Relevant bibliographies by topics / Chromosome polymorphism

Academic literature on the topic 'Chromosome polymorphism'

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Published: 4 June 2021
Last updated: 25 July 2024

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Journal articles on the topic "Chromosome polymorphism"

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Taran Kyzy, Jafar Aliyev. "Value heterochromatin and polymorphic varian gene folat cycle in women with miscarried and losses of pregnancy." HEALTH OF WOMAN, no. 9(115) (November 30, 2016): 148–51. http://dx.doi.org/10.15574/hw.2016.115.148.

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The article presents data from surveys of women of losses of pregnancy (LP) in history, conducted within the medical genetic counseling, given the urgency of specifying genetic factors that actually are in causal connection with the LP specification clinical effects of epigenetic variability. The objective: to clarify the meaning of the changes in women heterochromatin (chromosomal polymorphism) and polymorphic variants of genes folat cycle enzymes as potential risk factors and pathogenic primordial LP. Patients and methods. The study involved two groups of women: I - 154 observations with complicated obstetric history in LP and II - 32 healthy women with uncomplicated reproductive history, held preconception planning to prevent pregnancy. Studied genealogical history, especially of internal organs, genitalia. Special studies included cytogenetic analysis, identification of gene polymorphisms system folat cycle methylentetrahydrofolate reductase [MTHFR] (C677T, A1298C, G1793A); methionine synthase reductase [MTRR] (A66G). Results. Women with a history of LP in 36.4% identified chromosome polymorphisms (SNPs extreme variants of chromosome polymorphism) on the background of various risk alleles of polymorphic variants of genes folat cycle; 7.1% of them is a polymorphism of the 21st chromosome. These genetic features are interpreted as a significant risk factor for LP as grounds for targeted in-depth medical and genetic examination. Prevalence among women with a history of PL undifferentiated forms cjnnective tissue and mesoderm dysplasia, benign tumors and «precancerous» states, as well as the prevalence of cardiovascular and psycho-neurological disease in pedigree suggests pathogenetic link these phenomena, the role of chromosomal polymorphism and polymorphic variants of genes of pathogenic folat cycle as primordial. Conclusion. The data on the place and role of heterochromatin and gene polymorphisms folat cycle in the origin LP should be mandatory option when examining women within the medical genetic counseling. Key words: pregnancy, reproductive losses, chromosomal instability, folat cycle genes, ancestry.
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Nishioka, Yutaka. "Two types of mouse (Mus musculus domesticus) Y chromosomes in Quebec." Genome 35, no. 3 (June 1, 1992): 534–37. http://dx.doi.org/10.1139/g92-078.

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A Y chromosomal repetitive sequence identified two types of Y chromosomes in mice (Mus musculus domesticus) caught near Ste. Anne de Bellevue, Quebec. One type is apparently identical to the Y chromosome found in Maryland, Delaware, and California, whereas the other type is similar, but not identical, to the Y chromosome present in M.m. poschiavinus, an Alpine race of M.m. domesticus. These findings suggest that the domesticus Y chromosome is highly polymorphic and thus useful for elucidating the relationships among American and European house mouse populations.Key words: mouse Y chromosome, polymorphism, Mus musculus domesticus, repetitive sequence, Quebec.
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Angelova, Lyudmila, Maria Tsvetkova, and Mariya Levkova. "CHROMOSOMAL POLYMORPHISM IN BULGARIAN PATIENTS WITH REPRODUCTIVE PROBLEMS – ONE GENETIC CENTRE EXPERIENCE." Journal of IMAB - Annual Proceeding (Scientific Papers) 27, no. 4 (December 2, 2021): 4133–38. http://dx.doi.org/10.5272/jimab.2021274.4133.

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Chromosomal polymorphism is described as normal variants at chromosomal regions with no impact on the phenotype but a possible correlation to infertility and recurrent spontaneous abortions. The aim of this study was to evaluate the effect of the chromosomal polymorphisms involved in families with reproductive failures in the Bulgarian population. Material and methods: A total of 1733 patients with unexplained reproductive failures who visited the Laboratory of Medical Genetics – Varna, Bulgaria, (2004 - 2019) were investigated by conventional cytogenetic analysis GTG and CBG differential banding techniques and analyzed at the resolution 400-550 GTG bands. Results: Chromosomal polymorphisms were found in 173 infertile patients (9,98%). The sex distribution was 6,52% males and 3,46% females. The most frequent finding was inv(9)(qh) (23,7%). The other chromosomal variants, which were found, consisted: 9qh+/- variants (15,1%); polymorphisms on the short arms of the acrocentric chromosomes (21,4%); 16qh+ (12,7%) and 1qh+ (6,9%). Y chromosome polymorphism was found in 27,4% of the males with polymorphisms. Two rare cases of polymorphism involving the centromere regions - 19qcenh+ and 20pcenh+ were also found. Conclusion: There is growing evidence that polymorphisms may have a clinical impact on fertility and could take part in the etiology of RF. In this study, we found a significantly high percentage of polymorphisms (9,98%) among the tested patients, and they were more common among males. The statistical significance of increased incidence of chromosome variations found in our study emphasizes the need for routine evaluation of their role in families with RF in our country.
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Hatsumi, Machiko. "Karyotype polymorphism in Drosophila albomicans." Genome 29, no. 3 (June 1, 1987): 395–400. http://dx.doi.org/10.1139/g87-069.

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Supernumerary (B) chromosomes are present in Thai, Malay, and Burmese populations of Drosophila albomicans (2n = 6) in a polymorphic state. Although usually stable at mitosis, their numbers differed between individuals and their frequency was also different between isofemale lines and between populations. Arm 3 of the X3 chromosome was polymorphic for the presence and the size of a procentric heterochromatic segment. Chromosome 4 is polytypic for variation in length governed by differences in the amount of heterochromatin and the long variant is polymorphic for the location of its secondary constriction. Key words: Drosophila albomicans, karyotype polymorphism, B chromosome.
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Mukhopadhyay, Saswati, Sujoy Dasgupta, Kushagradhi Ghosh, and Tania Mukherjee. "Investigating the relation between chromosomal polymorphism and recurrent pregnancy loss: A cohort study." Indian Journal of Obstetrics and Gynecology Research 9, no. 3 (August 15, 2022): 391–96. http://dx.doi.org/10.18231/j.ijogr.2022.074.

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Chromosomal polymorphisms (CPM) are minor variation of karyotype, found in >1% of the general population. Heterochromatin, the inactive part of the chromosome, shows frequent polymorphism - increase/decrease in length. Recently, studies show that heterochromatin is not inert, but contains genes essential for spindle attachment, chromosome movement, meiotic pairing, and sister chromatid cohesion. Balanced translocation in parents, reciprocal and robertsonian, can disrupt important genes, and produce gametes with unbalanced gene dosage, causing spontaneous miscarriage. To correlate between chromosomal polymorphisms/ structural alterations and first trimester Recurrent Pregnancy Loss (RPL) primary infertility. : 100 couples with primary infertility or RPLs, were karyotyped by 72-h whole blood culture. Giemsa banding (GTG) was done in all cases. 20 metaphases were analysed according to the ISCN criteria. The total no. of RPLs was noted for each couple with abnormal karyotype. Of the 44 couples with abnormal karyotype, 36 (82%) had chromosomal polymorphism, 7 (16%) showed structural abnormality and 1 (2%) had numerical abnormality. Chromosome 9qh+ was present in the majority (33.33%). Among the D, G chromosomes, chromosome 15ps+/pstk+ were found in 22.22% but average no. of RPL was 2.15, whereas average RPL in Chr.22ps+ (incidence 5.55%.) was 3 (highest). Among male partners, Chr.Yqh+/Yqh- were found in 12 (33.33%) couples. Among the structural abnormalities (16%), balanced translocation accounted for 11.36%, maximum of which were Reciprocal translocations. The frequency of chromosomal abnormalities is higher among couples with RPLs and infertility, compared to the general population. Karyotyping gives important genetic information, thus acting as a good diagnostic tool, and helps to plan ART or perform prenatal testing.
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Rovatsos, Michail T., Juan A. Marchal, Ismael Romero-Fernández, Maria Arroyo, Eva B. Athanasopoulou, and Antonio Sánchez. "Extensive Sex Chromosome Polymorphism of Microtus thomasi/Microtus atticus Species Complex Associated with Cryptic Chromosomal Rearrangements and Independent Accumulation of Heterochromatin." Cytogenetic and Genome Research 151, no. 4 (2017): 198–207. http://dx.doi.org/10.1159/000477114.

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The sibling species Microtus thomasi and M. atticus represent probably the highest karyotypic diversity within the genus Microtus and are an interesting model for chromosomal evolution studies. In addition to variation in autosomes, they show a high intraspecific variation in the size and morphology of both sex chromosomes. We analyzed individuals with different sex chromosome constitutions using 3 painting probes, 2 from Y chromosome variants and 1 from the small arm of the submetacentric X chromosome. Our comparative painting approach uncovered 12 variants of Y and 14 variants of X chromosomes, which demonstrates that the polymorphism of sex chromosomes is substantially larger than previously reported. We suggest that 2 main processes are responsible for this sex chromosome polymorphism: change of morphology from acrocentric to submetacentric or metacentric chromosomes and increase in size due to accumulation of repetitive DNA sequences, generating heterochromatic blocks. Strong genetic drift in small and fragmented populations of these 2 species could be related to the origin and maintenance of the large polymorphism of sex chromosomes. We proposed that a similar polymorphism variation combined with random drift fixing the biggest sex chromosomes could have occurred in the origin of some of the actual Microtus species with giant sex chromosomes.
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Hashimoto, Diogo Teruo, and Fábio Porto-Foresti. "Chromosome polymorphism of heterochromatin and nucleolar regions in two populations of the fish Astyanax bockmanni (Teleostei: Characiformes)." Neotropical Ichthyology 8, no. 4 (2010): 861–66. http://dx.doi.org/10.1590/s1679-62252010000400016.

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Karyotype and other chromosomal markers as revealed by C-banding and silver (Ag) impregnation in two Astyanax bockmanni populations (Barra Seca Stream and Campo Novo River) were examined. The diploid chromosome number 2n = 50 and nearly identical karyotypes were documented. C-banding revealed heterochromatic blocks on the terminal regions of some chromosomes, with high frequencies of polymorphisms. The Ag-impregnation showed that the nucleolus organizer regions (NORs) varied in number, location and organization. Astyanax bockmanni revealed chromosome characteristics similar those of the species complex "A. scabripinnis". Mechanisms that may be responsible for the high degree of polymorphism are discussed.
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HENRIKSSON, J., J. C. DUJARDIN, C. BARNABÉ, S. BRISSE, G. TIMPERMAN, J. VENEGAS, U. PETTERSSON, M. TIBAYRENC, and A. SOLARI. "Chromosomal size variation in Trypanosoma cruzi is mainly progressive and is evolutionarily informative." Parasitology 124, no. 3 (March 2002): 277–86. http://dx.doi.org/10.1017/s0031182001001093.

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The evolutionary significance of chromosome size polymorphism was explored in a representative panel of 26 Trypanosoma cruzi stocks. We tested a progressive model (aCSDI) assuming that the larger the size difference between homologous chromosomes, the more divergent the parasites are. This was contrasted with a non-progressive model (Jaccard's distance), in which any chromosome size difference has the same weight. ACSDI-based dendrograms were very similar to those built-up from multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA (RAPD) data: structuring in 2 major lineages (T. cruzi I and T. cruzi II) and 5 small subdivisions within T. cruzi II was identical, and branching was very similar. Furthermore, a significant correlation (P<0·001) was observed between aCSDI and phenetic distances calculated from MLEE and RAPD data. In contrast, analysis of chromosome size polymorphism with Jaccard's distance generated dendrograms with relatively long branches, causing most branching points to cluster close together, which generates statistically uncertain branching points. Our results thus support a model of progressive chromosome size-variation and show that despite an extensive polymorphism, chromosomal sizes constitute valuable characters for evolutionary analyses. Furthermore, our data are consistent with the clonal evolution model previously proposed for T. cruzi.
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Vieira, Cristina P., Paula A. Coelho, and Jorge Vieira. "Inferences on the Evolutionary History of theDrosophila americanaPolymorphicX/4Fusion From Patterns of Polymorphism at theX-LinkedparalyticandelavGenes." Genetics 164, no. 4 (August 1, 2003): 1459–69. http://dx.doi.org/10.1093/genetics/164.4.1459.

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AbstractIn Drosophila there is limited evidence on the nature of evolutionary forces affecting chromosomal arrangements other than inversions. The study of the X/4 fusion polymorphism of Drosophila americana is thus of interest. Polymorphism patterns at the paralytic (para) gene, located at the base of the X chromosome, suggest that there is suppressed crossing over in this region between fusion and nonfusion chromosomes but not within fusion and nonfusion chromosomes. These data are thus compatible with previous claims that within fusion chromosomes the amino acid clines found at fused1 (also located at the base of the X chromosome) are likely maintained by local selection. The para data set also suggests a young age of the X/4 fusion. Polymorphism data on para and elav (located at the middle region of the X chromosome) suggest that there is no population structure other than that caused by the X/4 fusion itself. These findings are therefore compatible with previous claims that selection maintains the strong association observed between the methionine/threonine variants at fused1 and the status of the X chromosome as fused or unfused to the fourth chromosome.
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Zolan, M. E., N. K. Heyler, and N. Y. Stassen. "Inheritance of chromosome-length polymorphisms in Coprinus cinereus." Genetics 137, no. 1 (May 1, 1994): 87–94. http://dx.doi.org/10.1093/genetics/137.1.87.

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Abstract We have investigated the inheritance of chromosome-length polymorphisms in the basidiomycete Coprinus cinereus. The electrophoretic karyotypes of interfertile strains of C. cinereus are strikingly different, and crosses between strains with different karyotypes yield progeny with chromosomes of new sizes. Repeated backcrossing of a mutant to one parent often stabilizes the mutant chromosome at a unique size; this then becomes a chromosome-length polymorphism marker for that mutant gene. A comparison of mutant strains, their wild-type progenitor, and backcrossed strains revealed that these marker chromosomes are not caused by the initial mutagenic treatment and are found only in progeny of crosses between strains with polymorphic chromosomes. Thus, they are most likely formed by meiotic recombination. For the rad12 gene, the marker chromosome can further recombine to become the size of the homolog of the backcross parent. For the rad3 gene, both ectopic and homologous recombination events are likely involved in the generation of the marker chromosomes. As predicted by a recombination model, a cross to a new wild-type parent can change the size of a mutant marker chromosome. Therefore, changes in chromosome length are a common and prominent feature of the genome of this sexual fungus, and a variety of karyotypes is tolerated by the organism.
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Dissertations / Theses on the topic "Chromosome polymorphism"

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Wang, Weixin, and 王煒欣. "A fast and accurate model to detect germline SNPs and somatic SNVs with high-throughput sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/197115.

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The rapid development of high-throughput sequencing technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently and accurately call genetic variants in single base level (germline single nucleotide polymorphisms (SNPs) or somatic single nucleotide variants (SNVs)) is the fundamental challenge in sequencing data analysis, because these variants reported to influence transcriptional regulation, alternative splicing, non-coding RNA regulation and protein coding. Many applications have been developed to tackle this challenge. However, the shallow depth and cellular heterogeneity make those tools cannot attain satisfactory accuracy, and the huge volume of sequencing data itself cause this process inefficient. In this dissertation, firstly the performance of prevalent reads aligners and SNP callers for second-generation sequencing (SGS) is evaluated. And due to the high GC-content, the significantly lower coverage and poorer SNP calling performance in the regulatory regions of human genome by SGS is investigated. To enhance the capability to call SNPs, especially within the lower-depth regions, a fast and accurate SNP detection (FaSD) program that uses a binomial distribution based algorithm and a mutation probability is proposed. Based on the comparison with popular software and benchmarked by SNP arrays and high-depth sequencing data, it is demonstrated that FaSD has the best SNP calling accuracy in the aspects of genotype concordance rate and AUC. Furthermore, FaSD can finish SNP calling within four hours for 10X human genome SGS data on a standard desktop computer. Lastly, combined with the joint genotype likelihoods, an updated version of FaSD is proposed to call the cancerous somatic SNVs between paired tumor and normal samples. With extensive assessments on various types of cancer, it is demonstrated that no matter benchmarked by the known somatic SNVs and germline SNPs from database, or somatic SNVs called from higher-depth data, FaSD-somatic has the best overall performance. Inherited and improved from FaSD, FaSD-somatic is also the fastest somatic SNV caller among current programs, and can finish calling somatic mutations within 14 hours for 50X paired tumor and normal samples on normal server.
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Biochemistry
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Doctor of Philosophy
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O'Neill, Ann Marie Ewald Sandra J. "Polymorphism in chicken immune response genes and resistance to disease." Auburn, Ala., 2007. http://repo.lib.auburn.edu/2007%20Fall%20Dissertations/O'Neill_Ann_48.pdf.

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Liu, Shuk Ming. "Single nucleotide polymorphism in human microsomal glutathione s-transferase gene and colorectal cancer /." View Abstract or Full-Text, 2003. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202003%20LIU.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003.
Includes bibliographical references (leaves 95-105). Also available in electronic version. Access restricted to campus users.
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Davison, Jerry. "Polymorphism and replication of heterochromatic repeats in the DNA of Arabidopsis /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/5134.

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Myka, Jennifer Leigh. "COMPARATIVE GENE MAPPING FOR EQUUS PRZEWALSKII AND E. HEMIONUS ONAGER WITH INVESTIGATION OF A HOMOLOGOUS CHROMOSOME POLYMORPHISM IN EQUIDAE." UKnowledge, 2003. http://uknowledge.uky.edu/gradschool_diss/476.

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The ten extant species in the genus Equus are separated by less than 3.7 million years of evolution. Three lines of investigation were pursued to further characterize equid genome organization. 1.) The Przewalski.s wild horse (E. przewalskii, EPR) has a diploid chromosome number of 2n=66, while the domestic horse (E. caballus, ECA) has 2n=64. A comparative gene map for E. przewalskii was constructed using 46 bacterial artificial chromosome (BAC) probes previously mapped to 38 of 44 E. caballus chromosome arms and ECAX. BAC clones were hybridized to metaphase spreads of E. przewalskii and localized by fluorescent in situ hybridization (FISH). No exceptions to homology between E. przewalskii and E. caballus were identified, except for ECA5, a metacentric chromosome with homology to two acrocentric chromosome pairs, EPR23 and EPR24. 2.) The onager (E. hemionus onager, EHO) has a modal diploid chromosome number 2n=56 and a documented chromosome number polymorphism within its population, resulting in individuals with 2n=55. Construction of a comparative gene map of a 2n=55 onager by FISH using 52 BAC probes previously mapped to 40 of 44 E. caballus chromosome arms and ECAX identified multiple chromosome rearrangements between E. caballus and E. h. onager. 3.) A centric fission (Robertsonian translocation) polymorphism has been documented in 5 of the ten extant equid species, namely, E. h. onager, E. h. kulan, E. kiang, E. africanus somaliensis, and E. quagga burchelli. BAC clones containing equine (E. caballus, ECA) genes SMARCA5 (ECA2q21 homologue to human (HSA) chromosome 4p) and UCHL1 (ECA3q22 homologue to HSA4q) were FISH mapped to metaphase spreads for individuals possessing the chromosome number polymorphism. These probes mapped to a single metacentric chromosome and two unpaired acrocentrics showing that the centric fission polymorphism involves the same homologous chromosome segments in each species and has homology to HSA4. These data suggest the polymorphism is either ancient and conserved within the genus or has occurred recently and independently within each species. Since these species are separated by 1-3 million years of evolution, the persistence of this polymorphism would be remarkable and worthy of further investigations.
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Chung, Man-kin. "A study on the prevalence of AZFd Y-chromosome microdeletion in Hong Kong Chinese men with severe male factor infertility." Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31971696.

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Ehrenreich, Liezle Suzette. "The evaluation of Y-STR loci for use in forensics." Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_9766_1228396041.

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The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation.

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Chung, Man-kin, and 鍾文健. "A study on the prevalence of AZFd Y-chromosome microdeletion in Hong Kong Chinese men with severe male factor infertility." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31971696.

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Varney, Robin Lynne. "Assessment of nuclear DNA variation and population structure in the eastern oyster, Crassostrea virginica, through discovery and analysis of single nucleotide polymorphisms (SNPs)." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 216 p, 2009. http://proquest.umi.com/pqdweb?did=1891582831&sid=1&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Boschiero, Clarissa [UNESP]. "Mapeamento fino de qtls e polimorfismos de genes candidatos associados ao crescimento no cromossomo 1 da galinha." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/104869.

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Made available in DSpace on 2014-06-11T19:33:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-08-20Bitstream added on 2014-06-13T19:04:33Z : No. of bitstreams: 1 boschiero_c_dr_botfmvz.pdf: 635473 bytes, checksum: feca4297f6abf36be6a9c8cf72ce1eb6 (MD5)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Universidade Estadual Paulista (UNESP)
A partir de resultados de um estudo anterior, no qual foram mapeados QTLs para características de peso vivo, peso do coração e pulmões no GGA1, foi definida uma região no intervalo entre os marcadores ADL0234 e LEI0071, abrangendo 82,3 cM. Foram avaliadas três famílias de meios-irmãos paternos que compreendiam sete famílias de irmãos completos, num total de 652 F2 para as características: peso vivo aos 35 e 41 dias de idade, pesos do coração e pulmões e rendimentos de coração e pulmões. Os genótipos de seis marcadores microssatélites foram adicionados aos dez utilizados anteriormente. O mapa de ligação obtido da região compreendeu 110,8 cM com espaçamento médio entre os marcadores de 7,4 cM. Na análise de F2, em um único intervalo (LEI0146-LEI0174), compreendendo 28,8 cM, foram mapeados QTLs para todas as características estudadas, com exceção dos rendimentos de coração e pulmões. Neste intervalo estão localizados o gene IGF1 e o centrômero do cromossomo. A adição de seis marcadores confirmou os QTLs mapeados anteriormente, porém alguns em diferentes posições. A análise de meios-irmãos paternos indicou que os principais QTLs estavam segregando em apenas uma das famílias (7716), na qual cinco QTLs foram mapeados. Na análise de meios-irmãos maternos, duas famílias segregaram QTLs tanto na análise Individual como na Conjunta (7810 e 7971). As diferentes análises permitiram selecionar dois casais F1, que devem ser o alvo dos próximos estudos. Este estudo restringiu a busca por genes candidatos responsáveis pelas características de interesse a uma região de 28,8 cM (9,82 Mb) no GGA1.
Based on the results from a previous study, in which QTL for body weight, heart and lungs weights and heart and lungs percentages were mapped to GGA1, a region was defined between markers ADL0234 and LEI0071, spanning 82.3 cM. Three paternal half-sib families, comprising seven full-sib families, totaling 652 F2 were evaluated for body weight at 35 and 41 days of age, heart and lungs weights and heart and lungs yields. Genotypes of six microsatellite markers were added to those of ten previously used. The linkage map of this region spanned 110.8 cM, with average spacing of 7.4 cM between markers. In a single interval (LEI0146-LEI0174), comprising 28.8 cM, QTLs for all traits, except for heart and lungs yields were mapped in the F2 analysis. In this same interval the IGF1 gene, and the chromosome centromere, are located. The use of six additional markers confirmed the same QTLs mapped previously, but some of them, in different positions. The paternal half-sib analysis indicated that the main QTLs were segregating in one of the families only (7716), in which five QTLs were mapped. In the maternal half-sib analysis, two families segregated QTLs both, in the across and within families analyses (7810 and 7971). These analyses allowed the selection of two F1 couples to be the target for future studies. This study restricted the search for candidate genes responsible for the traits of interest to a region of 28.8 cM (9.82 Mb) in GGA1.
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Books on the topic "Chromosome polymorphism"

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1939-, Wyandt Herman Edwin, and Tonk Vijay S, eds. Atlas of human chromosome heteromorphisms. Dordrecht: Kluwer Academic Publishers, 2003.

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Wyandt, Herman E., and Vijay S. Tonk. Human Chromosome Variation: Heteromorphism and Polymorphism. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-0896-9.

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Wyandt, Herman E. Human Chromosome Variation: Heteromorphism and Polymorphism. Dordrecht: Springer Science+Business Media B.V., 2012.

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Wyandt, Herman E., Golder N. Wilson, and Vijay S. Tonk. Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-3035-2.

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Krimbas, Costas B. Drosophila subobscura: Biology, genetics, and inversion polymorphism. Hamburg: Kovač, 1993.

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University), National Seminar on Cytopolymorphism in Plants (1989 Annamalai. Proceedings of the National Seminar on Cytopolymorphism in Plants, 25th-27th February 1989. Annamalai Nagar: Annamalai University, 1991.

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R, Taylor G., ed. Laboratory methods for the detection of mutations and polymorphisms in DNA. Boca Raton: CRC Press, 1997.

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Ellegren, Hans. Genome analysis with microsatellite markers. Uppsala: Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 1993.

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Single nucleotide polymorphisms: Methods and protocols. 2nd ed. New York: Humana, 2009.

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Atlas of human chromosome heteromorphisms. Dordrecht: Kluwer Academic·, 2002.

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Book chapters on the topic "Chromosome polymorphism"

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 5." In Human Chromosome Variation: Heteromorphism and Polymorphism, 79–81. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_10.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 6." In Human Chromosome Variation: Heteromorphism and Polymorphism, 83–85. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_11.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 7." In Human Chromosome Variation: Heteromorphism and Polymorphism, 87–88. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_12.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 8." In Human Chromosome Variation: Heteromorphism and Polymorphism, 89–90. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_13.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 9." In Human Chromosome Variation: Heteromorphism and Polymorphism, 91–104. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_14.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 10." In Human Chromosome Variation: Heteromorphism and Polymorphism, 105–6. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_15.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 11." In Human Chromosome Variation: Heteromorphism and Polymorphism, 107–8. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_16.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 12." In Human Chromosome Variation: Heteromorphism and Polymorphism, 109. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_17.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 13." In Human Chromosome Variation: Heteromorphism and Polymorphism, 111–15. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_18.

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Wyandt, Herman E., and Vijay S. Tonk. "Chromosome 14." In Human Chromosome Variation: Heteromorphism and Polymorphism, 117–22. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0896-9_19.

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Conference papers on the topic "Chromosome polymorphism"

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Kozyreva, S. Yu, M. M. Gridina, A. A. Torgasheva, V. S. Fishman, K. S. Zadesenets, and L. P. Malinovskaya. "DISSECTING THE STRUCTURE OF THE CHROMOSOMAL REARRANGEMENTS IN CHROMOSOME 1A IN GREAT TITS (PARUS MAJOR) USING HI-C TECHNIQUE." In OpenBio-2023. ИПЦ НГУ, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-21.

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Polymorphism caused by complex rearrangement on chromosome 1A has been identified in the population of the Great Tit (Parus major). Сhromosomal rearrangement involves large inversion and regions with copy number variations, potentially spanning around 3.5 Mb. Using Hi-C technique we determined the inversion breakpoints with an accuracy of 1000 bp and developed an approach that allowed to discover additional 15 Mb of genomic sequences in the rearranged chromosome.
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Soboleva, E. S., V. S. Fedorova, V. A. Burlak, M. V. Sharakhova, and G. N. Artemov. "INVERSION POLYMORPHISM OF NATURAL POPULATIONS ANOPHELES BEKLEMISHEVI STEGNII ET KABANOVA IN WESTERN SIBERIA." 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/10.17223/978-5-94621-931-0-2020-35.

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The geographical distribution and inversion polymorphism of malaria mosquitoes Anopheles beklemishevi Stegnii et Kabanova in the West Siberia were investigated. X chromosome homozygous cytotypes were defined by fluorescent in situ hybridization of microdissected DNA-probe, labeling the breakpoints region of X chromosome inversions. For the first time the samples, which are homozygous and hemizygous by inversions X1 и X2 were detected. Cytotypes representation and frequencies have not differences between northern and southern (Altay) population of the malaria mosquitoes.
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Chan, Vivian, V. W. S. Liu, A. C. K. Wong, and T. K. Chan. "DNA POLYMORPHISMS IN OR LINKED TO THE FACTOR VIII GENE IN CHINESE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644049.

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78 unrelated X chromosomes from Southern Chinese (56 normal and 22 haemophiliac) were studied. DNA was restricted by Bel I, Bgl I or Taq I and hybridized to 3' factor VIII:C cDNA probe (5 kb, Chiron) or St 14.1 probe(3 kb, Oberle &Mandel) by standard techniques. The intragenic Bel I polymorphic site was positive in 82%, while Bgl I polymorphic site was positive in all. Thus, 29.5%(2 x×0.82 × 0.18) of Chinese females carried the Bel I polymorphism. Asto the Taq I polymorphism in the closely linked DXS52 DNA segment, the incidences for the various alleles were :System I - allele (3) 10.2%, (4) 2.6%, (5) 2.6%,(6) 17.9%, (7) 21.8% and (8) 44.9% System II - α a allele 56%, 6 allele 44%. Approximately 80% of females were heterozygous for two different alleles. Hence the Bel I and Taq I polymorphisms can be used to track the defective factor VIII gene for carrier detection and prenatal diagnosis. Furthermore, their frequencies in the Chinese are different from those previously reported in other ethnic groups.
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Karasev, E. P., E. E. Andronov, E. P. Chizevskaya, and N. A. Provorov. "Comparative analysis of nucleotide polymorphism of chromosomal and symbiotic genes in symbionts of eastern and medical goat’s rue from a population of the North Caucasus." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.112.

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The analysis of the nucleotide polymorphism in two goatfish rhizobia biovars showed that the diversity of all gene groups corresponds to the diversity of the host plant, and the general polymorphism of chromosomal genes is higher than the symbiotic gene polymorphysm in both biovars.
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Pei, Zhili, Ying Kong, Xiaohu Shi, Zhichao Lian, Xuning Tang, Lisha Liu, Zhongbo Cao, and Yanchun Liang. "A Populations Evolution Study Using the Genotype Frequency Data of Single Nucleotide Polymorphism from Y-Chromosome." In 2007 1st International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2007. http://dx.doi.org/10.1109/icbbe.2007.78.

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Jabasini, Mohammad, Lihua Zhang, Feng Xu, Fuquan Dang, and Yoshinobu Baba. "Rapid applicable separation of DNA polymorphism on the human Y-chromosome by micro fabricated electrophoresis chip." In 2002 International Conference on Solid State Devices and Materials. The Japan Society of Applied Physics, 2002. http://dx.doi.org/10.7567/ssdm.2002.p14-6.

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Muntyan, Victoria S., Alla S. Saksaganskaia, Alexey N. Muntyan, Mariia E. Vladimirova, and Marina L. Roumiantseva. "STRESS AND IMMUNITY OF NODULE BACTERIA SINORHIZOBIUM MELILOTI: LOCALIZATION, POLYMORPHISM AND PHYLOGENY OF GENETIC DETERMINANTS." In 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022/6.1/s25.15.

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Sinorhizobium meliloti are agriculturally valuable species of soil bacteria that form nitrogen-fixing symbiosis with alfalfa plants. Global climate changes lead to an increase of agricultural areas subjected to salinity. Current knowledge about about high-salt stress impact on soil saprophitic root nodulated microsymbionts of legumes is weakly studied and rhizobia gene pool responsible for salt tolerance are fragment and far from clear. An increase of bacteria nonspecific resistance (immune status) to unfavorable stress factors can occur through the induction of defense mechanisms like restrictionmodification systems and CRISPR/cas systems which are aimed to protect bacteria cells from bacteriophages widespread in soil microbiome. The aim of this research was to evaluate the role of the megaplasmid pSymA in the formation of ecological genome of S. meliloti, which is related to stress tolerance and to determine the location of elements of adaptive immune systems protecting root nodule bacteria against external foreign DNA. The analysis was done on 11 genes, products of which involved in response to ion stress and synthesis of osmoprotectors. It was found that 6 out of 11 genes were found in the genomes of all analyzed S. meliloti strains, while it was not a case for other 5 genes. It was found that, unlike chromosome, megaplasmid I of S. meliloti accumulated copies of 4 from 5 genes, except kdpA gene, which is represented by a single copy and localized on megaplasmid I in all so far studied strains. It was predicted that closest phylogenetic relatives of genes whose products are involved in response to ion stress as well in synthesis of osmoprotectors are homologous genes of closely related S. medicae species. The exception was for betI2, for which the closest phylogenetic relative was homologous gene of Klebsiella pneumonia, and another exception is kdpA gene introduced onto megaplasmid-I from actinobacteria. Regarding elements of immune systems it was revealed that nonsymbiotic plasmids of S. meliloti harbored incomplete elements of RMS-I, -II, and - III systems, while the 4 complete RMS-IV systems were detected on a single plasmid. It was found out that corresponding methylases had similarities with similar enzymes detected in nitrogen-fixing strains of Agrobacterium tumefaciens, Mezorhizobium sp., Bradyrhizobium sp. CRISPR sequences were not detected on megaplasmid-I, while they were on chromosome, megaplasmid-II and on cryptic plasmids. So, it was concluded that megaplasmid-I of S. meliloti are enriched in copies of genes related to osmotic stress tolerance, but it role in immune status of rhizobia is requested further elucidation.
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Choi, Yi Young. "Abstract 1146: A functional polymorphism on chromosome 15q25 associated with survival of early stage non-small cell lung cancer." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-1146.

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Ploos van Amstel, J. K., A. L. van der Zanden, P. H. Reitsma, and R. M. Bertina. "RESTRICTION ANALYSIS AND SOUTHERN BLOTTING OF TOTAL HUMAN DNA REVEALS THE EXISTENCE OF MORE THAN ONE GENE HOMOLOGOUS WITH PROTEIN S cDNA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644639.

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A deficiency in protein S, the cofactor of activated protein C, is associated with an increased risk for the development of venous thrombosis. It is inherited as an autosomal dominant disorder. To improve the detection of heterozygotes in affected families, we have started to search for restriction fragment length polymorphism (RFLP) in the protein S gene. This study revealed the existence of two genes containing sequences homologous to protein S cDNA.Three non-overlapping fragments of clone pSUL5, which codes for the carboxy-terminal part of protein S and contains the complete 3' untranslated region, were isolated and used as probes in search for RFLP of the protein S gene.Surprisingly the non-overlapping probes shared more than one hybridizing band. The hybridization took place under stringent assay conditions.This observation is contradictory to the intron-exon organization of a gene and suggests the existence of two genes, containing sequences homologous with pSUL5. Both genes could be assigned to chromosome 3 by mapping through somatic cell hybrids. Whether two functional protein S genes are present in the human genome remains to be established.
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Cheah, Peh Yean, Lai Fun Thean, Yik Ying Teo, Woon-Puay Koh, Jian-Min Yuan, Min Hoe Chew, and Choong Leong Tang. "Abstract 4587: Genome-wide copy number analysis identified a copy number polymorphism at chromosome 8p11 associated with sporadic colorectal cancer risk in Singapore Chinese." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4587.

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Reports on the topic "Chromosome polymorphism"

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Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.

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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Kistler, Harold Corby, Talma Katan, and Dani Zamir. Molecular Karyotypes of Pathogeic Strains of Fusarium oxysporum. United States Department of Agriculture, June 1995. http://dx.doi.org/10.32747/1995.7604927.bard.

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Genetic diversity of pathogenic strains of the fungus Fusarium oxysporum was determied by analysis of electrophoretic karyotype, as well as by DNA variation detected by Restriction Fragment Length Polymorphisms (RFLPs) and Random Amplified Polymorphic DNAs (RAPDs). The electrophoretic karyotypes for 130 isolates of the fungus pathogenic to tomato, melon, and banana were analyzed. Electrophoretic karyotype variation, reflected in differences in apparent chromosome number and genome size, was observed even among isolates from the same host and sub specific category. Sub specific categories studied were forma specialis, vegetative compatibility group (VCG) and race. Chromosome number and genome size variation was less for isolates within the same VCG than for the collection of isolates as a whole. RFLP and RAPD analysis were performed on 62 isolates of F. oxysporum from tomato and melon. Polygenetic trees were constructed from genetic diversity data. The results support the hypothesis that isolates belonging to the same VCG originate from a single ancestor compared to other isolates. The results do not support the hypothesis that all isolates belonging to the same forma specialis originate from a common ancestor. These conclusions have profound implication for breeding resistance to diseases caused by particular formae speciales of F. oxysporum.
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Reisch, Bruce, Pinhas Spiegel-Roy, Norman Weeden, Gozal Ben-Hayyim, and Jacques Beckmann. Genetic Analysis in vitis Using Molecular Markers. United States Department of Agriculture, April 1995. http://dx.doi.org/10.32747/1995.7613014.bard.

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Genetic analysis and mapping in grapes has been difficult because of the long generation period and paucity of genetic markers. In the present work, chromosome linkage maps were developed with RAPD, RFLP and isozyme loci in interspecific hybrid cultivars, and RAPD markers were produced in a V. vinifera population. In three cultivars, there were 19 linkage groups as expected for a species with 38 somatic chromosomes. These maps were used to locate chromosome regions with linkages to important genes, including those influencing powdery mildew and botrytis bunch rot resistance; flower sex; and berry shape. In V. vinifera, the occurrence of specific markers was correlated with seedlessness, muscat flavor and fruit color. Polymorphic RAPD bands included single copy as well as repetitive DNA. Mapping procedures were improved by optimizing PCR parameters with grape DNA; by the development of an efficient DNA extraction protocol; and with the use of long (17- to 24-mer) primers which amplify more polymorphic loci per primer. DNA fingerprint analysis with RAPD markers indicated that vinifera cultivars could be separated readily with RAPD profiles. Pinot gris, thought to be a sort of Pinot noir, differed by 12 bands from Pinot noir. This suggests that while Pinot gris may be related to Pinot noir, it is not likely to be a clone. The techniques developed in this project are now being further refined to use marker-assisted selection in breeding programs for the early selection of elite seedlings. Furthermore, the stage has been set for future attempts to clone genes from grapes based upon map locations.
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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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Levin, Ilan, John Thomas, Moshe Lapidot, Desmond McGrath, and Denis Persley. Resistance to Tomato yellow leaf curl virus (TYLCV) in tomato: molecular mapping and introgression of resistance to Australian genotypes. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7613888.bard.

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Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomatoes. Although first identified in the Mediterranean region, it is now distributed world-wide. Sequence analysis of the virus by the Australian group has shown that the virus is now present in Australia. Despite the importance of the disease and extensive research on the virus, very little is known about the resistance genes (loci) that determine host resistance and susceptibility to the virus. A symptom-less resistant line, TY-172, was developed at the Volcani Center which has shown the highest resistance level among all tested varieties. Preliminary results show that TY-172 is a good candidate to confer resistance to both TYLCV and to Tomato leaf curl virus (ToLCV) in Queensland conditions. Furthermore, Segregation analysis has previously indicated that the resistance is determined by 2-3 genes. In this proposal we aimed to substantiate that TY-172 can contribute to resistance breeding against TYLCV in Queensland, to develop DNA markers to advance such resistance breeding in both Israel and Queensland, and to exploit these markers for resistant breeding in Australian and Israeli lines. To map quantitative trait loci (QTLs) controlling TYLCVresistance in TY172, appropriate segregating populations were analyzed using 69 polymorphic DNA markers spanning the entire tomato genome. Results show that TYLCV resistance in TY172 is controlled by a previously unknown major QTL, originating from the resistant line, and four additional minor QTLs. The major QTL, termed Ty-5, maps to chromosome 4 and accounts for 39.7-to-46.6% of the variation in symptom severity among segregating plants (LOD score: 33-to-35). The minor QTLs, originated either from the resistant or susceptible parents, were mapped to chromosomes 1, 7, 9 and 11, and contributed 12% to the variation in symptom severity in addition to Ty-5. Further analysis of parental lines as well as large F₁, BC₁F₁, F₂ and BC₁F₂ populations originating from crosses carried out, in reciprocal manner, between TY172 and the susceptible processing line M-82 (LA3475) during spring-summer 2010, indicated that: (1) the minor QTLs we have previously identified are in effect not reproducible, (2)Ty-5 alone can yield highly resistant plants with practically no extra-chromosomal effects, and (3) the narrow-sense heritability estimate of resistance levels, attributed to additive factors responsive to selection, does not significantly deviate from 1. All of these results point to Ty-5 as the sole resistance locus in TY172 thus significantly increasing the likelihood of its successful molecular dissection. The DNA markers developed during the course of this study were transferred together with the TY172 genotype to Queensland. TY172 was crossed to a panel of Australian genotypes and the resulting populations were subjected to segregation analysis. Results showed that resistant locus, Ty-5, is highly reproducible in the Australian conditions as well. The Australian group was also able to make improvements to the marker assays by re-designing primer pairs to provide more robust PCR fragments. The Ty-5 locus has now been introgressed into elite Australian germplasm and selection for TYLCV resistance has begun. Cumulatively, our results show that Ty-5 can be effectively used, together with the TY172 genotype to expedite TYLCV resistance breeding and improve our understanding of the genetics that underline the response of tomato to TYLCV. Contributions to agriculture include: (1) the development of tools for more efficient resistance breeding, allowing the incorporation of resistance to local tomato varieties in Australia, Israel and elsewhere; and (2) establish a solid framework for a future attempt to clone the genes that encode such resistance. The latter will enable to decipher the resistance mechanisms that could be applied to other geminiviruses in tomato and possibly in other plant species.
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Ginzberg, Idit, and Walter De Jong. Molecular genetic and anatomical characterization of potato tuber skin appearance. United States Department of Agriculture, September 2008. http://dx.doi.org/10.32747/2008.7587733.bard.

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Potato (Solanum tuberosum L.) skin is composed of suberized phellem cells, the outer component of the tuber periderm. The focus of the proposed research was to apply genomic approaches to identify genes that control tuber skin appearance - smooth and shiny skin is highly preferred by the customers while russeted/netted skin potatoes are rejected. The breeding program (at Cornell University) seeks to develop smooth-skin varieties but has encountered frequent difficulties as inheritance of russeting involves complementary action by independently segregating genes, where a dominant allele at each locus is required for any degree of skin russeting. On the other hand, smooth-skin varieties frequently develop unsightly russeting in response to stress conditions, mainly high soil temperatures. Breeding programs in Israel aimed towards the improvement of heat tolerant varieties include skin quality as one of the desired characteristics. At the initiation of the present project it was unclear whether heat induced russeting and genetically inherited russeting share the same genes and biosynthesis pathways. Nevertheless, it has been suggested that russeting might result from increased periderm thickness, from strong cohesion between peridermal cells that prevents the outer layers from sloughing off, or from altered suberization processes in the skin. Hence, the original objectives were to conduct anatomical study of russet skin development, to isolate skin and russeting specific genes, to map the loci that determine the russet trait, and to compare with map locations the candidate russet specific genes, as well as to identify marker alleles that associated with russet loci. Anatomical studies suggested that russet may evolve from cracking at the outer layers of the skin, probably when skin development doesn’t meet the tuber expansion rate. Twodimensional gel electrophoresis and transcript profiling (cDNA chip, potato functional genomic project) indicated that in comparison to the parenchyma tissue, the skin is enriched with proteins/genes that are involved in the plant's responses to biotic and abiotic stresses and further expand the concept of the skin as a protective tissue containing an array of plantdefense components. The proteomes of skin from heat stressed tubers and native skin didn’t differ significantly, while transcript profiling indicated heat-related increase in three major functional groups: transcription factors, stress response and protein degradation. Exceptional was ACC synthase isogene with 4.6 fold increased level in the heat stressed skin. Russeting was mapped to two loci: rusB on chromosome 4 and rusC on chromosome 11; both required for russeting. No evidence was found for a third locus rusA that was previously proposed to be required for russeting. In an effort to find a link between the russeting character and the heat-induced russeting an attempt was made to map five genes that were found in the microarray experiment to be highly induced in the skin under heat stress in the segregating russet population. Only one gene was polymorphic; however it was localized to chromosome 2, so cannot correspond to rusB or rusC. Evaluation of AFLP markers tightly linked to rusB and rusC showed that these specific alleles are not associated with russeting in unrelated germplasm, and thus are not useful for MAS per se. To develop markers useful in applied breeding, it will be necessary to screen alleles of additional tightly linked loci, as well as to identify additional russet (heat-induced and/or native) related genes.
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8

Weller, Joel I., Harris A. Lewin, and Micha Ron. Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586473.bard.

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Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.
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