (WGS) data identified extremely strong and clear signals of association for several resistance genes which will facilitate gene cloning in concert with a wild barley pan-genome currently under construction. The cloning of multiple resistance gene can facilitate the development of durably resistant cultivars by inserting, through transgenesis, cassettes of multiple resistance genes.
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Knowlton, Nancy. Genetic Diversity and Stability of Coral - Algal Symbiosis. Fort Belvoir, VA: Defense Technical Information Center, March 1999. http://dx.doi.org/10.21236/ada361549.

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Ashraf, Quamrul, and Oded Galor. Genetic Diversity and the Origins of Cultural Fragmentation. Cambridge, MA: National Bureau of Economic Research, January 2013. http://dx.doi.org/10.3386/w18738.

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Fahima, Tzion, and Jorge Dubcovsky. Map-based cloning of the novel stripe rust resistance gene YrG303 and its use to engineer 1B chromosome with multiple beneficial traits. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598147.bard.

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Research problem: Bread wheat (Triticumaestivum) provides approximately 20% of the calories and proteins consumed by humankind. As the world population continues to increase, it is necessary to improve wheat yields, increase grain quality, and minimize the losses produced by biotic and abiotic stresses. Stripe rust, caused by Pucciniastriiformisf. sp. tritici(Pst), is one of the most destructive diseases of wheat. The new pathogen races are more virulent and aggressive than previous ones and have produced large economic losses. A rich source for stripe-rust resistance genes (Yr) was found in wild emmer wheat populations from Israel. Original Project goals: Our long term goal is to identify, map, clone, characterize and deploy in breeding, novel wild emmer Yr genes, and combine them with multiple beneficial traits. The current study was aiming to map and clone YrG303 and Yr15, located on chromosome 1BS and combine them with drought resistance and grain quality genes. Positional cloning of YrG303/Yr15: Fine mapping of these genes revealed that YrG303 is actually allelic to Yr15. Fine genetic mapping using large segregating populations resulted in reduction of the genetic interval spanning Yr15 to less than 0.1 cM. Physical mapping of the YrG303/Yr15 locus was based on the complete chromosome 1BS physical map of wheat constructed by our group. Screening of 1BS BAC library with Yr15 markers revealed a long BAC scaffold covering the target region. The screening of T. dicoccoidesaccession-specific BAC library with Yr15 markers resulted in direct landing on the target site. Sequencing of T. dicoccoidesBAC clones that cover the YrG303/Yr15 locus revealed a single candidate gene (CG) with conserved domains that may indicate a role in disease resistance response. Validation of the CG was carried out using EMS mutagenesis (loss-of- function approach). Sequencing of the CG in susceptible yr15/yrG303 plants revealed three independent mutants that harbour non-functional yr15/yrG303 alleles within the CG conserved domains, and therefore validated its function as a Pstresistance gene. Evaluation of marker-assisted-selection (MAS) for Yr15. Introgressions of Yr15 into cultivated wheat are widely used now. Recently, we have shown that DNA markers linked to Yr15 can be used as efficient tools for introgression of Yr15 into cultivated wheat via MAS. The developed markers were consistent and polymorphic in all 34 tested introgressions and are the most recommended markers for the introgression of Yr15. These markers will facilitate simultaneous selection for multiple Yr genes and help to avoid escapees during the selection process. Engineering of improved chromosome 1BS that harbors multiple beneficial traits. We have implemented the knowledge and genetic resources accumulated in this project for the engineering of 1B "super-chromosome" that harbors multiple beneficial traits. We completed the generation of a chromosome including the rye 1RS distal segment associated with improved drought tolerance with the Yr gene, Yr15, and the strong gluten allele 7Bx-over-expressor (7Bxᴼᴱ). We have completed the introgression of this improved chromosome into our recently released variety Patwin-515HP and our rain fed variety Kern, as well as to our top breeding lines UC1767 and UC1745. Elucidating the mechanism of resistance exhibited by Yr36 (WKS1). The WHEAT KINASE START1 (WKS1) resistance gene (Yr36) confers partial resistance to Pst. We have shown that wheat plants transformed with WKS1 transcript are resistant to Pst. WKS1 is targeted to the chloroplast where it phosphorylates the thylakoid-associatedascorbateperoxidase (tAPX) and reduces its ability to detoxify peroxides. Based on these results, we propose that the phosphorylation of tAPX by WKS1 reduces the ability of the cells to detoxify ROS and contributes to cell death. Distribution and diversity of WKS in wild emmer populations. We have shown that WKS1 is present only in the southern distribution range of wild emmer in the Fertile Crescent. Sequence analysis revealed a high level of WKS1 conservation among wild emmer populations, in contrast to the high level of diversity observed in NB-LRR genes. This phenomenon shed some light on the evolution of genes that confer partial resistance to Pst. Three new WKS1 haplotypes displayed a resistance response, suggesting that they can be useful to improve wheat resistance to Pst. In summary, we have improved our understanding of cereals’ resistance mechanisms to rusts and we have used that knowledge to develop improved wheat varieties.
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9

Malek Al-Marayati, Malek Al-Marayati. Genetic diversity across the Atlantic in a red seaweed. Experiment, January 2018. http://dx.doi.org/10.18258/10700.

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10

Research Institute (IFPRI), International Food Policy. Genetic resource policies what is diversity worth to farmers? Washington, DC: International Food Policy Research Institute, 2005. http://dx.doi.org/10.2499/ifpriragbriefs13-18.

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