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Статті в журналах з теми "Nucleotide sequence diversity"
1
Kami, James A., and Paul Gepts. "Phaseolin nucleotide sequence diversity in Phaseolus. I. Intraspecific diversity in Phaseolus vulgaris." Genome 37, no. 5 (October 1, 1994): 751–57. http://dx.doi.org/10.1139/g94-107.
Повний текст джерелаАнотація:
Most information about the molecular biology of phaseolin, the major seed storage protein in Phaseolus vulgaris, has been obtained from the T-type phaseolin, which is characteristic of the Andean gene pool of the species. In the work reported here, two cDNA clones for the S-type phaseolin representing the other major, Middle American gene pool were isolated and sequenced. Analysis of the DNA sequences revealed the presence of two subtypes of S phaseolin, α and β, depending on the presence or absence, respectively, of a 27-bp direct repeat. These are similar to the α- and β-phaseolin subtypes found in the Andean, T phaseolin; however, the additional 15-bp direct repeat also found in the T α-phaseolin gene type was apparently absent from the S α-phaseolin genes. The overall sequence identity was greater between the α or β subtypes of different gene pools than between the a or p subtypes within gene pools. This implies that the gene subtypes were formed prior to the formation of the two major gene pools of P. vulgaris. Analysis of the putative amino acid sequence revealed that both the 'Sanilac' phaseolin subtypes contained an additional methionine, however, not at the same site. This opens the possibility of increasing the nutritionally limiting methionine level in phaseolin either through protein engineering or by screening accessions for recombinant phaseolin sequences that combine both substitutions.Key words: seed storage protein, multigene family, direct repeat.
2
Suerbaum, Sebastian, Marc Lohrengel, Agnes Sonnevend, Florian Ruberg, and Manfred Kist. "Allelic Diversity and Recombination inCampylobacter jejuni." Journal of Bacteriology 183, no. 8 (April 15, 2001): 2553–59. http://dx.doi.org/10.1128/jb.183.8.2553-2559.2001.
Повний текст джерелаАнотація:
ABSTRACT The allelic diversity and population structure ofCampylobacter jejuni were studied by multilocus nucleotide sequence analysis. Sequences from seven housekeeping genes were obtained from 32 C. jejuni isolates isolated from enteritis patients in Germany, Hungary, Thailand, and the United States. Also included was strain NCTC 11168, the complete genomic sequence of which has recently been published. For all loci analyzed, multiple strains carried identical alleles. The frequency of synonymous and nonsynonymous sequence polymorphisms was low. The number of unique alleles per locus ranged from 9 to 15. These alleles occurred in 31 different combinations (sequence types), so that all but two pairs of strains could be distinguished from each other. Sequences were analyzed for evidence of recombination by the homoplasy test and split decomposition. These analyses showed that intraspecific recombination is frequent in C. jejuni and has generated extensive diversity of allelic profiles from a small number of polymorphic nucleotides.
3
Garcia Machado, Erik, Mario Oliva Suarez, Nicole Dennebouy, Monique Monnerot, and Jean-Claude Mounolou. "Mitochondrial 16S-rRna Gene of Two Species of Shrimps: Sequence Variability and Secondary Structure." Crustaceana 65, no. 3 (1993): 279–86. http://dx.doi.org/10.1163/156854093x00711.
Повний текст джерелаАнотація:
AbstractPart of the mitochondrial 16S-ribosomal RNA gene (around 400 nucleotides) of Penaeus notialis and Penaeus schmitti has been amplified and sequenced. The comparison of sequences reveals an 11% nucleotide divergence between the two species. When compared with that of the homologous fragment in Artemia salina and Drosophila yakuba, the secondary structure appears well conserved in spite of high nucleotide divergence due to numerous substitutions and additions/deletions. Sequences have been obtained for six individuals of P. notialis belonging to the same population, their comparison shows a 0.7% nucleotide diversity.
4
Geering, A. D. W., L. A. McMichael, R. G. Dietzgen, and J. E. Thomas. "Genetic Diversity Among Banana streak virus Isolates from Australia." Phytopathology® 90, no. 8 (August 2000): 921–27. http://dx.doi.org/10.1094/phyto.2000.90.8.921.
Повний текст джерелаАнотація:
Banana streak virus (BSV) is an important pathogen of bananas and plantains (Musa spp.) throughout the world. We have cloned and sequenced part of the genomes of four isolates of BSV from Australia, designated BSV-RD, BSV-Cav, BSV-Mys, and BSV-GF. These isolates originated from banana cvs. Red Dacca, Williams, Mysore, and Goldfinger, respectively. All clones contained a sequence covering part of open reading frame III and the intergenic region of the badnavirus genome. The sequences were compared with those of other badnaviruses, including BSV-Onne, a previously characterized isolate from Nigeria. The BSV-RD sequence was virtually identical to that of BSV-Onne, differing by only two nucleotides over 1,292 bp. However, BSV-Cav, -Mys, and -GF were divergent in nucleotide sequence. Phylogenetic analyses using conserved sequences in the ribonuclease H domain revealed that all BSV isolates were more closely related to each other than to any other badnavirus. BSV-Cav was most closely related to BSV-Onne, and there was 95.1% identity between the two amino acid sequences. Other relationships between the BSV isolates were less similar, with sequence identities ranging from 66.4 to 78.2%, which is a magnitude comparable to the distance between some of the recognized badnavirus species. Immunocapture-polymerase chain reaction assays have been developed, allowing specific detection and differentiation of the four isolates of BSV.
5
Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli, D. R. Grimm, S. M. Hyatt, E. W. Fickus, N. D. Young, and P. B. Cregan. "Single-Nucleotide Polymorphisms in Soybean." Genetics 163, no. 3 (March 1, 2003): 1123–34. http://dx.doi.org/10.1093/genetics/163.3.1123.
Повний текст джерелаАнотація:
Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.
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Begum, RA, MT Alam, H. Jahan, and MS Alam. "Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh." Journal of Biodiversity Conservation and Bioresource Management 5, no. 1 (July 13, 2019): 25–30. http://dx.doi.org/10.3329/jbcbm.v5i1.42182.
Повний текст джерелаАнотація:
Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular.
J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30
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Ren, Xifeng, Yonggang Wang, Songxian Yan, Dongfa Sun, and Genlou Sun. "Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley." Genome 57, no. 4 (April 2014): 239–44. http://dx.doi.org/10.1139/gen-2014-0039.
Повний текст джерелаАнотація:
Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.
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Zhang, Nian-Zhang, Ying Xu, Si-Yang Huang, Dong-Hui Zhou, Rui-Ai Wang, and Xing-Quan Zhu. "Sequence Variation inToxoplasma gondii rop17Gene among Strains from Different Hosts and Geographical Locations." Scientific World Journal 2014 (2014): 1–4. http://dx.doi.org/10.1155/2014/349325.
Повний текст джерелаАнотація:
Genetic diversity ofT. gondiiis a concern of many studies, due to the biological and epidemiological diversity of this parasite. The present study examined sequence variation in rhoptry protein 17 (ROP17) gene amongT. gondiiisolates from different hosts and geographical regions. Therop17gene was amplified and sequenced from 10T. gondiistrains, and phylogenetic relationship among theseT. gondiistrains was reconstructed using maximum parsimony (MP), neighbor-joining (NJ), and maximum likelihood (ML) analyses. The partialrop17gene sequences were 1375 bp in length and A+T contents varied from 49.45% to 50.11% among all examinedT. gondiistrains. Sequence analysis identified 33 variable nucleotide positions (2.1%), 16 of which were identified as transitions. Phylogeny reconstruction based onrop17gene data revealed two major clusters which could readily distinguish Type I and Type II strains. Analyses of sequence variations in nucleotides and amino acids among these strains revealed high ratio of nonsynonymous to synonymous polymorphisms (>1), indicating thatrop17shows signs of positive selection. This study demonstrated the existence of slightly high sequence variability in therop17gene sequences amongT. gondiistrains from different hosts and geographical regions, suggesting thatrop17gene may represent a new genetic marker for population genetic studies ofT. gondiiisolates.
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Raphael, Brian H., Mallory J. Choudoir, Carolina Lúquez, Rafael Fernández, and Susan E. Maslanka. "Sequence Diversity of Genes Encoding Botulinum Neurotoxin Type F." Applied and Environmental Microbiology 76, no. 14 (May 28, 2010): 4805–12. http://dx.doi.org/10.1128/aem.03109-09.
Повний текст джерелаАнотація:
ABSTRACT Botulism due to type F botulinum neurotoxin (BoNT/F) is rare (<1% of cases), and only a limited number of clostridial strains producing this toxin type have been isolated. As a result, analysis of the diversity of genes encoding BoNT/F has been challenging. In this study, the entire bont/F nucleotide sequences were determined from 33 type F botulinum toxin-producing clostridial strains isolated from environmental sources and botulism outbreak investigations. We examined proteolytic and nonproteolytic Clostridium botulinum type F strains, bivalent strains, including Bf and Af, and Clostridium baratii type F strains. Phylogenetic analysis revealed that the bont/F genes examined formed 7 subtypes (F1 to F7) and that the nucleotide sequence identities of these subtypes differed by up to 25%. The genes from proteolytic (group I) C. botulinum strains formed subtypes F1 through F5, while the genes from nonproteolytic (group II) C. botulinum strains formed subtype F6. Subtype F7 was composed exclusively of bont/F genes from C. baratii strains. The region of the bont/F5 gene encoding the neurotoxin light chain was found to be highly divergent compared to the other subtypes. Although the bont/F5 nucleotide sequences were found to be identical in strains harboring this gene, the gene located directly upstream (ntnh/F) demonstrated sequence variation among representative strains of this subtype. These results demonstrate that extensive nucleotide diversity exists among genes encoding type F neurotoxins from strains with different phylogenetic backgrounds and from various geographical sources.
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Ali, Shaymaa H., Jaladet M. S. Jubrael, and Caroline Bowsher. "Genetic diversity and nucleotide sequence analysis of powdery mildew marker and Vf2RAD resistant gene in apple (Malus domestica) land races." Innovaciencia Facultad de Ciencias Exactas, Físicas y Naturales 6, no. 1 (December 28, 2018): 1–10. http://dx.doi.org/10.15649/2346075x.460.
Повний текст джерелаАнотація:
Introduction: DNA sequencing-based methods and nucleotide sequence analysis have become the most common molecular approaches currently used for molecular typing purposes and phylogenetic diversity analysis. Methods: In this study, the nucleotide sequence variations of Powdery mildew resistance gene marker (CH03c02) and the apple scab resistance gene (Vf2RAD) beside phylogenetic diversity of seven apple landraces have been investigated. The two-locus have been successfully cloned and their nucleotide sequences were determined across all studied landraces. Results: Results of sequence alignment of the Powdery mildew resistant locus (CH03c02), compared with that of the published sequence of the same locus of Discovery genotype (HiDRAS), revealed that the nucleotide variations of this locus ranged from 1 to 28 nucleotide substitutions across all seven apple landraces. Whilst, the nucleotide variations of VF2RAD ranged from 2-8 nucleotide substitutions across all the investigated landraces. The highest genetic distance (0.062) was between Amara and Barwari. Whereas, the lowest genetic distance (0.0015) was found between each of the Lubnani, Rechard, Ispartal, and the Ahmadagha. The nucleotide sequences of the two loci were concatenated and implemented to build a Neighbor-Joining tree. The seven apple landraces were successfully grouped into two main genetic clusters (C1 and C2) in the phylogenetic tree. Conclusions: It can be concluded that the cloning approach used in the current study was found to be very successful and helpful for obtaining the full nucleotide sequences of these two loci. The investigated loci were displayed nucleotide variations among the studied landraces. And, finding of these variations was allowed the distinguishing and discrimination of these landraces.
Дисертації з теми "Nucleotide sequence diversity"
1
Ngwira, Patricia. "Nucleotide sequence diversity in maize and grass-infecting streak geminiviruses: A basis for nucleotide sequence classification and identification /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487945015618607.
Повний текст джерела
2
Fullerton, Stephanie Malia. "Allelic sequence diversity at the human beta-globin locus." Thesis, University of Oxford, 1994. http://ora.ox.ac.uk/objects/uuid:da897e20-7dae-4c77-9c4d-0be69cb024e1.
Повний текст джерела
3
Christensen, Shawn A. "Assessment of Chenopodium quinoa Willd. genetic diversity in the USDA and CIP-FAQ collections using SSR's and SNP's /." Diss., CLICK HERE for online access, 2005. http://contentdm.lib.byu.edu/ETD/image/etd1118.pdf.
Повний текст джерела
4
Geleta, Mulatu. "Genetic diversity, phylogenetics and molecular systematics of Guizotia Cass. (Asteraceae) /." Alnarp : Department of Plant Protection Biology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200727.pdf.
Повний текст джерела
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Robertson, Gail Alexandra. "Computerised methods for selecting a small number of single nucleotide polymorphisms that enable bacterial strain discrimination." Thesis, Queensland University of Technology, 2006. https://eprints.qut.edu.au/16284/1/Gail_Robertson_Thesis.pdf.
Повний текст джерелаАнотація:
The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net.
The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information.
Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered.
The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism.
A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.
6
Lawal, Zarah Yetunde. "The impact of immunosuppression on nucleotide sequence diversity in the first hypervariable region (HVR1) of hepatitis C virus (HCV)." Thesis, Open University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336980.
Повний текст джерела
7
Robertson, Gail Alexandra. "Computerised methods for selecting a small number of single nucleotide polymorphisms that enable bacterial strain discrimination." Queensland University of Technology, 2006. http://eprints.qut.edu.au/16284/.
Повний текст джерелаАнотація:
The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net. The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information. Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered. The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism. A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.
8
Pfeifer, Susanne. "Statistical challenges in the detection of mutation and variation using high throughput sequencing." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:e49ce2fa-aa2c-42d7-bb54-c63e50d14afb.
Повний текст джерелаАнотація:
The aim of this thesis is to obtain a better understanding of mutation rates within as well as between the genomes of humans and chimpanzees using data generated by high throughput sequencers. I will start with a review of the field and an overview of the technologies and protocols used to generate and analyse high throughput sequencing data. I apply some of the discussed techniques to show that there is evidence of a selective advantage of pathogenic de novo mutations in the Fibroblast Growth Factor Receptor 3 gene in the male germ line of humans. Furthermore, I use some of the methods to generate a map of genome-wide sequence variation in Western chimpanzees. Ever since Darwin [Darwin, 1871] and Huxley [Huxley, 1863] postulated more than a century ago that African great apes are our closest living evolutionary relatives, the study of chimpanzee individuals is of great scientific interest from an evolutionary point of view, as comparisons between the genomes of human and chimpanzee offer the potential to help to understand the molecular basis for similarities and differences between the two species. I use the generated data to explore the breadth of the nucleotide diversity in the chimpanzee genome in order to shed light on whether or not the local variation in mutation rate has been conserved since the divergence of the two species and to place human nucleotide diversity into perspective with an evolutionary closely related species. I explore the relationship of nucleotide diversity in chimpanzees with specific large-scale genome features to reveal a number of highly significant correlations which explain over 40% of the observed variation. I use data from the 1000 Genomes Project to examine the occurrence of ancestral polymorphisms shared between human and chimpanzee on a genome-wide scale. These ancestral polymorphisms do not only influence fine-scale divergence rates across the genome in very closely related species, they are also good candidates for regions under balancing selection and thus, they are a useful tool to study long-time population demographics and speciation. Using these variants, I postulate that long-term balancing selection may be more common than previously believed. I conclude with a discussion of the results contained in the body of the thesis and suggest a number of areas for future research.
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Manceau, Valérie. "Polymorphisme des séquences d'ADN mitochondrial dans le genre Capra : application à la conservation du bouquetin des Pyrénées (C. Pyrenaica)." Université Joseph Fourier (Grenoble ; 1971-2015), 1997. http://www.theses.fr/1997GRE10213.
Повний текст джерелаАнотація:
Le projet de reintroduction du bouquetin iberique (capra pyrenaica) sur le versant francais des pyrenees pose des questions de systematique. La systematique de l'espece capra pyrenaica et celle de l'ensemble du genre capra sont actuellement basees sur l'analyse des caracteres morphologiques. Au sein de l'espece iberique, quatre sous-especes dont une, c. P. Pyrenaica, typique des pyrenees sont definies. Ces systematiques sont cependant remises en question du fait de la plasticite des criteres morphologiques pris en compte. Afin de tester la position taxonomique du bouquetin iberique au sein du genre capra et celle de la sous-espece pyreneenne dans l'espece iberique, nous avons effectue une analyse phylogenetique de sequences partielles de l'adn mitochondrial (adnmt). Des portions de la region codant pour le cytochrome b et de la region de controle de l'adnmt ont ete etudiees. Les especes du genre ont ete echantillonnees majoritairement sous forme d'os preleves sur le terrain ou dans des musees. Les resultats de l'analyse phylogenetique confirment l'hypothese d'une domestication de la chevre a partir de populations d'aegagres d'iran et l'existence de deux formes bien differenciees de bouquetin a l'est et a l'ouest du caucase. En revanche, la monophylie du groupe des ibex (bouquetin des alpes, de siberie, de nubie ou d'abyssinie) est remise en question et donc la pertinence, dans ce cas, des criteres morphologiques pour etablir une phylogenie. Les haplotypes des bouquetins iberiques et des bouquetins alpins forment un clade monophyletique. De plus, la divergence nucleotidique moyenne entre les haplotypes pyreneens et les autres haplotypes iberiques est equivalente a la divergence moyenne entre les haplotypes iberiques et les haplotypes alpins. Ceci confirme l'existence d'une unite de conservation typique des pyrenees. Du fait de la presence de tres peu d'individus dans les pyrenees, nous suggerons cependant de renforcer cette population ou/et de reintroduire dans les pyrenees des individus provenant de la population la plus polymorphe ou de plusieurs populations iberiques.
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Gao, Xiaojiang. "Nucleotide sequence diversity of HLA class II genes in Australian Aborigines and populations of Asia-Oceania." Phd thesis, 1992. http://hdl.handle.net/1885/13687.
Повний текст джерелаАнотація:
The aim of this thesis was to investigate nucleotide
sequence diversity of HLA class II genes in Australian
Aborigines and indigenous peoples of Asia-Oceania. Nineteen
study populations represented eight major ethnic groups
including Australian Aborigines, Papua New Guinean
highlanders, coastal Melanesians, Polynesians, Micronesians,
Javanese, southern and northern Chinese, and a minority group
from northwestern China. Using PCR-based technologies, the
nucleotide sequence polymorphism in exon 2 DRB1, DRB3, DRB5,
DQA1 and DQB1 genes was examined in all these populations. The
DPB1 exon 2 polymorphism was examined in Australian Aborigines
and a Chinese population.
Six novel HLA class II alleles including four DRB1, one
DRB5 and one DPBl were discovered in this study by the
occurrence of unusual hybridization patterns in the PCR-SSO
typing procedure and were confirmed by DNA Sequencing. These
new alleles, DRB1*0412, 1408, 1409, 1410, DRB5*0203 and
DBP1*2201 have been recognized by the WHO Nomenclature
Committee. The nucleotide sequences and the deduced amino acid
sequences of the novel class II alleles indicated that
multiple molecular mechanisms were involved in generating
these alleles including point mutation and hypermutational
events of segmental transfer and intra-exonic recombination.
In two cases (DRB1*0412 and DRB1*1410), hypermutational events
have created unique peptide binding sites which are
drastically different from all their putative progenitor
molecules. Five of the six novel alleles were found in
Australian Aborigines and four novel DRB1 alleles were
detected in 45% of the Aboriginal individuals tested.
PCR-SSO typing revealed some HLA class II polymorphisms
previously difficult or impossible to detect with more
traditional typing techniques. Remarkable differences in the
V
class II HLA allele frequency distributions, especially in the
subtypes of major DR antigen groups, were observed between the
study populations. Australian Aborigines showed the most
divergent class II HLA profile; most of their DRB1 alleles did
not overlap with other study populations. PNG highlanders and
Javanese were highly homogeneous with quite restricted class
II HLA distributions. Other Oceanic populations of
Polynesians, Micronesians and coastal Melanesians were each
characterized with unique class II HLA distribution but shared
common features which indicated their historical ties.
Distinctive HLA distributions were observed between Chinese
populations from southern and northern China, while the
minority group from northwestern China demonstrated a mixed
ancestry of both Caucasoids and Orientals.
Further information came from the analysis of HLA-DR, -DQ
haplotypes. A total of 80 three-locus or four-locus DR-DQ
combinations including 16 DR2-related, 12 DR4-related, 11 DR5-
related, and 24 DR6-related haplotypes were inferred from the
study populations. Haplotype frequencies were used to
calculate genetic distances between these populations and to
reconstruct population phylogeny, which proved a sensitive
indicator of population affinities. The unusual linkage
relationships detected in the study populations also had
important implications for the understanding of MHC evolution.
Knowledge of the nucleotide sequence polymorphism of HLA
class II genes in general populations has fundamental
importance in HLA-related clinical investigations. The
apparent lack of susceptible alleles in the HLA gene pool of
native Australians and Pacific islanders, or the high
frequency of protective alleles, might partly explain the
extremely low incidence of autoimmune diseases in these
populations.
Книги з теми "Nucleotide sequence diversity"
1
Rocap, Gabrielle. Genetic diversity and ecotypic differentiation in the marine cyanobacteria Prochlorococcus and Synechococcus. Cambridge, Mass: Massachusetts Institute of Technology, 2000.
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2
Simone, Angila Ann. RNA editing and sequence diversity of 4f-rnp mRNA transcripts during development in Drosophila melanogaster. 1997.
Знайти повний текст джерелаЧастини книг з теми "Nucleotide sequence diversity"
1
Seal, Bruce S. "Analysis of Matrix Protein Gene Nucleotide Sequence Diversity Among Newcastle Disease Virus Isolates Demonstrates that Recent Disease Outbreaks Are Caused by Viruses of Psittacine Origin." In Molecular Evolution of Viruses — Past and Present, 145–52. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-1407-3_13.
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Sevanthi, Amitha Mithra V., Prashant Kale, Chandra Prakash, M. K. Ramkumar, Neera Yadav, V. Sureshkumar, Yugandhar Poli, et al. "National repository of EMS induced mutants of an upland rice cultivar Nagina 22: progress update on characterization and utilization." In Mutation breeding, genetic diversity and crop adaptation to climate change, 290–302. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0030.
Повний текст джерелаАнотація:
Abstract The Indian initiative for creating mutant resources in rice has generated 87,000 mutants in the background of a popular drought- and heat-tolerant upland cultivar, Nagina 22 (N22), through EMS mutagenesis. So far, 541 macro-mutants from this resource have been identified, maintained in the mutant garden and characterized in detail based on 44 descriptors pertaining to distinctness, uniformity and stability (DUS) of rice and other agronomic parameters. The similarity index of the mutants was more than 0.6 for nearly 90% of the mutants with respect to DUS descriptors, further establishing the validity of the mutants. The available high-quality sequence resource of N22 has been improved by reducing the gaps by 0.02% in the coding sequence (CDS) region. This was made possible using the newly synthesized whole-genome data of N22 which helped to remove 9006 'Ns' and replace 12,746 existing nucleotides with the accurate ones. These sequence and morphological details have been updated in the mutant database 'EMSgardeN22'. Further, 1058 mutants have been identified for low-P tolerance, tolerance to sheath blight, blast, drought, heat, higher photosynthetic efficiency and agronomic and root traits from this resource. A novel herbicide-tolerant (imazethapyr) mutant earlier identified and characterized from this resource is now being used in introgressing the herbicide-tolerant trait in eight major rice varieties in India. Further, robust and simpler screening systems have been tested for studying low-P tolerance of the mutants. A grain-size mutant, heat-tolerant mutant, drought-tolerant mutant, stay-green mutant and low-P tolerant and water-use efficient high-root-volume mutants have been characterized at morphological and molecular levels. A brief account of all these mutants, the entire mutant resource and the elaborate trait-based screenings is presented in this chapter.
3
Luján, R., J. A. Sáez-Nieto, J. V. Martinez-Suárez, B. G. Spratt, L. Bowler, and Q. Y. Zhang. "Nucleotide sequences and genetic diversity of the penA genes from penicillin sensitive and moderately penicillin resistant strains of Neisseria lactamica." In Neisseriae 1990, edited by Mark Achtman, Peter Kohl, Christian Marchal, Giovanna Morelli, Andrea Seiler, and Burghard Thiesen, 93–98. Berlin, Boston: De Gruyter, 1991. http://dx.doi.org/10.1515/9783110867787-019.
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4
Weigand, Michael R., Margaret M. Williams, and Glen Otero. "Temporal patterns of Bordetella pertussis genome sequence and structural evolution." In Pertussis, 144–65. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198811879.003.0009.
Повний текст джерелаАнотація:
Population genetics of Bordetella pertussis has long wrestled with a conflicting dichotomy of low gene sequence variation and high restriction fragment profile diversity. Recent applications of high-throughput sequencing and bioinformatics have deepened understanding of Bordetella evolution confirming that frequent chromosome rearrangement is a significant source of diversity in this species, in addition to gradual modification of protein-coding gene sequences. This chapter summarizes recent progress in the study of B. pertussis genomics to characterize temporal genetic shifts in the circulating population. Much of the presented work reinforces the dichotomy of B. pertussis genome evolution, concurrent mutation both of nucleotide sequences and gene arrangements, which still presents challenges in the genomic era. Disentangling the specific contributions of these processes to disease resurgence, as well as exploring their potential utility for vaccine development and novel therapeutics, provides a wealth of future research opportunities.
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Hartl, Daniel L. "Mutation, Gene Conversion, and Migration." In A Primer of Population Genetics and Genomics, 75–108. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780198862291.003.0004.
Повний текст джерелаАнотація:
Chapter 4 focuses on forward and reverse mutation, gene duplication and functional divergence, gene conversion, and equilibrium heterozygosity. It includes an introduction to the coalescent as well as the Wright–Fisher and Moran models of random genetic drift, measures of nucleotide polymorphism and diversity, and how these may be estimated from sequence data. Biased gene conversion is discussed in regard to its effects on homogeneity of nucleotide sequence across the genome. Several distinct types of effective population number are compared and contrasted including the inbreeding, variance, and coalescent effective numbers. Various models of migration are also examined including one-way migration, the island model, and stepping-stone models.
6
Raychaudhuri, Soumya. "An Introduction to Text Analysis in Genomics." In Computational Text Analysis. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198567400.003.0008.
Повний текст джерелаАнотація:
The February 16th, 2001 issue of Science magazine announced the completion of the human genome project—making the entire nucleotide sequence of the genome available (Venter, Adams et al. 2001). For the first time a comprehensive data set was available with nucleotide sequences for every gene. This marked the beginning of a new era, the ‘‘genomics’’ era, where molecular biological science began a shift from the investigation of single genes towards the investigation of all genes in an organism simultaneously. Alongside the completion of the genome project came the introduction of new high throughput experimental approaches such as gene expression microarrays, rapid single nucleotide polymorphism detection, and proteomics methods such as yeast two hybrid screens (Brown and Botstein 1999; Kwok and Chen 2003; Sharff and Jhoti 2003; Zhu, Bilgin et al. 2003). These methods permitted the investigation of hundreds if not thousands of genes simultaneously. With these high throughput methods, the limiting step in the study of biology began shifting from data collection to data interpretation. To interpret traditional experimental results that addressed the function of only a single or handful of genes, investigators needed to understand only those few genes addressed in the study in detail and perhaps a handful of other related genes. These investigators needed to be familiar with a comparatively small collection of peer-reviewed publications and prior results. Today, new genomics experimental assays, such as gene expression microarrays, are generating data for thousands of genes simultaneously. The increasing complexity and sophistication of these methods makes them extremely unwieldy for manual analysis since the number and diversity of genes involved exceed the expertise of any single investigator. The only practical solution to analyzing these types of data sets is using computational methods that are unhindered by the volume of modern data. Bioinformatics is a new field that emphasizes computational methods to analyze such data sets (Lesk 2002). Bioinformatics combines the algorithms and approaches employed in computer science and statistics to analyze, understand, and hypothesize about the large repositories of collected biological data and knowledge.
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Cann, R. L. "Nucleotide sequences, restriction maps, and human mitochondrial DNA diversity." In Genetic Variation and its Maintenance, 77–86. Cambridge University Press, 1986. http://dx.doi.org/10.1017/cbo9780511983603.007.
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Laugel, Marianne, Emilie Lecomte, Eduard Ayuso, Oumeya Adjali, Mathieu Mével, and Magalie Penaud-Budloo. "The Diversity of Parvovirus Telomeres." In Veterinary Medicine and Science. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.102684.
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Parvoviridae are small viruses composed of a 4–6 kb linear single-stranded DNA protected by an icosahedral capsid. The viral genes coding non-structural (NS), capsid, and accessory proteins are flanked by intriguing sequences, namely the telomeres. Telomeres are essential for parvovirus genome replication, encapsidation, and integration. Similar (homotelomeric) or different (heterotelomeric) at the two ends, they all contain imperfect palindromes that fold into hairpin structures. Up to 550 nucleotides in length, they harbor a wide variety of motifs and structures known to be recognized by host cell factors. Our study aims to comprehensively analyze parvovirus ends to better understand the role of these particular sequences in the virus life cycle. Forty Parvoviridae terminal repeats (TR) were publicly available in databases. The folding and specific DNA secondary structures, such as G4 and triplex, were systematically analyzed. A principal component analysis was carried out from the prediction data to determine variables signing parvovirus groups. A special focus will be put on adeno-associated virus (AAV) inverted terminal repeats (ITR), a member of the genus Dependoparvovirus used as vectors for gene therapy. This chapter highlights the diversity of the Parvoviridae telomeres regarding shape and secondary structures, providing information that could be relevant for virus-host interactions studies.
Тези доповідей конференцій з теми "Nucleotide sequence diversity"
1
Zhu, Li, Ming-zhou Li, Xue-wei Li, Su-rong Shuai, Qiang Li, Lei Chen, and Yi-ren Gu. "The Nucleotide Sequence Diversity Analysis of the Pig MyoG Gene." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering (ICBBE '08). IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.32.
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2
Prokhorova, E. E., and R. R. Usmanova. "GENETIC POLYMORPHISM OF SNAILS SUCCINEA PUTRIS (GASTROPODA, PULMONATA)." In V International Scientific Conference CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION. Tomsk State University Press, 2020. http://dx.doi.org/10.17223/978-5-94621-931-0-2020-33.
Повний текст джерелаАнотація:
Genotypic diversity of snails Succinea putris L. (Linnaeus, 1758) collected in the north-west of Russia and in the Republic of Belarus was analysed. Homology between the nucleotide sequences of snails from different population made up 100% by the nucleotide sequence of ITS1-5.8S-ITS2 region of rDNA. Genetic variability based on mitochondrial markers was insignificant. Average genetic distances between samples made up 0,009 for СOI gene loci and 0.008 for CytB gene loci. Was found ten haplotypes of the mitochondrial gene CytB and nine haplotypes of the mitochondrial gene СOI. Perhaps the genetic homogeneity of snails S. putris found in the study explains a low variability of their parasites, trematodes from the genus Leucochloridium.
Звіти організацій з теми "Nucleotide sequence diversity"
1
Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
2
Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7594399.bard.
Повний текст джерелаАнотація:
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.
3
Breiman, Adina, Jan Dvorak, Abraham Korol, and 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, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.
Повний текст джерелаАнотація:
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.