Gotowe bibliografie tematyczne / Haplotypes

Gotowa bibliografia na temat „Haplotypes”

Autor: Grafiati
Data publikacji: 4 czerwca 2021
Data aktualizacji: 3 marca 2023

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Artykuły w czasopismach na temat "Haplotypes"

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Pegueroles, Cinta, Verónica Mixão, Laia Carreté, Manu Molina i Toni Gabaldón. "HaploTypo: a variant-calling pipeline for phased genomes". Bioinformatics 36, nr 8 (13.12.2019): 2569–71. http://dx.doi.org/10.1093/bioinformatics/btz933.

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Abstract Summary An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. Availability and implementation HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. Supplementary information Supplementary data are available at Bioinformatics online.
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Li, Ruidong, Han Qu, Jinfeng Chen, Shibo Wang, John M. Chater, Le Zhang, Julong Wei i in. "Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes". Molecular Biology and Evolution 37, nr 12 (15.07.2020): 3684–98. http://dx.doi.org/10.1093/molbev/msaa176.

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Abstract Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.
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Kaufman, Letícia, Francisco R. Carnese, Alicia Goicoechea, Cristina Dejean, Francisco M. Salzano i Mara H. Hutz. "Beta-globin gene cluster haplotypes in the Mapuche Indians of Argentina". Genetics and Molecular Biology 21, nr 4 (grudzień 1998): 435–37. http://dx.doi.org/10.1590/s1415-47571998000400003.

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Haplotypes derived from five polymorphic restriction sites in the beta-globin gene cluster were investigated in 86 chromosomes from the Argentinian Mapuche. These results were integrated with those previously obtained for ten Brazilian Indian tribes. Eight haplotypes were identified, the most frequent being 2 (57%) and 6 (27%). The presence of haplotype 3 in 2% of the Mapuche chromosomes is probably an evidence of admixture with individuals of African ancestry. Due to the high number of haplotypes observed, heterozygosity as measured by the Gini-Simpson index was higher in the Mapuche than in Brazilian Indians. The haplotypic distribution in the Mapuche was also significantly different from those of all Brazilian tribes investigated. This heterogeneity could be at least partially explained by admixture with non-Indian populations.
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Kesik, Harun Kaya, Figen Celik, Seyma Gunyakti Kilinc, Sami Simsek, Haroon Ahmed, Yujuan Shen i Jianping Cao. "Genetic Diversity and Haplotype Analysis of Cattle Hydatid Cyst Isolates Using Mitochondrial Markers in Turkey". Pathogens 11, nr 5 (28.04.2022): 519. http://dx.doi.org/10.3390/pathogens11050519.

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Echinococcus granulosus sensu lato (s.l.) causes cystic echinococcosis in ungulates and humans. The current study was designed to find the genetic diversity and haplotypic profiles of hydatid cysts from the lungs of cattle in three provinces in eastern Turkey. Individual cyst isolates (n = 60) were collected from infected cattle lungs after slaughter and then samples were stored in ethanol (70%) until further use. From each isolate, total gDNA was extracted from the cysts’ germinal layers. A partial (875 bp) mt-CO1 gene was amplified by PCR and sequenced unidirectionally. The final size of the trimmed sequences was 530 bp for 60 sequences. Sequence and haplotype analyses were performed, followed by phylogenetic analyses. According to BLAST searches, all sequences were detected as E. granulosus s.s. (G1 and G3 strains). Forty-nine point mutations were identified. In addition, five conserved fragments were detected in all sequences. The haplotype analysis diagram showed E. granulosus s.s. haplotypes organized in a star-like configuration. The haplotypes were characterized by 1–17 mutations compared with the fundamental focal haplotype. Thirty-three haplotypes were determined in 60 samples of which 17 (28.3%) belonged to the main haplotype (Hap_06). The mt-CO1 sequences revealed 49 polymorphic sites, 34.5% (20/49) of which were informative according to parsimony analysis.
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Roberts, Amity R., Louise H. Appleton, Adrian Cortes, Matteo Vecellio, Jonathan Lau, Laura Watts, Matthew A. Brown i Paul Wordsworth. "ERAP1 association with ankylosing spondylitis is attributable to common genotypes rather than rare haplotype combinations". Proceedings of the National Academy of Sciences 114, nr 3 (3.01.2017): 558–61. http://dx.doi.org/10.1073/pnas.1618856114.

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We investigated the proposal that ankylosing spondylitis (AS) is associated with unusual ERAP1 genotypes. ERAP1 haplotypes were constructed for 213 AS cases and 46 rheumatoid arthritis controls using family data. Haplotypes were generated from five common ERAP1 single nucleotide polymorphisms (SNPs)—rs2287987 (M349V), rs30187 (K528R), rs10050860 (D575N), rs17482078 (R725Q), and rs27044 (Q730E). Haplotype frequencies were compared using Fisher’s exact test. ERAP1 haplotypes imputed from the International Genetics of AS Consortium (IGAS) Immunochip study were also studied. In the family study, we identified only four common ERAP1 haplotypes (“VRNQE,” “MKDRQ,” “MRDRE,” and “MKDRE”) in both AS cases and controls apart from two rare (<0.5%) previously unreported haplotypes. There were no examples of the unusual ERAP1 haplotype combination (“*001/*005”) previously reported by others in 53% of AS cases. As expected, K528-bearing haplotypes were increased in the AS family study (AS 43% vs. control 35%), due particularly to an increase in the MKDRQ haplotype (AS 35% vs. control 25%, P = 0.01). This trend was replicated in the imputed Immunochip data for the two K528-bearing haplotypes MKDRQ (AS 33% vs. controls 27%, P = 1.2 × 10–24) and MKDRE (AS 8% vs. controls 7%, P = 0.004). The ERAP1 association with AS is therefore predominantly attributable to common ERAP1 haplotypes and haplotype combinations.
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Sugiura, Nami, Dingqin Tang, Hiroyuki Kurokochi, Yoko Saito i Yuji Ide. "Genetic structure of Quercus gilva Blume in Japan as revealed by chloroplast DNA sequences". Botany 93, nr 12 (grudzień 2015): 873–80. http://dx.doi.org/10.1139/cjb-2015-0025.

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Quercus gilva (Blume) is an evergreen oak species that is native to Japan, China, and Taiwan. Because of a long history of human impact, this species is threatened with extinction in several regions of Japan. The objective of this study was to identify the genetic structure of Q. gilva based on chloroplast DNA (cpDNA) sequencing analysis. We collected 123 samples from 25 populations in Japan, 8 samples from 1 population in China, and 46 samples from 5 populations in Taiwan. Approximately 1815 bp of cpDNA was sequenced for each of the 177 samples. Thirteen haplotypes were detected, with no cross-region distribution of haplotypes among the three geographically separated countries. There were large genetic differences among populations (GST = 0.824, [Formula: see text] = 0.937). Six haplotypes (haplotypes 1, 2, 3, 4a, 4b, and 5) were detected in Japan; haplotype 4a was the most common, detected from 20 populations, and the other rare haplotypes, except for haplotype 4b, occurred at the edge of the species’ distribution. In addition, four haplotypes (haplotypes 1, 2, 3, and 5) were quite different from the predominant haplotype (haplotype 4a), with more than four cpDNA mutations except for a mononucleotide repeat, suggesting that populations with these rare haplotypes should be conserved separately.
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Vathipadiekal, Vinod, Abdulrahman Alsultan, John Farrell, A. M. Al-Rubaish, Fahad Al-Muhanna, Z. Naserullah, A. Alsuliman i in. "Polymorphisms Associated with the Arab-Indian Haplotype of Sickle Cell Anemia Are Candidate Fetal Hemoglobin Gene Modulators". Blood 126, nr 23 (3.12.2015): 3388. http://dx.doi.org/10.1182/blood.v126.23.3388.3388.

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Abstract Fetal hemoglobin (HbF) inhibits HbS polymerization. Because of this, sufficient HbF in most sickle erythrocytes can lead to a milder disease phenotype. HbF levels differ amongst the β-globin gene (HBB) cluster haplotypes of sickle cell anemia. In the Arab-Indian (AI) haplotype, HbF was about 20% compared with 5-10% in the Bantu, Benin, and Senegal haplotypes. Functional elements linked to the HBB haplotype are likely to regulate the expression of HbF in addition to the effects of trans-acting modulators. To identify cis-acting SNPs in the HBB gene cluster that differentiate the AI haplotype from all others, including the Senegal haplotype-the Senegal haplotype shares some SNPs with the AI haplotype but its carriers have lower HbF-we studied patients with sickle cell anemia who were homozygous for HBB haplotypes by genome-wide SNP association analysis (GWAS; Table). First, we compared the results of GWAS of 42 Saudi AI haplotype homozygotes with GWAS in 71 Saudi Benin haplotype homozygotes. The only variants distinguishing these 2 populations with genome-wide significance (p-values between 9.6E-07 and 2.7E-45) were 223 SNPs in chromosome 11p15 from positions 3.5 to 6.5 mb. This region included the HBB gene cluster, its locus control region (LCR) and the upstream and downstream olfactory receptor gene clusters. The minor allele frequency of SNPs in MYB (chr 6q23), BCL11A (chr 2p16) and KLF1 (chr 19), trans-acting loci that affect expression of the HbF genes, were similar in these 2 cohorts. A novel candidate trans-acting locus was not found, however our power to detect such an association was low. We followed-up these observations by comparing allele frequencies in 303 African American cases homozygous for the haplotypes shown in the Table. Thirteen GWAS-significant SNPs, in addition to rs7482144 and rs10128556, were present in all AI haplotype cases but not in 83 Senegal haplotype chromosomes. The allele frequency of these SNPs was replicated in 62 independent AI haplotype cases. Rs2472530 is in the coding region of OR52A5; rs16912979, rs4910743 and rs4601817 are in the HBB gene cluster LCR; rs16912979 in DNase I hypersensitive site-4 altered motifs for POLR2A, GATA1, and GATA2 binding.The minor allele of rs10837771 causes a missense mutation in OR51B4 an upstream olfactory receptor gene. To see if any of these or other alleles might sometimes be associated with HbF in the Bantu and Benin haplotyes, we selected homozygotes and compound heterozygous for these haplotypes who had unexplained and uncharacteristically high HbF. Thirty-one African Americans, aged ≥5 yrs. who had a HbF of 21% were compared with 350 similar cases who had a mean HbF of 3%. Four additional SNPs on chromosome 11, from positions ranging from 5536415 to 5543705 in the UBQLNL/HBG2, region and present in 45-48% of AI haplotype and 3-13% of other haplotypes, were found at higher frequencies in the high HbF group compared with the low HbF group. These SNPs also altered transcription factor binding motifs. Loci marked by SNPs that distinguish the AI from the Senegal and other HBB haplotypes might contain functionally important polymorphisms and account in part for high HbF in AI haplotype sickle cell anemia, independent of, or in addition to, the effects associated with rs7482144 or rs10128556. They might also be rarely associated with high HbF found in other haplotypes. These observations provide a foundation for mechanistic studies focused on the role of these variants in the expression of their linked HbF genes.Table 1.non-codedallelegenomic locationSaudi AI(n=42)Saudi ben.ben(n=71)AA ben.ben(n=264)AA ban.ban(n=31)AA sen.sen(n=8)HbF (%)1711669rs10837771Gexon OR51B410.020.0200rs4601817GLCR10.020.0400rs4910743CLCR10.010.0100rs16912979CLCR00.960.920.111rs10488675Gintron HBE110.01000rs7482144*AHBG210001rs10128556#TIntron HBBP110001rs7935470COR51V110.020.0300rs10837582GOR51V1100.0200rs11036227TOR51V110000rs10734485COR51A1P00.990.9711rs10837461AOR52A110.01000rs2472522GOR52A110.01000rs2472530Gexon OR52A510.01000rs2499948TOR52A510.020.010.020Allele frequencies in haplotypes of sickle cell anemia. * Xmn1 5' HBG 2 restriction site. This SNP, not present on the SNP microarray, was genotyped independently; # LD with rs7482144; AA designates African Americans; ben-Benin; ban-Bantu; sen-Senegal. Disclosures No relevant conflicts of interest to declare.
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Patel, Suprava, Rachita Nanda, Nighat Hussain, Eli Mohapatra i Pradeep Kumar Patra. "Interactions of Combined Haplotypes of Methylenetetrahydrofolate Reductase on Clinical Events in Children with Sickle Cell Disorder". Journal of Evolution of Medical and Dental Sciences 10, nr 25 (21.06.2021): 1889–94. http://dx.doi.org/10.14260/jemds/2021/390.

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BACKGROUND Methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C variants are considered as potential genetic risk factors for vaso-occlusive complications in sickle cell disorder (SCD). The purpose of the study was to determine the interaction of the combined haplotypes on the clinical presentations in children with sickle cell disorder. METHODS A cross-sectional study was conducted on 249 children, confirmed for sickle cell disorder. Clinical details and frequencies of clinical episodes in the past one year were noted and a severity index number was allotted to each child and evaluated for their relationship with the combined haplotypes of C677T and A1298C single nucleotide polymorphisms genotyped by real-time PCR. RESULTS The frequency for 677T / 1298A haplotype was 46.4 % and that of 677C / 1298C was 12.4 %. The three variant combined haplotypes had higher plasma homocysteine values than the wild 677C / 1298A haplotypes (P < 0.001). Clinical events like vasoocclusive crisis (VOC), homocysteinemia, hospitalization frequency and SI were found significantly related among the children in sickle cell trait (SCT) group (P < 0.001) but not so in SCD group. Chances for anemia was 1.93 times more in presence of dual variant alleles (95 %CI: 0.95 to 3.92, P = 0.07) in SCT. The 677T / 1298C haplotype accounted for higher SI was 7.85 times more than the wild haplotypic children even in SCT children and 1.67 times in SCD children. CONCLUSIONS Presence of the variant haplotypes had significant implication on crisis events in children with sickle cell trait and make them more prone for the clinical severity. A preliminary allelic screening might be helpful in them. KEY WORDS Dual Variant Alleles, Heterozygous, Homozygous, MTHFR, Variant Haplotypes
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Vadva, Larsen, Propp, Trautwein, Alford i Alper. "A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies". Cells 8, nr 8 (5.08.2019): 835. http://dx.doi.org/10.3390/cells8080835.

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Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage rate (the frequency of phased haplotypes in which each SNP is defined) and genomic location. Redundant SNPs were eliminated, overall haplotype polymorphism was optimized and the number of undefined haplotypes was minimized. These edited SNP haplotypes from a region containing HLA-DRB1 (DR) and HLA-DQB1 (DQ) both correlated well with HLA-typed DR,DQ haplotypes and differentiated HLA-DR,DQ fragments shared by three pairs of previously identified megabase-length conserved extended haplotypes. In a pedigree-based genetic association assay for type 1 diabetes, edited SNP haplotypes and HLA-typed HLA-DR,DQ haplotypes from the same families generated essentially identical qualitative and quantitative results. Therefore, this edited SNP haplotype method is useful for both genomic polymorphic architecture and genetic association evaluation using SNP markers with diverse minor allele frequencies.
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Slade, D., Ž. Škvorc, D. Ballian, J. Gračan i D. Papes. "The Chloroplast DNA Polymorphisms of White Oaks of Section Quercus in The Central Balkans". Silvae Genetica 57, nr 1-6 (1.12.2008): 227–34. http://dx.doi.org/10.1515/sg-2008-0035.

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Abstract A total of 444 oak trees from 110 populations from a previously under-sampled area in the central Balkans were analysed using four primer/enzyme combinations which amplified and restricted four, largely non-coding regions of the maternally inherited chloroplast DNA. Using the nomenclature of PETIT et al. (2002 a) to classify the haplotypes and lineages, the seven haplotypes that were found in Croatia, Bosnia and Herzegovina, Montenegro, Albania, Macedonia and southern Kosovo consisted of haplotypes 2, 4, 5, 6, 7, 17, 31, as well as the subtypes of haplotypes 4 (a), 5 (a, b, c), and 17 (a). Five of these haplotypes belong to lineage A. One of these, haplotype 5, is present throughout the sampled area. The distributions of the other haplotypes from this lineage are more geographically structured. The other two haplotypes, haplotype 2 and haplotype 17, belong to lineages C and E, respectively. The data are combined with previous data by PETIT et al. (2002 b) to provide more detailed information of the postglacial routes of colonisation taken by oaks in south-eastern Europe.
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Rozprawy doktorskie na temat "Haplotypes"

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Xia, Shuang. "Detecting Rare Haplotype-Environment Interaction and Dynamic Effects of Rare Haplotypes using Logistic Bayesian LASSO". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1406246686.

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Janyakhantikul, Somwang. "Evolution of CCL3L1/CCL4L1 haplotypes". Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/13404/.

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CCL3LI and CCL4LI are chemokine genes, located on chromosome 17q12. They are copy number variable genes which share 95% sequence identity with their non-copy number variable paralogues CCL3 and CCL4. The copy number of these genes varies between populations and has been reported to be associated with phenotypes such as susceptibility to HIV infection, hepatitis C virus infection, Kawasaki disease and SLE. The aim of this study is to understand the evolutionary history of variation at the CCL3L1/CCL4LI cluster. To accomplish this goal, several approaches including typing microsatellites, single nucleotide polymorphisms (SNPs) and CCL3L 1/CCL4L 1 sequence haplotypes were used to investigate the association with CCL3L 1 and CCL4L 1 copy number. However, the results showed that there is no strong association between a single-copy marker and CCL3L 1 and CCL4LI copy number, but there is evidence of recombination. Therefore, this may suggest that CCL3L 1/CCL4L 1 is a complex region and one plausible hypothesis is that there is a high rate of recombination in this region. This study of the evolution of CCL3L 1/CCL4L 1 haplotypes showed that a major one-copy CCL3L 1/CCL4L I haplotype (about 70% haplotype frequency) identified in humans, represents the ancestral state, as inferred from comparison with chimpanzee.
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Zhang, Han. "Detecting Rare Haplotype-Environmental Interaction and Nonlinear Effects of Rare Haplotypes using Bayesian LASSO on Quantitative Traits". The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu149969433115895.

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Martinez, Cadenas Conrado. "Y chromosome haplotypes and Spanish surnames". Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559800.

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In most societies, surnames are passed down from fathers to sons, just like the Y chromosome. It follows that, theoretically, men sharing the same surnames would also be expected to share related Y chromosomes. Previous investigations have explored such relationships but most data has been collected so far only from the British Isles. In order to provide additional in sights into the con-elation between surnames and Y chromosomes, this study focuses on the Spanish population and investigates Y chromosome SNP/STR variation by analysing a total of 1,766 DNA samples from unrelated Spanish male volunteers belonging to 37 surnames and 355 controls. The results suggest that the degree of coancestry within surnames is highly dependent on surname frequency. Within-surname genetic variation, as measured by different statistics, con-elates well with surname frequency, though a few exceptions are found. In addition, geographic distance between the individuals' place of origin influences Significantly the con-elation between Y chromosome and surnames: men with the same surname tend to have more similar Y chromosomes if their paternal grandfathers were born geographically close to each other. Therefore, it seems that Y chromosome coancestry within surnames is as much about surname frequency as it is about geographical proximity.
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Brennan, Patrick J. "An Investigation of Personal Ancestry Using Haplotypes". University of Toledo / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744.

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Nicholls, Samuel. "Computational recovery of enzyme haplotypes from a metagenome". Thesis, Aberystwyth University, 2018. http://hdl.handle.net/2160/cfc1d884-cc17-439f-be6e-c3ab6d79ee1d.

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Population-level diversity of microbial communities (microbiomes) represent a biotechnological resource for biomining, biorefining and synthetic biology; but industrial exploitation of enzymes responsible for catalyzing reactions of interest requires the recovery of the exact DNA sequences (or "haplotypes") that encode the genes. However, haplotype reconstruction is an extremely difficult computational problem, further complicated by the infancy of techniques for the handling of environmental sequencing data (metagenomics). Current haplotyping approaches cannot choose between alternative haplotype reconstructions and fail to provide biological evidence of correct predictions. Additionally, there is no philosophical framework under which we can consider the variation of genes within a microbial community, such as those that encode isoforms of enzymes of interest to us. To address this, my thesis proposes the "metahaplome" as a definition for the set of haplotypes for a genomic region of interest within a microbial community. This work will offer the first formalisation of the problem of recovering haplotypes from a metagenomic data set, and present Hansel and Gretel: a novel probabilistic framework that reconstructs the most likely haplotypes from complex microbiomes. The framework is robust to sequencing error and uses all available evidence from aligned reads, without altering or discarding observed variation. The approach is verified with multiple in silico experiments, including two de facto data sets that are currently used to benchmark algorithms for the recovery of viral quasispecies, and strain identification. With long-read sequencing, this thesis will demonstrate in vitro verification of the approach, presenting the first biologically validated method for the recovery of haplotypes from a microbial community. Finally, I will introduce the "Rumen Landscape" pilot study to demonstrate the sort of research questions and novel biological insight that can be obtained through exploration of the metahaplome.
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Higgins, Thomas John Diatchenko Luda. "Molecular characterization of [beta]2 adrenergic receptor haplotypes". Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,1602.

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Thesis (M.S.)--University of North Carolina at Chapel Hill, 2008.
Title from electronic title page (viewed Sep. 16, 2008). "... in partial fulfillment of the requirements for the degree of Master's of Science in the Curriculum in Neurobiology." Discipline: Neurobiology; Department/School: Medicine. On title page, [beta] appers as Greek character and 2 appears in subscript.
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Bradman, Neil. "A Y chromosome history of the Jews". Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275330.

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Lo, Wing Sze. "Association of SNPs and haplotypes in GABRB2 with schizophrenia /". View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BICH%202006%20LO.

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King, Turi E. "The relationship between British surnames and Y-chromosomal haplotypes". Thesis, University of Leicester, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.484806.

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Abstract In Britain surnames are paternally inherited and they are thus analogous to the paternally inherited Y chromosome. Therefore, males who share surnames might be expected to share Y-chromosomes. However, this simple relationship is complicated by the multiple origins of many surnames, non-paternity, and mutations on the Y chromosome. Y-chromosomal DNA polymorphisms provide us with a set of tools to directly test, at a molecular level, this hypothetical link. Since surnames are highly geographically localized, local geographical patterning of Y haplotypes is a potential confounding factor: genetic structure within names could arise as a result of geographical structure within Britain, rather than due to descent. Geographical structure was examined using samples from this research but little evidence of such structure was found. Then, to ask if a signal of haplotype sharing exists within surnames, 150 pairs of men were recruited, each sharing a British surname, and Y-haplotype sharing assessed within each pair. The signal of coancestry exhibited constituted powerful evidence for common origins of men sharing surnames. It also has forensic implications and this research shows that it could allow the prediction of surname from crime-scene samples. . These findings for pairs of men sharing surnames suggested that a larger scale' study of larger sample sizes would be worthwhile, so a set of 40 surnames with an average sample size of 42 apparently unrelated men was investigated using Y markers. Correlations between surname rank and degree of diversity exist: the more common the surname, the greater the diversity of Y-chromosomal haplotypes associated with the name. Furthermore, an individual is far more likely to share a Y-chromosome haplotype with another person sharing their surname if the surname is rare. While a handful of surnames show some evidence of having a single founder, overall the picture is one of far more complex surnames histories.
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Książki na temat "Haplotypes"

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New mathematical methods in human gene mapping. [New York]: [Columbia University], 1993.

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Perry, Claire Louise. A search for novel MHC-encoded IDDM susceptibility genes using oriental haplotypes. Birmingham: University of Birmingham, 1997.

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Iliadis, Alexandros. Haplotype Inference through Sequential Monte Carlo. [New York, N.Y.?]: [publisher not identified], 2013.

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Istrail, Sorin, Michael Waterman i Andrew Clark, red. Computational Methods for SNPs and Haplotype Inference. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/b96286.

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Pound, Michelle C. Deletion screening and haplotype analysis in the Fraxe region at Xq28. [Portsmouth]: [University of Portsmouth], 2000.

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Svensson, Ann-Cathrin. Molecular analyses of human endogenous retrovirus ERV9: Marker for HLA-DR haplotype evolution. Uppsala: Sveriges Lantbruksuniversitet, 1996.

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Sorin, Istrail, Waterman Michael S i Clark Andrew G. 1954-, red. Computational methods for SNPs and Haplotype inference: DIMACS/RECOMB satellite workshop, Piscataway, NJ, USA, November 21-22, 2002 : revised papers. Berlin: Springer-Verlag, 2004.

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Kay, Chris, Emily Fisher i Michael R. Hayden. Epidemiology. Oxford University Press, 2014. http://dx.doi.org/10.1093/med/9780199929146.003.0007.

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The prevalence and persistence of Huntington’s disease (HD) is crucially informed by the causative mutation. Diagnostic and predictive testing has enabled a new era of epidemiologic study of HD, whereby only those who carry an expanded CAG repeat are included in such measures. In Western populations, estimated prevalence of the disease is higher following the introduction of genetic testing, and prevalence may also be increasing in absolute terms. There are worldwide differences in the prevalence of HD by ethnicity and population, which may be accounted for in part by genetic diversity of the CAG repeat and the surrounding haplotype. HD is endemic to all populations, but is most common in populations of European ancestry in which specific disease haplotypes are found. New mutations maintain HD in a population, and genetic differences by population may contribute to differences in the de novo mutation rate.
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Morell-Ducos, Fausto. COMT and morphine use in cancer pain. Redaktorzy Paul Farquhar-Smith, Pierre Beaulieu i Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0082.

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The landmark paper discussed in this chapter is ‘Genetic variation in the catechol-O-methyltransferase (COMT) gene and morphine requirements in cancer patients with pain’, published by Rakvåg et al. in 2008. Genetic variation contributes to differences in pain sensitivity and response to analgesics. Catecholamines are involved in the modulation of pain and are metabolized by catchol-O-methyltransferase (COMT). Genetic variability in the COMT gene may therefore contribute to differences in pain sensitivity and response to analgesics. It has been shown that a polymorphism in the COMT gene, Rs4680 (val158met), influences pain sensitivity and efficacy for morphine in cancer pain treatment. This study investigated whether the variability in other regions in the COMT gene also contributes to the inter-individual variability of morphine efficacy by mapping 11 single nucleotide polymorphisms, constructing haplotypes from them, and then comparing genotypes and haplotypes against pharmacological, demographic, and patient symptom measurements in patients receiving morphine for cancer pain.
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Mészáros, Gábor, Marco Milanesi, Paolo Ajmone Marsan i Yuri Tani Utsunomiya, red. Haplotype Analysis Applied to Livestock Genomics. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-968-4.

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Części książek na temat "Haplotypes"

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Martin, Marcel, Peter Ebert i Tobias Marschall. "Read-Based Phasing and Analysis of Phased Variants with WhatsHap". W Methods in Molecular Biology, 127–38. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2819-5_8.

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AbstractWhatsHap is a command-line tool for phasing and phasing-related tasks. It allows to infer haplotypes in diploid and polyploid samples based on (preferably long) reads covering at least two heterozygous variants. It offers additional tools for working with phased variant calls such as computing statistics, comparing different phasings and assigning reads in alignment files to their haplotype.
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Betuel, H., E. D. Du Toit, L. Gebuhrer, M. P. LaBonne, M. Oudshoorn, L. Dombrausky, C. Gorodezky i D. Cohen. "Unusual DR-DQ Haplotypes". W Immunobiology of HLA, 888–90. New York, NY: Springer New York, 1989. http://dx.doi.org/10.1007/978-1-4612-3552-1_259.

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Lefferts, Juliet W., Vera Boersma, Marne C. Hagemeijer, Karima Hajo, Jeffrey M. Beekman i Erik Splinter. "Targeted Locus Amplification and Haplotyping". W Methods in Molecular Biology, 31–48. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2819-5_2.

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AbstractTargeted locus amplification (TLA) allows for the detection of all genetic variation (including structural variation) in a genomic region of interest. As TLA is based on proximity ligation, variants can be linked to each other, thereby enabling allelic phasing and the generation of haplotypes. This allows for the study of genetic variants in an allele-specific manner. Here, we provide a step-by-step protocol for TLA sample preparation and a complete bioinformatics pipeline for the allelic phasing of TLA data. Additionally, to illustrate the protocol, we show the ability of TLA to re-sequence and haplotype the complete cystic fibrosis transmembrane (CFTR) gene (> 200 kb in size) from patient-derived intestinal organoids.
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Hurley, Carolyn Katovich, Noriko Steiner, Peter Gregersen, Jack Silver, Robert Hartzman, Gerald Nepom i Armead H. Johnson. "Evolution of DQw2-Related Haplotypes". W Immunobiology of HLA, 283–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-662-39946-0_100.

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Klein, Jan, Colm O’hUigin, Masanori Kasahara, Vladimir Vincek, Dagmar Klein i Felipe Figueroa. "Frozen Haplotypes in Mhc Evolution". W Molecular Evolution of the Major Histocompatibility Complex, 261–86. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-84622-9_23.

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Kirkpatrick, Bonnie. "Haplotypes versus Genotypes on Pedigrees". W Lecture Notes in Computer Science, 136–47. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-15294-8_12.

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Cotner, Tom, Elizabeth Mellins i Donald A. Pious. "Characterization of Multiple HLA-DR3 Haplotypes". W Immunobiology of HLA, 200–201. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-662-39946-0_58.

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Takahashi, T. C., H. T. Kao, J. C. Tang, P. Gregersen, J. Silver i C. Y. Wang. "Molecular Diversity of HLA-DRw6 Haplotypes". W Immunobiology of HLA, 218–19. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-662-39946-0_67.

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Cheng, Yun, Arthur Berg, Song Wu, Yao Li i Rongling Wu. "Computing Genetic Imprinting Expressed by Haplotypes". W Methods in Molecular Biology, 189–212. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-247-6_11.

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Sinha, Sumit, i Cheng-Zhong Zhang. "Determining Complete Chromosomal Haplotypes by mLinker". W Methods in Molecular Biology, 149–59. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2819-5_10.

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Streszczenia konferencji na temat "Haplotypes"

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Pe'er, Itsik, i Jacques S. Beckmann. "Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples". W the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640107.

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Tejera, P., Z. Wang, R. Zhai, L. Su, CC Sheu i DC Christiani. "Functional Analysis of Haplotypes inPI3Promoter." W American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California. American Thoracic Society, 2009. http://dx.doi.org/10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a1884.

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Đuretanović, Simona, Tijana Veličković, Aleksandra Milošković, Milena Radenković, Marijana Nikolić, Ivana Maguire i Vladica Simić. "PRELIMINARY RESULTS REGARDING PHYLOGENY OF THE NOBLE CRAYFISH (DECAPODA, ASTACIDAE, „ASTACUS ASTACUS“) IN SERBIA". W 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.222dj.

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The noble crayfish is one of the three autochthonous species that inhabit the freshwater ecosystems of Serbia, along with stone and Danube crayfish. The noble crayfish has a complex historical and genetic status shaped by geological events, habitat loss, pollution, translocations, and reintroductions of both autochthonous and allochthonous crayfish species. That led to the disruption of the species genetic structure, mixing, and loss of populations across Europe. According to recent data, its populations in the freshwater ecosystems of Serbia are significantly reduced, so it has the status of a "strictly protected species". The genetic structure of the species must be known for endangered species conservation. Unfortunately, there is lack of such data for the territory of Serbia, which due to its position on the Balkan Peninsula, was an important refuge during the glaciation period. In this paper, the genetic structure of seven crayfish populations in freshwater ecosystems of Serbia was examined. Analyzes were performed on the COI and 16S rRNA genes of mitochondrial DNA. The study results showed a significant diversity of COI and 16S rRNA haplotypes compared to already described haplotypes. Three haplotypes were detected, of which Hap26 is the most common and was detected in five studied populations. Haplotypes Hap47 and Hap49 were detected in one and two populations, respectively. The results obtained in this study, together with previously published morphometric data, represent a good starting point for further genetic and population research, which are the basis for the proposal of conservation measures.
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Bafna, Vineet, Bjarni V. Halldorsson, Russell Schwartz, Andrew G. Clark i Sorin Istrail. "Haplotypes and informative SNP selection algorithms". W the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640078.

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Prokhorova, E. E., i R. R. Usmanova. "GENETIC POLYMORPHISM OF SNAILS SUCCINEA PUTRIS (GASTROPODA, PULMONATA)". W 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.

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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.
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Blazhko, Natalia, Sultan Vyshegurov, Alevtina Khodakova i Sergei Loginov. "Polymorphism of Haplotypes of Bovine Leukemia Virus". W Proceedings of the International Scientific Conference The Fifth Technological Order: Prospects for the Development and Modernization of the Russian Agro-Industrial Sector (TFTS 2019). Paris, France: Atlantis Press, 2020. http://dx.doi.org/10.2991/assehr.k.200113.140.

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Permaul, P., BA Raby, BD Levy i E. Israel. "ALOX-15 Haplotypes and Association with Asthma." W American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California. American Thoracic Society, 2009. http://dx.doi.org/10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2746.

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Karp, Richard M. "Large scale reconstruction of haplotypes from genotype data". W the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640088.

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Piras, Ignazio, Maria Elena Ghiani, Laurent Varesi, Carla Calo, Alessandra Falchi, Giuseppe Vona i Laurianne Giovannoni. "Distribution of ݭGlobin Cluster Haplotypes in Sardinia (Italy)". W 2006 First International Symposium on Environment Identities and Mediterranean Area. IEEE, 2006. http://dx.doi.org/10.1109/iseima.2006.344992.

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ERONEN, L., F. GEERTS i H. TOIVONEN. "A MARKOV CHAIN APPROACH TO RECONSTRUCTION OF LONG HAPLOTYPES". W Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0011.

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Raporty organizacyjne na temat "Haplotypes"

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Yan, Jingjing, Mahdi Saatchi, Hailin Su, Jungjae Lee, Rohan L. Fernando i Dorian J. Garrick. Characterization and Associations of Haplotypes Containing PLAG1 in Cattle. Ames (Iowa): Iowa State University, styczeń 2014. http://dx.doi.org/10.31274/ans_air-180814-1137.

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Hayr, Melanie K., Xiaochen Sun, Tom Druet i Dorian J. Garrick. Genomic Prediction of Milk Fat using Fixed Length Haplotypes. Ames (Iowa): Iowa State University, styczeń 2016. http://dx.doi.org/10.31274/ans_air-180814-201.

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Sun, Xiaochen, Rohan L. Fernando, Dorian J. Garrick i Jack C. M. Dekkers. Improved Accuracy of Genomic Prediction for Traits with Rare QTL by Fitting Haplotypes. Ames (Iowa): Iowa State University, styczeń 2015. http://dx.doi.org/10.31274/ans_air-180814-1339.

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Sun, Xiaochen, Hailin Su i Dorian J. Garrick. Improved Accuracy of Across-breed Genomic Prediction Using Haplotypes in Beef Cattle Populations. Ames (Iowa): Iowa State University, styczeń 2016. http://dx.doi.org/10.31274/ans_air-180814-527.

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Sun, Xiaochen, Hailin Su i Dorian J. Garrick. Genetic Difference of Five Beef Cattle Breeds Characterized by Genome-wide SNPs and Haplotypes. Ames (Iowa): Iowa State University, styczeń 2016. http://dx.doi.org/10.31274/ans_air-180814-498.

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Weng, Ziqing, Dorian J. Garrick, Mahdi Saatchi, Robert Schnabel i Jeremy Taylor. Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle. Ames (Iowa): Iowa State University, styczeń 2013. http://dx.doi.org/10.31274/ans_air-180814-632.

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Michelmore, Richard, Eviatar Nevo, Abraham Korol i Tzion Fahima. Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca. United States Department of Agriculture, luty 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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Su, Hailin, James E. Koltes, Mahdi Saatchi, Jungjae Lee, Rohan L. Fernando i Dorian J. Garrick. Characterizing Haplotype Diversity in Ten US Beef Cattle Breeds. Ames (Iowa): Iowa State University, styczeń 2014. http://dx.doi.org/10.31274/ans_air-180814-1132.

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Roecklein, Kathryn A. Haplotype Analysis of the Melanopsin Gene in Seasonal Affective Disorder and Controls. Fort Belvoir, VA: Defense Technical Information Center, maj 2007. http://dx.doi.org/10.21236/ad1014058.

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Weng, Ziqing, Anna Wolc, Jesus Arango, Petek Settar, Janet E. Fulton, Neil P. O'Sullivan, Rohan L. Fernando, Jack C. M. Dekkers i Dorian J. Garrick. Estimation of Haplotype Diversity and Recombination Rate on Chromosomes 5 and 15 in Layer Chickens. Ames (Iowa): Iowa State University, styczeń 2015. http://dx.doi.org/10.31274/ans_air-180814-1322.

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