Relevant bibliographies by topics / Haplotype analysi

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Academic literature on the topic 'Haplotype analysi'

Author: Grafiati
Published: 11 March 2023

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Journal articles on the topic "Haplotype analysi"

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Kesik, Harun Kaya, Figen Celik, Seyma Gunyakti Kilinc, Sami Simsek, Haroon Ahmed, Yujuan Shen, and Jianping Cao. "Genetic Diversity and Haplotype Analysis of Cattle Hydatid Cyst Isolates Using Mitochondrial Markers in Turkey." Pathogens 11, no. 5 (April 28, 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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Epifanio, John M., Bonnie L. Brown, Peter E. Smouse, and Carol J. Kobak. "Mitochondrial DNA divergence among popylations of American shad (Alosa sapidissima): how much variation is enough for mixed-stock analysis?" Canadian Journal of Fisheries and Aquatic Sciences 52, no. 8 (August 1, 1995): 1688–702. http://dx.doi.org/10.1139/f95-761.

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We investigated the geographic distribution of the mitochondrial DNA (mtDNA) diversity of American shad from 15 North American rivers in 1992 with the intent of assessing sampling efficiency for future mixed-stock analysis. We observed 116 haplotypes among the 988 individuals assayed. Because no single or group of haplotypes completely discriminated river stocks or regional complexes, we investigated haplotype frequencies as stock descriptors. Analysis of four unique indices of haplotype divergence indicated that including rather than suppressing restriction site heteroplasmy increased resolution; however, the final results were not overwhelmingly dependent on this choice. A redundancy of variation among restriction enzymes diminished information returns rapidly after considering the six best enzymes, caused by physical linkage of restriction sites on the mtDNA molecule. Stock discriminatory power was tested by computing allocation efficiencies of mtDNA characters. When each individual was temporarily removed from the data set and reallocated to the various candidate populations on the basis of haplotypic similarity, 28% of the reallocations were correct, a fourfold increase over random success. We demonstrate that although the specific stock identity of individuals cannot be confidently established, the haplotypic arrays from baseline stocks can support stock identification and mixed-stock analysis for shad because rivers support stock-specific haplotype frequencies.
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Santos, Daniel Wagner C. L., Vania Aparecida Vicente, Vinicius Almir Weiss, G. Sybren de Hoog, Renata R. Gomes, Edith M. M. Batista, Sirlei Garcia Marques, Flávio de Queiroz-Telles, Arnaldo Lopes Colombo, and Conceição de Maria Pedrozo e. Silva de Azevedo. "Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network." Journal of Fungi 6, no. 4 (October 3, 2020): 204. http://dx.doi.org/10.3390/jof6040204.

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Chromoblastomycosis (CBM) is a neglected implantation mycosis prevalent in tropical climate zones, considered an occupational disease that affects impoverished rural populations. This retrospective study described clinical aspects of CBM in a hyperendemic area in Brazil and constructed a worldwide haplotype network of Fonsecaea spp. strains. The variables were collected from medical records using a standard report form, reporting 191 patients with CBM from Maranhão, Brazil. The mean age was 56.1 years, 168 (88%) patients were male and predominantly farmers (85.8%). The mean time of evolution of the disease until diagnosis was 9.4 years. Lower limbs (81.2%) and upper limbs (14.2%) were the main sites affected. Most patients exhibited verrucous (55%) and infiltrative plaque (48.2%). Fonsecaea spp. were identified in 136 cases and a haplotype network constructed with ITS sequences of 185 global strains revealed a total of 59 haplotypes exhibiting high haplotypic and low nucleotide diversities. No correlation was observed between the different haplotypes of Fonsecaea species and dermatological patterns, severity of disease or geographic distribution inside Maranhão. Data from this area contributed to better understanding the epidemiology of CBM. For the first time, a robust haplotype network with Fonsecaea strains reveals an evolutionary history with a recent population expansion.
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Kaul, Noyonika, Prem Lal Kashyap, Sudheer Kumar, Deepti Singh, and Gyanendra Pratap Singh. "Genetic Diversity and Population Structure of Head Blight Disease Causing Fungus Fusarium graminearum in Northern Wheat Belt of India." Journal of Fungi 8, no. 8 (August 5, 2022): 820. http://dx.doi.org/10.3390/jof8080820.

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Head blight or scab caused by Fusarium graminearum (FG), once ranked as a minor disease in wheat, is now emerging as one of the economically important diseases in India. The present study represents the first in-depth population genetic analysis of the FG from the northern wheat belt of India. In this study, multiple conserved gene sequences comprised of β-tubulin (TUB), translation elongation factor 1-α (TEF), and histone-3 (HIS) regions were used for multi-locus phylogenetic analysis of 123 geographically distinct F. graminearum isolates collected from four different states (Haryana (HR), Punjab (PB), Rajasthan (RJ) and West Bengal (WB)) of India. The phylogenetic and haplotype analysis showed the presence of thirty haplotypes in all the analyzed populations. The haplotypic diversity in the RJ population (Hd = 0.981) was higher than in the HR (Hd = 0.972), PB (Hd = 0.965) and WB population (Hd = 0.962). Recombination events (Rm = 12) and mutation events (485) were also detected. Analysis of molecular variance (AMOVA) indicated that genetic diversity was exclusively due to the differences within populations. The haplotype network was widely dispersed and not associated with specific populations, as a single common haplotype was not detected. The PB population contained both unique (H9, H10 and H11) and shared haplotypes (27 haplotypes) in a higher number in comparison to other geographical locations. Except for haplotype H22 (contains highly aggressive isolates), there was no specific linkage noticed between the isolate aggressiveness and haplotype. The concatenated sequences of all the three genes demonstrated a low level of genetic differentiation (Fst = −0.014 to 0.02) in the analyzed population. Positive values for the neutrality tests in PB, HR and RJ reveal a balancing selection mechanism behind the FG population structure. The WB population showed both positive and negative values of neutrality indices, indicating the role of both population expansion as well as balancing selection in structuring the FG population.
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Bhattacharyya, Nitai Pada, Priyadarshi Basu, Madhusudan Das, Srimanta Pramanik, Rajat Banerjee, Bidyut Roy, Susanta Roychoudhury, and Partha P. Majumder. "Negligible Male Gene Flow Across Ethnic Boundaries in India, Revealed by Analysis of Y-Chromosomal DNA Polymorphisms." Genome Research 9, no. 8 (August 1, 1999): 711–19. http://dx.doi.org/10.1101/gr.9.8.711.

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From the historically prevalent social structure of Indian populations it may be predicted that there has been very little male gene flow across ethnic boundaries. To test this finding, we have analyzed DNA samples of individuals belonging to 10 ethnic groups, speaking Indo-European or Austroasiatic languages and inhabiting the eastern and northern regions of India. Eight Y-chromosomal markers, two biallelic and six microsatellite, were studied. All populations were monomorphic for the deletion allele at the YAP (DYS287) locus and for the 119-bp allele at the DYS288 locus. Y-chromosomal haplotypes were constructed on the basis of one RFLP locus and five microsatellite loci. The haplotype distribution among the groups showed that different ethnic groups harbor nearly disjoint sets of haplotypes. This indicates that there has been virtually no male gene flow among ethnic groups. Analysis of molecular variance revealed that there was significant haplotypic variation between castes and tribes, but nonsignificant variation among ranked caste clusters. Haplotypic variation attributable to differences in geographical regions of habitat was also nonsignificant.
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Vathipadiekal, Vinod, Abdulrahman Alsultan, John Farrell, A. M. Al-Rubaish, Fahad Al-Muhanna, Z. Naserullah, A. Alsuliman, et al. "Polymorphisms Associated with the Arab-Indian Haplotype of Sickle Cell Anemia Are Candidate Fetal Hemoglobin Gene Modulators." Blood 126, no. 23 (December 3, 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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Tjensvoll, Kjersti, Ove Bruland, Ylva Floderus, Øyvind Skadberg, Sverre Sandberg, and Jaran Apold. "Haplotype Analysis of Norwegian and Swedish Patients with Acute Intermittent Porphyria (AIP): Extreme Haplotype Heterogeneity for the Mutation R116W." Disease Markers 19, no. 1 (2003): 41–46. http://dx.doi.org/10.1155/2003/384971.

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Acute intermittent porphyria (AIP), the most common of the acute porphyrias, is caused by mutations in the gene encoding hydroxymethylbilane synthase (HMBS) also called porphobilinogen deaminase (PBGD). The mutation spectrum in the HMBS gene is characterized by a majority of family specific mutations. Among the exceptions are R116W and W198X, with high prevalence in both the Dutch and Swedish populations. These two mutations were also detected in unrelated Norwegian patients. Thus, Norwegian and Swedish patients were haplotyped using closely linked flanking microsatellites and intragenic single nucleotide polymorphisms (SNPs) to see if the high frequency of these two mutations is due to a founder effect. Twelve intragenic SNPs were determined by a method based on fluorescent restriction enzyme fingerprinting single-strand conformation polymorphism (F-REF-SSCP).W198X occurred exclusively on one haplotype in both Norwegian and Swedish patients, showing that it has originated from a common gene source. In contrast, R116W was found on three different haplotypes in three Norwegian families, and in five Swedish families on four or five haplotypes. This extreme haplotype heterogeneity indicates that R116W is a recurrent mutation, maybe explained by the high mutability of CpG dinucleotides. This can also explain why it is the only AIP mutation reported to occur in seven different populations (Norway, Sweden, Finland, Netherlands, France, Spain and South Africa).
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TAN, QIHUA, LENE CHRISTIANSEN, KAARE CHRISTENSEN, LISE BATHUM, SHUXIA LI, JING HUA ZHAO, and TORBEN A. KRUSE. "Haplotype association analysis of human disease traits using genotype data of unrelated individuals." Genetical Research 86, no. 3 (November 25, 2005): 223–31. http://dx.doi.org/10.1017/s0016672305007792.

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Haplotype inference has become an important part of human genetic data analysis due to its functional and statistical advantages over the single-locus approach in linkage disequilibrium mapping. Different statistical methods have been proposed for detecting haplotype – disease associations using unphased multi-locus genotype data, ranging from the early approach by the simple gene-counting method to the recent work using the generalized linear model. However, these methods are either confined to case – control design or unable to yield unbiased point and interval estimates of haplotype effects. Based on the popular logistic regression model, we present a new approach for haplotype association analysis of human disease traits. Using haplotype-based parameterization, our model infers the effects of specific haplotypes (point estimation) and constructs confidence interval for the risks of haplotypes (interval estimation). Based on the estimated parameters, the model calculates haplotype frequency conditional on the trait value for both discrete and continuous traits. Moreover, our model provides an overall significance level for the association between the disease trait and a group or all of the haplotypes. Featured by the direct maximization in haplotype estimation, our method also facilitates a computer simulation approach for correcting the significance level of individual haplotype to adjust for multiple testing. We show, by applying the model to an empirical data set, that our method based on the well-known logistic regression model is a useful tool for haplotype association analysis of human disease traits.
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Anantaphruti, Malinee, Urusa Thaenkham, Teera Kusolsuk, Wanna Maipanich, Surapol Saguankiat, Somjit Pubampen, and Orawan Phuphisut. "Genetic Variation and Population Genetics ofTaenia saginatain North and Northeast Thailand in relation toTaenia asiatica." Journal of Parasitology Research 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/310605.

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Taenia saginatais the most common humanTaeniain Thailand. Bycox1sequences, 73 isolates from four localities in north and northeast were differentiated into 14 haplotypes, 11 variation sites and haplotype diversity of 0.683. Among 14 haplotypes, haplotype A was the major (52.1%), followed by haplotype B (21.9%). Clustering diagram of Thai and GenBank sequences indicated mixed phylogeny among localities. By MJ analysis, haplotype clustering relationships showed paired-stars-like network, having two main cores surrounded by minor haplotypes. Tajima’sDvalues were significantly negative inT. saginataworld population, suggesting population expansion. Significant Fu’sFsvalues in Thai, as well as world population, also indicate that population is expanding and may be hitchhiking as part of selective sweep. Haplotype B and its dispersion were only found in populations from Thailand. Haplotype B may evolve and ultimately become an ancestor of future populations in Thailand. Haplotype A seems to be dispersion haplotype, not just in Thailand, but worldwide. High geneticT. saginataintraspecies divergence was found, in contrast to its sister species,T. asiatica; among 30 samples from seven countries, its haplotype diversity was 0.067, while only 2 haplotypes were revealed. This extremely low intraspecific variation suggests thatT. asiaticacould be an endangered species.
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Pae, C. U. "Association Analysis of Heat Shock Protein 70 Gene Polymorphisms in Schizophrenia." European Psychiatry 24, S1 (January 2009): 1. http://dx.doi.org/10.1016/s0924-9338(09)71415-4.

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Objectives:This study investigated the association between an enlarged set of SNPs at Heat shock proteins (HSPs) 70 gene and schizophrenia.Methods:Two hundred and ninety four patients with schizophrenia and 287 controls were enrolled in the study. Genotypings of 5 SNPs of HSP70 were performed using pyrosequencing method.Results:Significant association was detected at rs2075799 (allele A, Chi suare =8.03, d.f.=1 p=0.0046), but not at rs2227956 (p=0.28), rs1043618 (p=0.88), rs562047 (p=0.47) or rs539689 (p=0.32). in fact, the rs2075799*G/A genotype was more represented in patients with schizophrenia than in controls (Chi-sq=8.23, d.f.=1, p=0.0041). Haplotype based associations were also detected (global p value 0.000003); the T-A-C-C-G haplotype was more prevalent among the patients (odds ratio, OR 5.95). Sliding windows analysis revealed a major contribution from rs2227956 and rs2075799 (global-p value 0.0075), with T-A haplotype significantly associated with schizophrenia. There was no evidence of an association between the clinical variables and schizophrenia across the genotypes.Conclusion:Our results raise the possibility that HSP70 gene (i.e., haplotypes of rs2075799) might be implicated in the development of schizophrenia, although limited by rare haplotypic association with the disease. Hence further studies from different ethnics should be performed to confirm these results.
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Dissertations / Theses on the topic "Haplotype analysi"

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Waldron, Edward. "Analysis of genetic association studies via haplotype clustering." Thesis, Imperial College London, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.497253.

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Tai, Bik-wah Diana, and 戴碧華. "Haplotype analysis of the family with Lynch syndrome." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B45153772.

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Yatskiv, Yuriy Romanovich. "A Haplotype Analysis of an Archaic Denisovan Genome." University of Toledo Health Science Campus / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=mco1481145733356233.

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Zhao, Jiantao. "Combining Association and Haplotype Studies Towards the Improvement of Fruit Quality in Tomato Multiple haplotype-based analyses provide genetic and evolutionary insights into tomato fruit weight and composition Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor Genomic designing for climate smart tomato." Thesis, Avignon, 2019. http://www.theses.fr/2019AVIG0712.

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Les consommateurs se plaignent de la qualité gustative des tomates depuis des décennies. Celle-ci est influencée principalement par les sucres, les acides et un ensemble de divers composés volatils. L’amélioration de la saveur de la tomate reste l’un des principaux défis à relever pour améliorer la qualité de la tomate et l’acceptabilité des consommateurs pour l’amélioration moderne des tomates. Le but principal de cette thèse était de disséquer le contrôle génétique de la saveur de la tomate en utilisant des SNP à haute densité et un ensemble divers de traits liés à la saveur, notamment les sucres, les acides, les acides aminés et les composés volatils. Dans la première partie, j'ai effectué plusieurs analyses basées sur l’exploration des haplotypes dans une collection d’accessions. Plusieurs approches ont été utilisées et comparées pour identifier les régions génomiques en cours de sélection. Les modèles bayésiens de génétique d’association basés sur les haplotypes et une partie des SNP ont identifié 108 associations significatives pour 26 caractères. Parmi ces associations, certains gènes candidats prometteurs ont été identifiés. Certains avantages de l’utilisation des haplotypes ont également été présentés. Dans la deuxième partie, j'ai réalisé une méta-analyse d'études d'association pangénomique à l'aide de trois panels d'associations de tomates. J'ai démontré l'efficacité de l'imputation des génotypes pour augmenter la couverture de SNP à l'échelle du génome. Des méta-analyses de modèles à effets fixes et à effets aléatoires (pour les SNP présentant une hétérogénéité I2 > 25) ont été effectuées afin de contrôler l'hétérogénéité croisée des études. Au total, 305 locus significatifs ont été identifiés, dont 211 nouveaux. Parmi ceux-ci, 24 locus ont présenté des cis-eQTL lors d'une précédente étude d'association à l'échelle du transcriptome de fruits. L'analyse d'enrichissement pour toutes les associations a montré que jusqu'à 10 processus biologiques étaient enrichis de manière significative et que tous étaient étroitement impliqués dans les métabolites liés aux arômes. Une liste de gènes candidats prometteurs a été fournie, qui pourraient présenter un grand intérêt pour la validation fonctionnelle. J'ai également démontré la possibilité d'augmenter de manière significative le contenu en composés volatils qui contribuent de manière positive aux préférences des consommateurs tout en réduisant les volatils désagréables, en sélectionnant les combinaisons d'allèles pertinentes. Globalement, cette thèse augmente les connaissances du contrôle génétique du goût de la tomate, ce qui devrait contribuer à son amélioration
Consumers have been complaining about tomato flavor for decades. Tomato taste is mainly influenced by sugars, acids and a diverse set of volatiles. Improving tomato flavor remains one of the main challenges for improving tomato sensory quality and consumer acceptability in modern tomato breeding. The main purpose of this thesis was to decipher the genetic and evolutionary control of tomato flavor by using high density SNPs and a diverse set of flavor-related metabolites, including sugars, acids, amino acids and volatiles. In the first part, I performed multiple haplotype-based analyses on a tomato core collection. Several approaches were used and compared to identify the genomic regions under selection. Haplotype and SNP-based Bayesian models identified 108 significant associations for 26 traits. Among these associations, some promising candidate genes were identified. I also compared marker local haplotype sharing (mLHS) with LD in determining the candidate regions. In addition, some general benefits of using haplotypes were also provided as general discussions. In the second part, I pioneered in introducing meta-analysis of genome-wide association studies using three tomato association panels. I demonstrated the efficiency of genotype imputation in increasing the genome-wide SNP coverage. Both fixed-effect and random-effect models (for those SNPs with heterogeneity I2 > 25) of meta-analysis were performed in order to control cross-study heterogeneity. A total of 305 significant loci were identified and 211 of which were new. Among them, 24 loci exhibited cis-eQTLs in a previous transcriptome-wide association study in fruit tissue. Enrichment analysis for all associations showed that up to 10 biological processes were significantly enriched and all of which were closely involved in flavor-related metabolites. A list of promising candidate genes was provided, which could be of great interest for functional validation. I also demonstrated the possibility to significantly increase the content of volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Taken together, this thesis provides a comprehensive knowledge of the genetic control of tomato flavor, which will promote its improvement
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Lächelt, Sandra [Verfasser]. "Funktionelle Analyse von ABCC2-Haplotypen / Sandra Lächelt." Kiel : Universitätsbibliothek Kiel, 2009. http://d-nb.info/1019869933/34.

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Hughes, David J. "Mutation characterisation and microsatellite haplotype analysis of the CFTR gene." Thesis, Queen's University Belfast, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361278.

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Osman, Abdimajid. "Studies on warfarin treatment with emphasis on inter-individual variations and drug monitoring." Doctoral thesis, Linköping : Linköping University, 2007. http://www.bibl.liu.se/liupubl/disp/disp2007/med1000s.pdf.

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ROSA, Rogério dos Santos. "Associating genotype sequence properties to haplotype inference errors." Universidade Federal de Pernambuco, 2015. https://repositorio.ufpe.br/handle/123456789/16011.

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Haplotype information has a central role in the understanding and diagnosis of certain illnesses, and also for evolution studies. Since that type of information is hard to obtain directly, computational methods to infer haplotype from genotype data have received great attention from the computational biology community. Unfortunately, haplotype inference is a very hard computational biology problem and the existing methods can only partially identify correct solutions. I present neural network models that use different properties of the data to predict when a method is more prone to make errors. I construct models for three different Haplotype Inference approaches and I show that our models are accurate and statistically relevant. The results of our experiments offer valuable insights on the performance of those methods, opening opportunity for a combination of strategies or improvement of individual approaches. I formally demonstrate that Linkage Disequilibrium (LD) and heterozygosity are very strong indicators of Switch Error tendency for four methods studied, and I delineate scenarios based on LD measures, that reveal a higher or smaller propension of the HI methods to present inference errors, so the correlation between LD and the occurrence of errors varies among regions along the genotypes. I present evidence that considering windows of length 10, immediately to the left of a SNP (upstream region), and eliminating the non-informative SNPs through Fisher’s Test leads to a more suitable correlation between LD and Inference Errors. I apply Multiple Linear Regression to explore the relevance of several biologically meaningful properties of the genotype sequences for the accuracy of the haplotype inference results, developing models for two databases (considering only Humans) and using two error metrics. The accuracy of our results and the stability of our proposed models are supported by statistical evidence.
Haplótipos têm um papel central na compreensão e diagnóstico de determinadas doenças e também para estudos de evolução. Este tipo de informação é difícil de obter diretamente, diante disto, métodos computacionais para inferir haplótipos a partir de dados genotípicos têm recebido grande atenção da comunidade de biologia computacional. Infelizmente, a Inferência de Halótipos é um problema difícil e os métodos existentes só podem predizer parcialmente soluções corretas. Foram desenvolvidos modelos de redes neurais que utilizam diferentes propriedades dos dados para prever quando um método é mais propenso a cometer erros. Foram calibrados modelos para três abordagens de Inferência de Haplótipos diferentes e os resultados validados estatisticamente. Os resultados dos experimentos oferecem informações valiosas sobre o desempenho e comportamento desses métodos, gerando condições para o desenvolvimento de estratégias de combinação de diferentes soluções ou melhoria das abordagens individuais. Foi demonstrado que Desequilíbrio de Ligação (LD) e heterozigosidade são fortes indicadores de tendência de erro, desta forma foram delineados cenários com base em medidas de LD, que revelam quando um método tem maior ou menor propensão de cometer erros. Foi identificado que utilizando janelas de 10 SNPs (polimorfismo de um único nucleotídeo), imediatamente a montante, e eliminando os SNPs não informativos pelo Teste de Fisher leva-se a uma correlação mais adequada entre LD e a ocorrência de erros. Por fim, foi aplicada análise de Regressão Linear para explorar a relevância de várias propriedades biologicamente significativas das sequências de genótipos para a precisão dos resultados de Inferência de Haplótipos, estimou-se modelos para duas bases de dados (considerando apenas humanos) utilizando duas métricas de erro. A precisão dos resultados e a estabilidade dos modelos propostos foram validadas por testes estatísticos.
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Nettelblad, Carl. "Two Optimization Problems in Genetics : Multi-dimensional QTL Analysis and Haplotype Inference." Doctoral thesis, Uppsala universitet, Avdelningen för beräkningsvetenskap, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-180920.

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The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools. The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures. The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS).
eSSENCE
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Neville, Catherine E. "The high resolution haplotype analysis and origin of the myotonic dystrophy mutation." Thesis, University of Ottawa (Canada), 1994. http://hdl.handle.net/10393/9857.

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The objective of this thesis was to determine the origin of the myotonic dystrophy (DM) mutation. I have used PCR-based assays of nine polymorphisms spanning a physical distance of 30 kb, within and immediately flanking the DM kinase gene, in order to examine patterns of allelic association with respect to the DM mutation. Four main haplotypes (A-D) were observed in the normal population using these nine markers at the DM locus. Significantly, DM is in complete association with haplotype A, the most common haplotype in the normal population. Our data suggest the presence of two founding chromosomes: one containing a stretch of five contiguous Alu elements (the progenitor for haplotype A) and the other in which three of these have been deleted (the progenitor for haplotypes B, C and D). Individuals with haplotype A displayed the full spectrum of (CTG)$\sb{\rm n}$ number, ranging from 5 to 35 repeats. The (CTG)$\sb5$ alleles as well as alleles with greater than 19 repeats are exclusively linked to haplotype A. In contrast, alleles in which the three Alu elements are deleted possess only (CTG)$\sb{11-14}$ repeats. Although the inference that the loss of the three Alu repeats may confer increased stability on the (CTG)$\sb{\rm n}$ repeat is speculative, the narrow size range of the (CTG)$\sb{\rm n}$ repeat on chromosomes in which the Alu elements have been deleted, relative to the variation seen on normal chromosomes with the DM haplotype (i.e. haplotype A), is striking. (Abstract shortened by UMI.)
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Books on the topic "Haplotype analysi"

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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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Sorin, Istrail, Waterman Michael S, and Clark Andrew G. 1954-, eds. 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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Mészáros, Gábor, Marco Milanesi, Paolo Ajmone Marsan, and Yuri Tani Utsunomiya, eds. 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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Waterman, Michael, Clark Andrew, and Sorin Istrail. Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satellite Workshop, Piscataway, NJ, USA, November 21-22, 2002, Revised Papers. Springer London, Limited, 2004.

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Crawford, Michael, and Rohina C. Rubicz. Molecular Genetic Evidence from Contemporary Populations for the Origins of Native North Americans. Edited by Max Friesen and Owen Mason. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199766956.013.4.

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An overview of the current molecular genetic evidence for the origins of North American populations is presented, including specific examples from the authors’ work with the Aleutian Island inhabitants. Shared mitochondrial DNA and Y-chromosome DNA markers among Siberians and Native Americans point to a Pleistocene migration from Siberia into the Americas via Beringia. There was likely a later migration from Siberia to Alaska, based on the analysis of whole-genome sequence data from a Greenland Paleoeskimo that clusters this individual with Siberian populations. Coalescence date estimates for Native American mitochondrial DNA and Y-chromosome DNA haplogroups indicate that there was a population expansion approximately 15,000–18,000 that was associated with a pre-Clovis settlement of the Americas and coastal migration, and then a later expansion of circum-Arctic populations. Settlement of the Aleutian Archipelago took place via east-to-west migration of Aleut kin groups, accompanied by a clinal loss in mitochondrial DNA haplotype diversity.
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Lewis, Myles, and Tim Vyse. Genetics of connective tissue diseases. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0042.

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The advent of genome-wide association studies (GWAS) has been an exciting breakthrough in our understanding of the genetic aetiology of autoimmune diseases. Substantial overlap has been found in susceptibility genes across multiple diseases, from connective tissue diseases and rheumatoid arthritis (RA) to inflammatory bowel disease, coeliac disease, and psoriasis. Major technological advances now permit genotyping of millions of single nucleotide polymorphisms (SNPs). Group analysis of SNPs by haplotypes, aided by completion of the Hapmap project, has improved our ability to pinpoint causal genetic variants. International collaboration to pool large-scale cohorts of patients has enabled GWAS in systemic lupus erythematosus (SLE), systemic sclerosis and Behçet's disease, with studies in progress for ANCA-associated vasculitis. These 'hypothesis-free' studies have revealed many novel disease-associated genes. In both SLE and systemic sclerosis, identified genes map to known pathways including antigen presentation (MHC, TNFSF4), autoreactivity of B and T lymphocytes (BLK, BANK1), type I interferon production (STAT4, IRF5) and the NFκ‎B pathway (TNIP1). In SLE alone, additional genes appear to be involved in dysregulated apoptotic cell clearance (ITGAM, TREX1, C1q, C4) and recognition of immune complexes (FCGR2A, FCGR3B). Future developments include whole-genome sequencing to identify rare variants, and efforts to understand functional consequences of susceptibility genes. Putative environmental triggers for connective tissue diseases include infectious agents, especially Epstein-Barr virus; cigarette smoking; occupational exposure to toxins including silica; and low vitamin D, due to its immunomodulatory effects. Despite numerous studies looking at toxin exposure and connective tissue diseases, conclusive evidence is lacking, due to either rarity of exposure or rarity of disease.
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Book chapters on the topic "Haplotype analysi"

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Martin, Marcel, Peter Ebert, and Tobias Marschall. "Read-Based Phasing and Analysis of Phased Variants with WhatsHap." In 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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Delaneau, Olivier, and Jean-François Zagury. "Haplotype Inference." In Data Production and Analysis in Population Genomics, 177–96. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-870-2_11.

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Epstein, Michael P., and Lydia C. Kwee. "Haplotype Association Analysis." In Handbook on Analyzing Human Genetic Data, 241–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-69264-5_8.

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Stram, Daniel O. "Haplotype Imputation for Association Analysis." In Design, Analysis, and Interpretation of Genome-Wide Association Scans, 183–211. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-9443-0_5.

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Wetmur, James G., and Jia Chen. "Linking Emulsion PCR Haplotype Analysis." In Methods in Molecular Biology, 165–75. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-944-4_11.

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Zheng, Gang, Yaning Yang, Xiaofeng Zhu, and Robert C. Elston. "Haplotype Analysis for Case-Control Data." In Analysis of Genetic Association Studies, 209–33. Boston, MA: Springer US, 2012. http://dx.doi.org/10.1007/978-1-4614-2245-7_7.

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Graça, Ana, João Marques-Silva, and Inês Lynce. "Haplotype Inference Using Propositional Satisfiability." In Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 127–47. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-6800-5_7.

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Roeder, Kathryn. "Evolutionary-Based Association Analysis Using Haplotype Data." In Computational Methods for SNPs and Haplotype Inference, 144. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_24.

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Stram, Daniel O., and Venkatraman E. Seshan. "Multi-SNP Haplotype Analysis Methods for Association Analysis." In Methods in Molecular Biology, 423–52. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-555-8_23.

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Stram, Daniel O. "Multi-SNP Haplotype Analysis Methods for Association Analysis." In Methods in Molecular Biology, 485–504. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7274-6_24.

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Conference papers on the topic "Haplotype analysi"

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Lin, Shili, and Terence P. Speed. "An algorithm for haplotype analysis." In the first annual international conference. New York, New York, USA: ACM Press, 1997. http://dx.doi.org/10.1145/267521.267548.

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Tejera, P., Z. Wang, R. Zhai, L. Su, CC Sheu, and DC Christiani. "Functional Analysis of Haplotypes inPI3Promoter." In 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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Sadovnychenko, Iurii, and Nataliia Pastukhova. "Open data of molecular genetic research through the prism of global trends." In First International Conference "Open Science and Innovation in Ukraine 2022". State Scientific and Technical Library of Ukraine, 2022. http://dx.doi.org/10.35668/978-966-479-129-5-7-18.

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The availability analysis of genetic databases in the articles of Ukrainian and foreign scientists was performed. Only 6.4 % of articles in domestic journals provided data on the subjects’ genotype and haplotype distribution. Most journals are open access, but their editorial policy does not postulate their commitment to open data sharing.
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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.

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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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Uddin, Mohammed, Mitch Sturge, Courtenay Griffin, Steve Benteau, and Proton Rahman. "Variability of haplotype phase and its effect on genetic analysis." In 2008 Canadian Conference on Electrical and Computer Engineering - CCECE. IEEE, 2008. http://dx.doi.org/10.1109/ccece.2008.4564604.

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KHRABROVA, Lyudmila A., Alexander M. ZAITSEV, Larisa L. VIKULOVA, Marina V. ADAMKOVSKAYA, Nina V. BLOKHINA, and Sergey I. SOROKIN. "MtDNA Haplotype Analysis in Dam Families of the Thoroughbred Riding Horses." In XVIII International Scientific and Practical Conference "Modern Trends in Agricultural Production in the World Economy". Sibac, 2020. http://dx.doi.org/10.32743/kuz.agri.2020.34-42.

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"Haplotype Block Analysis of FSHR Gene in Sragen and Jabres Cattle." In Technology Innovations and Collaborations in Livestock Production for Sustainable Food Systems. IAARD Press, 2021. http://dx.doi.org/10.14334/proc.intsem.lpvt-2021-p.16.

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NG, MICHAEL K., ERIC S. FUNG, WAI-KI CHING, and YIU-FAI LEE. "A RECURSIVE METHOD FOR SOLVING HAPLOTYPE FREQUENCIES IN MULTIPLE LOCI LINKAGE ANALYSIS." In 4th Asia-Pacific Bioinformatics Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2005. http://dx.doi.org/10.1142/9781860947292_0016.

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Karkar, S., A. Gloaguen, Y. Le Guen, M. Pierre-Jean, C. Dandine-Roulland, E. Le Floch, C. Philippe, A. Tenenhaus, and V. Frouin. "Multivariate Haplotype Analysis Of 96 Sulci Opening For 15,612 UK-Biobank Sujects." In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI). IEEE, 2019. http://dx.doi.org/10.1109/isbi.2019.8759497.

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Devatha Venkatesh, Sowmya, Mathew Varghese, Ravi Yadav, Sanjeev Jain, and Meera Purushottam. "C10 Haplotype structure analysis of Indian Huntington’s disease patients at HTT gene locus." In EHDN 2022 Plenary Meeting, Bologna, Italy, Abstracts. BMJ Publishing Group Ltd, 2022. http://dx.doi.org/10.1136/jnnp-2022-ehdn.54.

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Reports on the topic "Haplotype analysi"

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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, May 2007. http://dx.doi.org/10.21236/ad1014058.

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

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

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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.
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Fahima, Tzion, and Jorge Dubcovsky. Map-based cloning of the novel stripe rust resistance gene YrG303 and its use to engineer 1B chromosome with multiple beneficial traits. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598147.bard.

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