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1
Tarr, Phillip I., Laura M. Schoening, Yoo-Lee Yea, Teresa R. Ward, Srdjan Jelacic, and Thomas S. Whittam. "Acquisition of the rfb-gnd Cluster in Evolution of Escherichia coli O55 and O157." Journal of Bacteriology 182, no. 21 (November 1, 2000): 6183–91. http://dx.doi.org/10.1128/jb.182.21.6183-6191.2000.
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ABSTRACT The rfb region specifies the structure of lipopolysaccharide side chains that comprise the diverse gram-negative bacterial somatic (O) antigens. The rfb locus is adjacent to gnd, which is a polymorphic gene encoding 6-phosphogluconate dehydrogenase. To determine if rfb andgnd cotransfer, we sequenced gnd in five O55 and 13 O157 strains of Escherichia coli. E. coli O157:H7 has a gnd allele (allele A) that is only 82% identical to the gnd allele (alleleD) of closely related E. coli O55:H7. In contrast, gnd alleles of E. coli O55 in distant lineages are >99.9% identical to gnd alleleD. Though gnd alleles B andC in E. coli O157 that are distantly related toE. coli O157:H7 are more similar to allele Athan to allele D, there are nucleotide differences at 4 to 6% of their sites. Alleles B and C can be found in E. coli O157 in different lineages, but we have found allele A only in E. coli O157 belonging to the DEC5 lineage. DNA 3′ to the O55 gnd allele in diverse E. coli lineages has sequences homologous totnpA of the Salmonella enterica serovar Typhimurium IS200 element, E. coli Rhs elements (including an H-rpt gene), and portions of the O111 and O157rfb regions. We conclude that rfb andgnd cotransferred into E. coli O55 and O157 in widely separated lineages and that recombination was responsible for recent antigenic shifts in the emergence of pathogenic E. coli O55 and O157.
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Manivasakam, P., Susan M. Rosenberg, and P. J. Hastings. "Poorly Repaired Mismatches in Heteroduplex DNA are Hyper-Recombinagenic in Saccharomyces cerevisiae." Genetics 142, no. 2 (February 1, 1996): 407–16. http://dx.doi.org/10.1093/genetics/142.2.407.
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Abstract In yeast meiotic recombination, alleles used as genetic markers fall into two classes as regards their fate when incorporated into heteroduplex DNA. Normal alleles are those that form heteroduplexes that are nearly always recognized and corrected by the mismatch repair system operating in meiosis. High PMS (postmeiotic segregation) alleles form heteroduplexes that are inefficiently mismatch repaired. We report that placing any of several high PMS alleles very close to normal alleles causes hyperrecombination between these markers. We propose that this hyperrecombination is caused by the high PMS allele blocking a mismatch repair tract initiated from the normal allele, thus preventing corepair of the two alleles, which would prevent formation of recombinants. The results of three point crosses involving two PMS alleles and a normal allele suggest that high PMS alleles placed between two alleles that are normally corepaired block that corepair.
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Suprovych, T., N. Suprovych, T. Karchevska, I. Chornyy, and V. Chepurna. "АЛЕЛЬНИЙ ПОЛІМОРФІЗМ ГЕНА BOLA–DRB3.2 В ЗВ’ЯЗКУ З ТИПАМИ ВИВІДНОЇ СИСТЕМИ ВИМЕНІ ТА МАСТИТАМИ КОРІВ УКРАЇНСЬКОЇ ЧОРНО–РЯБОЇ МОЛОЧНОЇ ПОРОДИ." Scientific Messenger of LNU of Veterinary Medicine and Biotechnologies 18, no. 3(71) (October 7, 2016): 117–23. http://dx.doi.org/10.15421/nvlvet7127.
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The results comparing the two types of markers associated with susceptibility (by resistance) cows to mastitis presented in the article. Previous studies indicated 2 markers. There are allele gene BOLA–DRB3.2 and placer or magistral type of excretory ducts udder. The study was conducted by identifying spectrum allele's and types of excretory ducts udder of cows in 47 Ukrainian Black Pied dairy breed. Some of the animals (28 caw) have in the genotype «informative» alleles that indicate association with mastitis or resistance to the disease. Susceptible cows to the disease often have a placer type (half of the animals). Healthy cows have oftener magistral type of main excretory system (35.7%). With magistral type have genotype 9 cows «positive» alleles (32.1%); 11 animals with placer type have only «negative»alleles (39.3%). Comparing the presence of two types of markers in healthy and susceptible animals found two predominant choices:– healthy animals have the oftener magistral type of excretory system of the udder, and at least one allele associated with resistance to mastitis (9 cases);– in diseased animals have the oftener placer type of excretory system and at least one allele associated with susceptibility to mastitis (11 cases).The high incidence of these options indicates that there are natural connections between the type of excretory ducts udder, by alleles BoLA–DRB3.2 and mastitis.
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Searle, Susan, and Jenefer M. Blackwell. "Evidence for a functional repeat polymorphism in the promoter of the human NRAMP1 gene that correlates with autoimmune versus infectious disease susceptibility." Journal of Medical Genetics 36, no. 4 (April 1, 1999): 295–99. http://dx.doi.org/10.1136/jmg.36.4.295.
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A polymorphism in the promoter of human NRAMP1 encodes a Z-DNA forming dinucleotide repeat with four alleles: (1) t(gt)5ac(gt)5ac(gt)11g; (2) t(gt)5ac(gt)5 ac(gt)10g; (3) t(gt)5ac(gt)5ac(gt)9g; and (4) t(gt)5ac(gt)9g. Alleles 1 and 4 are rare (gene frequencies ∼0.001); alleles 2 and 3 occur at gene frequencies ∼0.20−0.25 and ∼0.75− 0.80, respectively. Here, luciferase reporter gene constructs are used to show that the four alleles differ in their ability to drive gene expression. In the absence of exogenous stimuli, alleles 1, 2, and 4 are poor promoters; allele 3 drives high expression, indicating that the repeat itself has endogenous enhancer activity. All four alleles show a similar percentage enhancement of reporter gene expression in the presence of interferon-γ, consistent with the multiple interferon-γ response elements both 5′ and 3′ of the Z-DNA forming repeat. However, while the addition of bacterial lipopolysaccharide (LPS) has no effect on alleles 1 and 4, it causes significant reduction in expression driven by allele 2 and enhances expression driven by allele 3, suggesting that the juxtaposition of LPS related response elements (NFκB, AP-1, NF-IL6) may be differentially affected by the two commonly occurring alleles. These results are consistent with the hypothesis that chronic hyperactivation of macrophages associated with allele 3 is functionally linked to autoimmune disease susceptibility, while the poor level of NRAMP1 expression promoted by allele 2 contributes to infectious disease susceptibility. Conversely, allele 3 protects against infectious disease and allele 2 against autoimmune disease. Hence, alleles that are detrimental in relation to autoimmune disease susceptibility may be maintained in the population because they improve survival to reproductive age following infectious disease challenge.
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Mortin, M. A., W. J. Kim, and J. Huang. "Antagonistic interactions between alleles of the RpII215 locus in Drosophila melanogaster." Genetics 119, no. 4 (August 1, 1988): 863–73. http://dx.doi.org/10.1093/genetics/119.4.863.
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Abstract The RpII215 locus encodes the large subunit of RNA polymerase II (polII). Three of 22 RpII215 alleles cause a synergistic enhancement of the mutant phenotype elicited by mutations in the Ultrabithorax (Ubx) locus. We have recovered and analyzed three new mutations that suppress this enhancement. All three mutations map to the RpII215 locus. In addition to suppressing the Ubx enhancement of other RpII215 alleles, two of the new mutations, JH1 and WJK2, themselves enhance Ubx. RpII215 alleles can be placed into three classes based on their ability to enhance Ubx. Class I alleles, including Ubl, C4, C11, JH1, and WJK2, enhance Ubx when heterozygous with class II alleles, which include wild-type RpII215. Class III alleles, which include amorphic alleles, do not enhance Ubx. The third new mutation, WJK1, is a conditional amorphic allele, which behaves like a class III allele at 29 degrees but like a class II allele at 19 degrees. Another mutant phenotype is caused by certain RpII215 alleles, including all class I alleles. This phenotype is a synergistic enhancement of a mutant phenotype elicited by mutations at the Delta (Dl) locus. Unlike the enhancement of Ubx, the enhancement of Dl is not dependent upon antagonistic interactions between different classes of RpII215 alleles.
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Ji, Ling, Shixiu Pan, Jacqueline Marti-Jaun, Edgar Hänseler, Katharina Rentsch, and Martin Hersberger. "Single-Step Assays to Analyze CYP2D6 Gene Polymorphisms in Asians: Allele Frequencies and a Novel *14B Allele in Mainland Chinese." Clinical Chemistry 48, no. 7 (July 1, 2002): 983–88. http://dx.doi.org/10.1093/clinchem/48.7.983.
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Abstract Background: Cytochrome P450-dependent monooxygenase 2D6 (CYP2D6) activity can be estimated by investigating the metabolism of model drugs or by genotyping the most common CYP2D6 alleles. For Caucasians, the CYP2D6 allele frequencies are well investigated, and single-step assays are available for genotyping, whereas allele analysis in mainland Chinese is limited. Methods: Two tetra-primer assays and one allele-specific amplification assay were developed to easily genotype the CYP2D6 alleles *8, *10, and *14 previously detected in Asians. Applying these assays in combination with established single-tube assays, we analyzed 223 DNA samples from Chinese volunteers for the CYP2D6 alleles *3, *4, *5, *6, *8, *10, and *14 and for duplication of CYP2D6. Results: Six different alleles were detected in mainland Chinese. The most frequent mutant allele was the intermediate metabolizer allele, CYP2D6*10, with a prevalence of 51.3%, followed by the poor metabolizer alleles CYP2D6*5 (7.2%) and a novel variant of CYP2D6*14. This novel *14B allele (2.0%) differs from the *14 allele by the absence of the C188T substitution and by the additional G1749C substitution. Furthermore, six duplication alleles of CYP2D6 were detected, including one duplication of the *10 allele (*10X2). Conclusions: The CYP2D6 allele frequencies in mainland Chinese shows some genetic diversity compared with Chinese from other regions: a novel *14B allele, a slightly higher frequency of the *5 allele, and a slightly lower frequency of the *10 allele than in most other Chinese populations.
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Sharma, B. S., C. P. Verschoor, and N. A. Karrow. "Short Communication: Associations of BoLA alleles DRB3.2*16 and DRB3.2*23 with health-related traits in Holstein bulls." Canadian Journal of Animal Science 91, no. 4 (December 2011): 597–600. http://dx.doi.org/10.4141/cjas2010-040.
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Sharma, B. S., Verschoor, C. P. and Karrow, N. A. 2011. Short communication:Associations of BoLA alleles DRB3.2*16 and DRB3.2*23 with health-related traits in Holstein bulls. Can. J. Anim. Sci. 91: 597–600. The relationships between bovine leukocyte antigen (BoLA) DRB3.2 alleles and health and fertility traits were investigated. A group of 548 Canadian and American Holstein bulls was genotyped for the presence of DRB3.2*16 and DRB3.2*23 alleles using the multi-primer target polymerase chain reaction technique. The traits of interest included somatic cell score (SCS), lactation persistency, daughter fertility (DF), and herd life (HL). Higher frequencies were observed for alleles DRB3.2*16 and DRB3.2*23 in this bull population compared with previous reports. In a comparison-wise level, some significant contrasts were detected; however, no association was detected between the DRB3.2 alleles and SCS. Allele DRB3.2*16 had a favorable effect on HL compared with allele DRB3.2*23. On the other hand, these two alleles had a favorable influence on DF, additionally, individuals carrying both of these two alleles performed better than the individuals carrying either allele. Further investigation is warranted to examine the effects of these alleles on HL and reproduction performance.
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Selby, Sandra, and Phillip Posch. "TNF promoter region allele frequencies in the White population and their expression levels (34.11)." Journal of Immunology 184, no. 1_Supplement (April 1, 2010): 34.11. http://dx.doi.org/10.4049/jimmunol.184.supp.34.11.
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Abstract Tumor necrosis factor (TNF) is a pro-inflammatory cytokine that plays a variety of roles in immune regulation and disease. The TNF regulatory region contains numerous SNPs some of which affect expression. We previously identified nine alleles of TNF promoter region from random samples, but allele frequencies in different populations and diversity of the gene, as well as expression levels driven by the promoter alleles are not known. The TNF promoter and gene were sequenced from 82 random healthy White individuals. Three novel promoter alleles and two novel SNPs were identified. Novel SNPs also were found in intron 1 and the 3’ UTR. Promoter allele p*001 was the most common allele (55.49%). Allele p*002 (15.85%), p*006 (14.02%) and p*003 (7.32%) also were frequent, while all other alleles were found at less than 5% frequency. Differences were noted in an initial analysis of expression levels in T cells driven by the TNF promoter alleles. Allele p*004 was significantly increased in unstimulated and PMA/ionomycin conditions when compared to allele p*001. Expression was decreased for alleles p*005, p*006, and p*008 in comparison to allele p*001 in stimulated and unstimulated conditions. Allele p*007 showed decreased expression only in unstimulated conditions, while allele p*002 showed reduced expression only under stimulated conditions. These data confirm some of the previously reported impacts of SNPs on TNF expression and suggest an impact of additional SNPs on TNF levels.
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Vässin, Harald, and Jose A. Campos-Ortega. "Genetic Analysis of Delta, a Neurogenic Gene of Drosophila melanogaster." Genetics 116, no. 3 (July 1, 1987): 433–45. http://dx.doi.org/10.1093/genetics/116.3.433.
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ABSTRACT We report here the results of a genetic analysis of the gene Delta (Dl) of Drosophila melanogaster. Dl has been mapped to the band 92A2, on the basis of two pieces of evidence: (1) this band is the common breakpoint of several chromosomal aberrations associated with Dl mutations and (2) recombination mapping of alleles of five different lethal complementation groups that are uncovered by Df(3R)DlFX3 (breakpoints at 91F11; 92A3). Dl was found to map most distally of all five complementation groups. The analysis of a large number of Dl alleles demonstrates the considerable genetic and functional complexity of Dl. Three types of Dl alleles are distinguishable. Most alleles behave as amorphic or hypomorphic recessive embryonic lethal alleles, which in addition cause various defects in heterozygosity over the wild-type allele. The defects are due to haplo-insufficient expression of the locus and can be suppressed by a duplication of the wild-type allele. The second class is comprised of three alleles with antimorphic expression. The phenotype of these alleles can only be reduced, rather than suppressed, by a duplication of the wild-type allele. The third group is comprised of three visible, predominantly hypomorphic alleles with an antimorphic component of phenotypic expression. The pattern of interallelic complementation is complex. On the one hand, there is a group of hypomorphic, fully penetrant embryonic lethal alleles which complement each other. On the other hand, most alleles, including all amorphic alleles, are viable over the visible ones; alleles of antimorphic expression, however, are lethal over visible alleles. These results are compatible with a rather complex genetic organization of the Dl locus.
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Manga, I., and J. Dvořák. "TaqMan allelic discrimination assay for A1 and A2 alleles of the bovine CSN2 gene." Czech Journal of Animal Science 55, No. 8 (August 19, 2010): 307–12. http://dx.doi.org/10.17221/89/2009-cjas.
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Alleles A1 and A2 of the Bos taurus CSN2 gene are the most frequent in a number of dairy cattle breeds. In this study, a new allelic discrimination assay using TaqMan fluorogenic probes was developed to detect single nucleotide substitution characterizing the A1/A2 alleles of the CSN2 gene. The method was validated using DNA samples of known genotypes with different concentrations and the results were compared with those for the commonly used problematic ACRS-PCR. We found the TaqMan method to be more effective, 100% reliable and hundred times more sensitive for testing the CSN2 genetic marker in cattle than the ACRS-PCR. As it enabled a rapid analysis of a large number of DNA samples in uniform format without previous DNA quality assessment and without the requirement for post-amplification manipulations, it presents an effective tool for the analysis of large-scale sample sets. The method was applied for testing on a sample of 120 Czech Holstein dairy cows. The observed relative genotype and allele frequencies were as follows: A1A1–0.20, A1A2–0.51, A2A2–0.29; A1–0.45, A2–0.55.
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Iqbal, Muhammad, Alireza Navabi, Rong-Cai Yang, Donald F. Salmon, and Dean Spaner. "Molecular characterization of vernalization response genes in Canadian spring wheat." Genome 50, no. 5 (May 2007): 511–16. http://dx.doi.org/10.1139/g07-028.
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Vernalization response (Vrn) genes play a major role in determining the flowering/maturity times of spring-sown wheat. We characterized a representative set of 40 western Canadian adapted spring wheat cultivars/lines for 3 Vrn loci. The 40 genotypes were screened, along with 4 genotypes of known Vrn genes, using previously published genome-specific polymerase chain reaction primers designed for detecting the presence or absence of dominant or recessive alleles of the major Vrn loci: Vrn-A1, Vrn-B1, and Vrn-D1. The dominant promoter duplication allele Vrn-A1a was present in 34 of 40 cultivars/lines, whereas the promoter deletion allele Vrn-A1b was present in only 1 of the western Canadian cultivars ( Triticum aestivum L. ‘Rescue’) and 2 of its derivative chromosomal substitution lines. The intron deletion allele Vrn-A1c was not present in any line tested. Only 4 of the western Canadian spring wheat cultivars tested here carry the recessive vrn-A1 allele. The dominant allele of Vrn-B1 was detected in 20 cultivars/lines. Fourteen cultivars/lines had dominant alleles of Vrn-A1a and Vrn-B1 in combination. All cultivars/lines carried the recessive allele for Vrn-D1. The predominance of the dominant allele Vrn-A1a in Canadian spring wheat appears to be due to the allele's vernalization insensitivity, which confers earliness under nonvernalizing growing conditions. Wheat breeders in western Canada have incorporated the Vrn-A1a allele into spring wheats mainly by selecting for early genotypes for a short growing season, thereby avoiding early and late season frosts. For the development of early maturing cultivars with high yield potential, different combinations of Vrn alleles may be incorporated into spring wheat breeding programs in western Canada.
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Huang, Shu-Pang, and B. S. Weir. "Estimating the Total Number of Alleles Using a Sample Coverage Method." Genetics 159, no. 3 (November 1, 2001): 1365–73. http://dx.doi.org/10.1093/genetics/159.3.1365.
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Abstract Previously reported methods for estimating the number of different alleles at a single locus in a population have not described a useful general result. Using the number of alleles observed in a sample gives an underestimate for the true number of alleles. The similar problem of estimating the number of species in a population was first investigated in 1943. In this article we use the sample coverage method proposed by Chao and Lee in 1992 to estimate the number of alleles in a population when there are unequal allele frequencies. Simulation studies under the recurrent mutation model show that, for reasonable sample sizes, a significantly better estimate of the true number can be obtained than that using only the observed alleles. Results under the stepwise mutation model and infinite-allele model are presented. Possible applications include improving the characterization of the prior distribution for the allele frequencies, adjusting the estimates of genetic diversity, and estimating the range of microsatellite alleles.
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Zoteyeva, Nadezhda, Ilze Skrabule, Ieva Mežaka, Daiga Vilcāne, Guna Usele, and Nils Rostoks. "The impact of R1and R3a genes on tuber resistance to late blight of the potato breeding clones." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. 70, no. 2 (April 1, 2016): 58–63. http://dx.doi.org/10.1515/prolas-2016-0010.
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Abstract Potato breeding clones were evaluated for resistance to late blight (agent Phytophthora infestans) using tuber inoculation tests and for presence of the resistance alleles of R1 and R3a genes in polymerase chain reaction tests. Among clones tested those expressing high, moderate and low resistance were identified. The data were analysed for the impact of R1 and R3a genes on tuber resistance to late blight in tested plant material. In previous evaluations performed on smaller amount of clones the tuber resistance levels significantly depended on presence/absence of the resistance allele of R3a gene and did not depend on presence of R1 gene allele. In the current study the statistical analyses did not prove the significant difference in resistance levels depending on presence of the resistance alleles, neither of R1 gene, nor of R3a gene. Tuber resistant clones bearing R3a gene resistance alleles still noticeably prevailed over the clones bearing the alleles of R1 gene as well as over the clones bearing the no resistance alleles of both genes. In several cases the resistance of clones with detected resistance allele of R1 gene was higher compared to those derived from the same crosses and showing amplification of the allele of R3a gene or those with no resistance alleles. Clones accumulating the resistance alleles of both (R1 and R3a) genes expressed high tuber resistance accompanied by necrotic reaction.
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Hauck, Nathanael R., Amy F. Iezzoni, Hisayo Yamane, and Ryutaro Tao. "Revisiting the S-allele Nomenclature in Sweet Cherry (Prunus avium) Using RFLP Profiles." Journal of the American Society for Horticultural Science 126, no. 6 (November 2001): 654–60. http://dx.doi.org/10.21273/jashs.126.6.654.
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Correct assignment of self-incompatibility alleles (S-alleles) in sweet cherry (Prunus avium L.) is important to assure fruit set in field plantings and breeding crosses. Until recently, only six S-alleles had been assigned. With the determination that the stylar product of the S-locus is a ribonuclease (RNase) and subsequent cloning of the S-RNases, it has been possible to use isoenzyme and DNA analysis to genotype S-alleles. As a result, numerous additional S-alleles have been identified; however, since different groups used different strategies for genotype analysis and different cultivars, the nomenclature contained inconsistencies and redundancies. In this study restriction fragment-length polymorphism (RFLP) profiles are presented using HindIII, EcoRI, DraI, or XbaI restriction digests of the S-alleles present in 22 sweet cherry cultivars which were chosen based upon their unique S-allele designations and/or their importance to the United States sweet cherry breeding community. Twelve previously published alleles (S1, S2, S3, S4, S5, S6, S7, S9, S10, S11, S12, and S13) could be differentiated by their RFLP profiles for each of the four restriction enzymes. Two new putative S-alleles, both found in `NY1625', are reported, bringing the total to 14 differentiable alleles. We propose the adoption of a standard nomenclature in which the sweet cherry cultivars `Hedelfingen' and `Burlat' are S3S5 and S3S9, respectively. Fragment sizes for each S-allele/restriction enzyme combination are presented for reference in future S-allele discovery projects.
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Lee, K. W., A. H. Johnson, and C. K. Hurley. "Two divergent routes of evolution gave rise to the DRw13 haplotypes." Journal of Immunology 145, no. 9 (November 1, 1990): 3119–25. http://dx.doi.org/10.4049/jimmunol.145.9.3119.
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Abstract The HLA class II genes and haplotypes have evolved over a long period of evolutionary time by mechanisms such as gene conversion, reciprocal recombination and point mutation. The extent of the diversity generated is most clearly evident in an analysis of the HLA class II alleles present within DRw13 haplotypes. This study uses cDNA sequencing to examine the first domains of DRB1, DRB3, DQA1, and DQB1 alleles from several American black individuals expressing seven different DRw13 haplotypes, five with undefined HLA-D specificities (i.e., not Dw18 or Dw19). Two new DRw13 alleles described in this study are the first examples of convergent evolution of DR alleles in which gene conversion has apparently combined segments of DRB1 alleles encoding DRw11 and DRw8 to generate two new DRB1 alleles, DRB1*1303 and DRB1*1304, that encode molecules bearing serologic determinants of a third allele, DRw13. These new DRw13 alleles are found embedded in haplotypes of DRw11 origin distinct from haplotypes encoding previously identified DRw13 alleles, DRB1*1301 and DRB1*1302. These data suggest that two evolutionary pathways may have given rise to two subgroups of alleles encoding molecules that share DRw13 serologic determinants yet which possess different structural and, likely, functional motifs. Reciprocal gene recombination events resulting in different DR, DRw52 and DQ allele combinations also appear to have played a crucial role in augmenting the level of diversity found in DRw13 haplotypes. Recombination has resulted in the association of one of the new DRw13 alleles with a DQw2 allele normally found associated with DR7 and the association of the DRw52c-associated DRw13 allele (DRB1*1302) with three different DQw1 alleles. The seven DRw13 haplotypes that have resulted from the effect of recombination on haplotypes formed by the two pathways of DRw13 allelic diversification have resulted in different repertoires of class II molecules and, most likely, different immune response profiles in individuals with these haplotypes.
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Sakurai, Kenji, Susan K. Brown, and Norman F. Weeden. "Determining the Self-incompatibility Alleles of Japanese Apple Cultivars." HortScience 32, no. 7 (December 1997): 1258–59. http://dx.doi.org/10.21273/hortsci.32.7.1258.
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The S alleles of 15 Japanese apple cultivars were determined by using the allele-specific polymerase chain reaction amplification and restriction enzyme digestion system developed by Janssens et al. (1995). Both S alleles were identified in eight diploid cultivars, two S alleles in three triploid cultivars, and one S allele in the remaining four diploid cultivars. Two cultivars had S alleles different than those predicted by their parentage, and in one comparison of a cultivar with its sport, an identity problem was discovered. The technique helped to indicate the parent contributing the unreduced gamete in triploids.
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Antonio, Nieto, Tobes Raquel, Vinasco Javier, Martin Javier, and Pareja Eduardo. "HLA DRB1*04 alleles typing by allele walking." Human Immunology 47, no. 1-2 (April 1996): 48. http://dx.doi.org/10.1016/0198-8859(96)84942-1.
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Tan, Geok Wee, Peijia Jiang, Ilja M. Nolte, Kushi Kushekhar, Rianne N. Veenstra, Bouke G. Hepkema, Ruth F. Jarrett, Anke van den Berg, and Arjan Diepstra. "HLA Expression in Relation to HLA Type in Classic Hodgkin Lymphoma Patients." Cancers 13, no. 22 (November 20, 2021): 5833. http://dx.doi.org/10.3390/cancers13225833.
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Several human leukocyte antigen (HLA) alleles are strongly associated with susceptibility to classic Hodgkin lymphoma (cHL), also in subgroups stratified for presence of the Epstein–Barr virus (EBV). We tested the hypothesis that the pressure on cHL tumour cells to lose HLA expression is associated with HLA susceptibility alleles. A meta-analysis was carried out to identify consistent protective and risk HLA alleles in a combined cohort of 839 cHL patients from the Netherlands and the United Kingdom. Tumour cell HLA expression was studied in 338 cHL cases from these two cohorts and correlated to the presence of specific susceptibility HLA alleles. Carriers of the HLA-DRB1*07 protective allele frequently lost HLA class II expression in cHL overall. Patients carrying the HLA-DRB1*15/16 (DR2) risk allele retained HLA class II expression in EBV− cHL and patients with the HLA-B*37 risk allele retained HLA class I expression more frequently than non-carriers in EBV+ cHL. The other susceptibility alleles showed no significant differences in expression. Thus, HLA expression by tumour cells is associated with a subset of the protective and risk alleles. This strongly suggests that HLA associations in cHL are related to peptide binding capacities of specific HLA alleles.
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Djukic, Nevena, Desimir Knezevic, Daniela Horvat, Dragan Zivancev, and Aleksandra Torbica. "Similarity of cultivars of wheat (Triticum durum) on the basis of composition of Gliadin alleles." Genetika 43, no. 3 (2011): 527–36. http://dx.doi.org/10.2298/gensr1103527d.
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Twenty one durum wheat cultivars originating from different world countries were investigated. Composition of gliadins was analyzed by acid polyacrylamide gel electrophoresis. Allele composition of gliadins was determined on the basis of identified gliadin blocks. Polymorphisms of Gli- loci was established and 27 different gliadin alleles were identified, namely, 5 at Gli-A1, 4 at Gli-B1, 9 at Gli-A2 and 9 alleles at Gli-B2 locus. The catalogue of determined alleles was presented. Frequency of alleles ranged from 4.76% to 42.86%. Heterozygous Gli-loci were identified at two durum cultivars. Similarity among cultivars was studied on composition of Gli-alleles and presented by UPGMA dendogram. On the base of Gli-allele composition, similarity varied from 0% to 100%.
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BĂCILĂ, Ioan, Voichița HAȘ, Dana ȘUTEU, Mihai MICLĂUȘ, Ana COSTE, Edward MUNTEAN, Carmen D. VANA, Andrei VARGA, Roxana CĂLUGĂR, and Ana COPÂNDEAN. "Screening of the Romanian maize (Zea mays L.) germplasm for crtRB1 and lcyE alleles enhancing the provitamin A concentration in endosperm." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 50, no. 3 (September 27, 2022): 12621. http://dx.doi.org/10.15835/nbha50312621.
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Maize occupies a significant place in the world agriculture. Yellow kernel maize contains mainly non-provitamin A carotenoids: lutein and zeaxanthin. The accumulation of provitamin A carotenoids is regulated by favourable alleles of lcyE and crtRB1 genes and could be used for the enhancement of these carotenoids in the maize grain through breeding. In this study, molecular screening of the Romanian germplasm was performed, looking for favourable alleles of the crtRB1 and lcyE genes, and the level of carotenoids was determined in a few selected lines. A number of 2746 inbred lines from seven research stations were subjected to a PCR amplification of crtRB1 and lcyE genes in order to identify the favourable alleles. It was selected 27 lines carrying the favourable alleles and nine lines with unfavourable alleles (four groups in total), from which total carotenoids, lutein, zeaxanthin, β-cryptoxanthin, β-carotene and retinol equivalents were determined by HPLC. Out of 2746 inbred lines analysed, 23.53% contained one or both genes with favourable alleles. The favourable allele of the crtRB1 gene was the most widespread (584 lines), followed by the lcyE gene (55 lines), while alleles favourable for both genes were detected in only 7 lines. Inbred lines with the favourable allele of the crtRB1 gene showed the highest levels of β-carotene and β-cryptoxanthin, while those with favourable allele of lcyE gene showed a high level of β-cryptoxanthin; the lines with favourable alleles for both genes had a level of β-carotene 60% higher than the lines with two unfavourable alleles.
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Gabay-Laughnan, Susan, Christine D. Chase, Victor M. Ortega, and Liming Zhao. "Molecular-Genetic Characterization of CMS-S Restorer-of-Fertility Alleles Identified in Mexican Maize and Teosinte." Genetics 166, no. 2 (February 1, 2004): 959–70. http://dx.doi.org/10.1093/genetics/166.2.959.
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Abstract Restorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm.
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Ahn, Jeong Hwan, Soo-Kyung Lee, and Chul Soo Park. "Evaluation of genetic variations at glutenin loci in Korean wheat landraces using allele-specific DNA markers." Plant Genetic Resources 12, no. 3 (October 30, 2014): 353–56. http://dx.doi.org/10.1017/s1479262114000926.
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The allelic variations at glutenin loci could significantly affect the bread baking quality, and specific glutenin alleles might be closely associated with greater gluten strength, which, in turn, is related to superior bread baking quality. In this study, allelic variations at Glu-1, Glu-A3 and Glu-B3 loci were evaluated in 222 Korean wheat landraces using gene-specific polymerase chain reaction (PCR) markers. Ten alleles were identified at Glu-1 loci. Glu-A1c, Glu-B1b, and Glu-D1a or Glu-D1f alleles were predominantly found at the respective loci and their frequencies were 86.5, 87.8 and 96.9 %, respectively. Seven Korean wheat landraces carried the Glu-D1d allele, and only one Korean wheat landrace (IT173162) achieved 10 points for the Glu-1 score. Fifteen alleles were identified at Glu-A3 and Glu-B3 loci; Glu-A3c and Glu-B3d or Glu-B3i alleles were commonly found at the respective loci and their frequencies were 77.0, 33.3 and 37.8 %, respectively. Glu-B3 alleles exhibited the highest genetic diversity than other alleles, while Glu-B1 and Glu-A1 alleles exhibited the lowest genetic diversity than other alleles. Twenty Korean wheat landraces had the Glu-A3d and Glu-B3b, Glu-B3d, Glu-B3f, Glu-B3g or Glu-B3i alleles, which were correlated with superior bread baking quality. Among these wheat lines, two (IT59787 and IT236544) carried the Glu-D1d allele.
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Westerdahl, Helena, Muhammad Asghar, Dennis Hasselquist, and Staffan Bensch. "Quantitative disease resistance: to better understand parasite-mediated selection on major histocompatibility complex." Proceedings of the Royal Society B: Biological Sciences 279, no. 1728 (July 6, 2011): 577–84. http://dx.doi.org/10.1098/rspb.2011.0917.
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We outline a descriptive framework of how candidate alleles of the immune system associate with infectious diseases in natural populations of animals. Three kinds of alleles can be separated when both prevalence of infection and infection intensity are measured—qualitative disease resistance, quantitative disease resistance and susceptibility alleles. Our descriptive framework demonstrates why alleles for quantitative resistance and susceptibility cannot be separated based on prevalence data alone, but are distinguishable on infection intensity. We then present a case study to evaluate a previous finding of a positive association between prevalence of a severe avian malaria infection (GRW2, Plasmodium ashfordi ) and a major histocompatibility complex (MHC) class I allele (B4b) in great reed warblers Acrocephalus arundinaceus . Using the same dataset, we find that individuals with allele B4b have lower GRW2 infection intensities than individuals without this allele. Therefore, allele B4b provides quantitative resistance rather than increasing susceptibility to infection. This implies that birds carrying B4b can mount an immune response that suppresses the acute-phase GRW2 infection, while birds without this allele cannot and may die. We argue that it is important to determine whether MHC alleles related to infections are advantageous (quantitative and qualitative resistance) or disadvantageous (susceptibility) to obtain a more complete picture of pathogen-mediated balancing selection.
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Eagles, H. A., Karen Cane, and Neil Vallance. "The flow of alleles of important photoperiod and vernalisation genes through Australian wheat." Crop and Pasture Science 60, no. 7 (2009): 646. http://dx.doi.org/10.1071/cp09014.
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The photoperiod sensitivity gene Ppd-D1 and the vernalisation genes Vrn-A1, Vrn-B1, and Vrn-D1 are known to contribute to optimal adaptation to specific environments. Diagnostic molecular markers for detecting important alleles of these genes are now available, including for 2 distinct spring alleles of Vrn-A1 (a and b). As a first step for determining the relative importance of these alleles, they were characterised in Australian cultivars released from the late 19th until the early 21st Century. The photoperiod-insensitive Ppd-D1a allele did not occur in the Australian cultivars we assessed until after the release of cultivars containing CIMMYT germplasm in 1973. Thereafter, this allele became common; however, cultivars with an alternative, presumably photoperiod-sensitive, allele have continued to be released for all parts of the Australian wheatbelt, including for latitudes less than 28°S. In contrast to other parts of the world, Vrn-A1b was frequent in cultivars released during the first 70 years of the 20th Century and is still present in modern cultivars. Before the use of CIMMYT germplasm, the spring allele of Vrn-B1 and the winter allele of Vrn-D1 were common. Four major combinations of alleles of these major genes were identified in modern cultivars: first, those similar to WW15 (Anza), with the Ppd-D1a allele, the spring Vrn-A1a allele, and winter alleles at Vrn-B1 and Vrn-D1; second, those similar to Spear or Kite, with the alternative, photoperiod-sensitive allele at Ppd-D1, the spring Vrn-A1a allele, the spring Vrn-B1a allele, and the winter allele at Vrn-D1; third, those similar to Pavon F 76, with the Ppd-D1a allele, the winter allele at Vrn-A1, and the spring alleles at Vrn-B1 and Vrn-D1; fourthly, those similar to Gabo, with the winter allele at Vrn-A1, the spring allele at Vrn-B1, the winter allele at Vrn-D1, but the Ppd-D1a allele. Other combinations were found, including those for winter cultivars and those for early heading cultivars. A hypothesis was suggested for the facultative cv. Oxley. Evidence was presented to suggest that modern full-season cultivars head ~1 week earlier in a Mallee environment than cultivars from the late 19th Century.
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Spencer, H. G., and R. W. Marks. "The maintenance of single-locus polymorphism. IV. Models with mutation from existing alleles." Genetics 130, no. 1 (January 1, 1992): 211–21. http://dx.doi.org/10.1093/genetics/130.1.211.
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Abstract The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.
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Knezevic, Desimir, and Aleksandra Novoselskaya-Dragovich. "Polymorphism of Gli-D1 alleles of Kragujevac’s winter wheat cultivars (Triticum aestivum L.)." Genetika 39, no. 2 (2007): 273–82. http://dx.doi.org/10.2298/gensr0702273k.
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Composition of gliadins encoded by Gli-D1 allele as well polymorphisms of Gli-D1 allele investigated in 25 wheat cultivars by using acid polyacrylamide gel electrophoresis. Electrophoregrams obtained by polyacrylamide gel electrophoresis were used for estimation variability of gliadin components and identification of gliadin blocks. Five gliadin blocks encoded by different alleles at Gli-D1 locus were apparently expressed and identified. Gliadin blocks differed according to number of components and their molecular mass. Variability of determined block components indicates that existing polymorphisms of gliadins alleles. Frequency of identified 5 alleles at Gli-D1 locus was in ratio from 4% to 52%. The highest frequency of b allele and the of g allele was found.
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Mersiyanova, I. I., Yu A. Knyazev, M. V. Burdenko, T. V. Sebko, and О. V. Yevgrafov. "Associations between insulin-dependent diabetes mellitus and HLA-DQA1 alleles." Problems of Endocrinology 41, no. 4 (August 15, 1995): 3–5. http://dx.doi.org/10.14341/probl11449.
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The incidence of HLA-DQA1 alleles was assessed in patients with insulin-dependent diabetes mellitus (IDDM), their relatives, and healthy controls using HLA-DQA1 genotyping by digestion of PCR amplified DNA with allele-specific restriction enzymes. A significant increase in the incidence of HLA-DQA1*0301 allele was observed in diabetics although the ratio of DQA1*0301 homozygotes to heterozygotes was similar in the patients and controls. The presence of one DQA 1*0301 allele in the genome appeared to be sufficient for susceptibility to IDDM. Comparison of the incidence of other DQA1 "Arg52" alleles in diabetics and healthy controls revealed no differences between the groups. The incidence of DQA1 "non-Arg52" alleles (specifically DQA1*0201) was reduced in diabetics as compared to normal controls. The presence of these alleles may be considered as the "protective" factor.
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Batra, T. R., P. A. Macdonald, and M. J. Stear. "Association of class I bovine lymphocyte antigens with production traits in the Ayrshire breed." Canadian Journal of Animal Science 74, no. 4 (December 1, 1994): 703–5. http://dx.doi.org/10.4141/cjas94-102.
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Ninety progeny tested Canadian Ayrshire bulls were serologically typed for the BoLA-A locus to determine the association of these alleles with production traits. After exclusion of bulls carrying alleles that occurred at frequencies lower than 2% or whose production proofs were not available, records from 78 bulls remained for analysis. A gene substitution model, which included the effects of BoLA alleles and the breeding value of the sire of the bull as covariate, was used to evaluate the additive effects of BoLA alleles of bulls (ETAs) on the production traits of their daughters. Allele W17 was significantly associated with ETA for milk, fat and protein yields. Allele CA96 was associated with significant increases in ETA for fat yield. There was no significant association of BoLA alleles with either ETA for fat or protein percentage. Key words: BoLA, production traits, Ayrshire
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Wang, Zaolin, P. Scott White, Michelle Petrovic, Owatha L. Tatum, Lee S. Newman, Lisa A. Maier, and Babetta L. Marrone. "Differential Susceptibilities to Chronic Beryllium Disease Contributed by Different Glu69 HLA-DPB1 and -DPA1 Alleles." Journal of Immunology 163, no. 3 (August 1, 1999): 1647–53. http://dx.doi.org/10.4049/jimmunol.163.3.1647.
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Abstract Chronic beryllium disease (CBD) is associated with the allelic substitution of a Glu69 in the HLA-DPB1 gene. Although up to 97% of CBD patients may have the Glu69 marker, about 30–45% of beryllium-exposed, unaffected individuals carry the same marker. Because CBD occurs in only 1–6% of exposed workers, the presence of Glu69 does not appear to be the sole genetic factor underlying the disease development. Using two rounds of direct automated DNA sequencing to precisely assign HLA-DPB1 haplotypes, we have discovered highly significant Glu69-containing allele frequency differences between the CBD patients and a beryllium-exposed, nondiseased control group. Individuals with DPB1 Glu69 in both alleles were almost exclusively found in the CBD group (6/20) vs the control group (1/75). Whereas most Glu69 carriers from the control group had a DPB1 allele *0201 (68%), most Glu69 carriers from the CBD group had a non-*0201 DPB1 Glu69-carrying allele (84%). The DPB1 allele *0201 was almost exclusively (29/30) associated with DPA1 *01 alleles, while the non-*0201 Glu69-containing DPB1 alleles were closely associated with DPA1 *02 alleles (26/29). Relatively rare Glu69-containing alleles *1701, *0901, and *1001 had extremely high frequencies in the CBD group (50%), as compared with the control group (6.7%). Therefore, the most common Glu69-containing DPB1 allele, *0201, does not seem to be a major disease allele. The results suggest that it is not the mere presence of Glu69, per se, but specific Glu69-containing alleles and their copy number (homozygous or heterozygous) that confer the greatest susceptibility to CBD in exposed individuals.
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Khavkin, E. E., M. V. Zabrodina, and D. Ya Silis. "Isoenzymes of aspartate aminotransferase in perennial and annual rye and their hybrids." Genome 39, no. 3 (June 1, 1996): 513–19. http://dx.doi.org/10.1139/g96-065.
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Aspartate aminotransferase patterns were screened in a collection of rye genotypes that included 24 accessions of wild perennial rye (Secale montanum Guss.), 6 accessions of cultivated perennial Derzhavin and Tsitsin rye (Secale cereale × S. montanum), 15 accessions of winter and spring rye cultivars (S. cereale L.), and 9 accessions of perennial and annual rye genotypes bred from S. montanum ssp. kuprijanovii, Derzhavin rye, and winter rye for their resistance to fungal diseases. Aspartate aminotransferase is coded for by four loci. The data fit the model where AAT 1/4 is coded by Aat 1 and Aat 4, two duplicate loci, with null and two active alleles for each locus, alleles 1 and 3 for locus Aat 1 and alleles 2 and 4 for locus Aat 4; dimeric AAT 1/4 enzyme molecules are the products of both intralocus and interloci complementation. Allele 1 of Aat 1 was the most prominent in the isoenzyme patterns of the rye species. Alleles null and 2 of Aat 4 were twice as frequent in the perennial rye accessions, including Derzhavin and Tsitsin rye, than in winter and spring rye. In contrast, allele 4 of Aat 4 was characteristic of S. cereale. Within the screened collection, locus Aat 2 was monomorphic. Among three alleles of Aat 3, allele 2 dominated isoenzyme profiles of both rye species, whereas the other two alleles were species-specific: allele 1 was characteristic of S. montanum and allele 3 was found only in S. cereale. Key words : rye, Secale cereale, Secale derzhavinii, Secale montanum, aspartate aminotransferase, isoenzymes, perennial habit, polymorphism.
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Kruger, F. J. "Enzyme polymorphism in Schistosoma mattheei from cattle in the Eastern Transvaal Lowveld." Journal of Helminthology 63, no. 3 (September 1989): 191–96. http://dx.doi.org/10.1017/s0022149x0000897x.
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ABSTRACTEnzyme electrophoresis was conducted on 10 Schistosoma mattheei adult worm samples, comprising 270 individuals, collected from cattle in the Eastern Transvaal Lowveld. Glucose-6-phosphate dehydrogenase (G6PDH) was studied in all the samples and phosphoglucomutase (PGM) and malate dehydrogenase (MDH) in five populations each. Only one population was polymorphic for G6PDH. In this population, in addition to the allele found in all the other samples, a second allele occurred with a similar Rf value to S. haematobium. The two alleles were in Hardy-Weinberg equilibrium. MDH-1 exhibited two alleles. However, these alleles were not in equilibrium. In certain populations, heterozygotes occurred together with homozygotes of one of the alleles only. PGM was monomorphic in all the populations studied.
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Paradkar, Minal U., Swarup A. V. Shah, Alpa J. Dherai, Dhanashri Shetty, and Tester F. Ashavaid. "Distribution of CYP2D6 genotypes in the Indian population – preliminary report." Drug Metabolism and Personalized Therapy 33, no. 3 (September 25, 2018): 141–51. http://dx.doi.org/10.1515/dmpt-2018-0011.
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Abstract Background Cytochrome P450 2D6 (CYP2D6) allelic distribution exhibits differences amongst worldwide populations. There is lack of data from Mumbai, Western India, on the major CYP2D6 alleles *2, *3, *4, *5, *10 and *41, and gene multiplication alleles. Hence, the present study was undertaken to determine the distribution of these clinically relevant CYP2D6 alleles. Methods Fifty-two healthy individuals were screened using TaqMan SNP genotyping and copy number variation (CNV) assays by real-time polymerase chain reaction. Results The allele frequencies of CYP2D6*2, *3, *4, *5, *10 and *41 alleles were observed to be 30.8%, 0%, 11.5%, 3.9%, 19.2% and 17.3%, respectively. The frequency of CYP2D6 gene one copy, two copies, three copies and four copies were observed to be 7.7%, 76.9%, 13.5% and 1.9%, respectively. The predicted phenotype frequency was observed to be 78.9%, 3.9% and 9.6% for extensive, intermediate, and ultrarapid metabolizers, respectively, whereas poor metabolizers were not detected. Conclusions CYP2D6 allele frequencies showed heterogeneous distribution in the present study as compared to worldwide populations. High frequency of CYP2D6*41 allele, gene duplication alleles and UMs was observed. The scarcity and/or lack of data from the Indian population on these alleles further substantiates the need for screening of CYP2D6 genotyping.
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Madrigal, J. A., M. P. Belich, W. H. Hildebrand, R. J. Benjamin, A. M. Little, J. Zemmour, P. D. Ennis, F. E. Ward, M. L. Petzl-Erler, and E. D. du Toit. "Distinctive HLA-A,B antigens of black populations formed by interallelic conversion." Journal of Immunology 149, no. 10 (November 15, 1992): 3411–15. http://dx.doi.org/10.4049/jimmunol.149.10.3411.
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Abstract Alleles encoding five HLA-A and B Ag characteristic of black populations have been isolated and their nucleotide sequences determined. In each case, the "black" allele is similar to a "related" allele found in caucasoid populations. The primary differences between these pairs of alleles are localized clusters of nucleotide substitutions that change two to five residues of the Ag recognition site. The pattern of differences indicates that the pairs of black and caucasoid alleles diverged primarily as a result of interallelic conversion events.
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Johnson, Toby, and Nick H. Barton. "The Effect of Deleterious Alleles on Adaptation in Asexual Populations." Genetics 162, no. 1 (September 1, 2002): 395–411. http://dx.doi.org/10.1093/genetics/162.1.395.
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Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.
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Schierup, Mikkel H., Xavier Vekemans, and Freddy B. Christiansen. "Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants." Genetics 150, no. 3 (November 1, 1998): 1187–98. http://dx.doi.org/10.1093/genetics/150.3.1187.
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Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.
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Mounkes, Leslie C., and Margaret T. Fuller. "Molecular Characterization of Mutant Alleles of the DNA Repair/Basal Transcription Factor haywire/ERCC3 in Drosophila." Genetics 152, no. 1 (May 1, 1999): 291–97. http://dx.doi.org/10.1093/genetics/152.1.291.
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Abstract The haywire gene of Drosophila encodes a putative helicase essential for transcription and nucleotide excision repair. A haywire allele encoding a dominant acting poison product, lethal alleles, and viable but UV-sensitive alleles isolated as revertants of the dominant acting poison allele were molecularly characterized. Sequence analysis of lethal haywire alleles revealed the importance of the nucleotide-binding domain, suggesting an essential role for ATPase activity. The viable haync2 allele, which encodes a poison product, has a single amino acid change in conserved helicase domain VI. This mutation results in accumulation of a 68-kD polypeptide that is much more abundant than the wild-type haywire protein.
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Wu, H., K. Taniguchi, F. Wakasugi, S. Ukae, S. Chiba, M. Ohseto, A. Hasegawa, Tomoko Urasawa, and Shozo Urasawa. "Survey on the distribution of the gene 4 alleles of human rotaviruses by polymerase chain reaction." Epidemiology and Infection 112, no. 3 (June 1994): 615–22. http://dx.doi.org/10.1017/s0950268800051311.
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SUMMARYThe presence of six gene 4 alleles (or VP4 genotypes) in human rotaviruses has been recognized. Using 16 representative cultivable human rotavirus strains, we confirmed the specificity of VP4 genotyping by polymerase chain reaction (PCR) using the nested oligonucleotides specific to each of the four representative gene 4 alleles. Using the PCR. we surveyed the gene 4 alleles of 199 human rotaviruses in stools collected in Japan and Thailand. Strains with the gene 4 allele, corresponding to P1A serotype. were shown to be the most prevalent, but two strains with P2 gene 4 allele and one strain with P3 gene 4 allele were detected in Thailand and in Japan, respectively.
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Fujii, Hiroshi, Keisuke Nonaka, Mai F. Minamikawa, Tomoko Endo, Aiko Sugiyama, Kosuke Hamazaki, Hiroyoshi Iwata, Mitsuo Omura, and Takehiko Shimada. "Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population." PLOS ONE 16, no. 2 (February 4, 2021): e0246468. http://dx.doi.org/10.1371/journal.pone.0246468.
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To enrich carotenoids, especially β-cryptoxanthin, in juice sac tissues of fruits via molecular breeding in citrus, allele mining was utilized to dissect allelic variation of carotenoid metabolic genes and identify an optimum allele on the target loci characterized by expression quantitative trait (eQTL) analysis. SNPs of target carotenoid metabolic genes in 13 founders of the Japanese citrus breeding population were explored using the SureSelect target enrichment method. An independent allele was determined based on the presence or absence of reliable SNPs, using trio analysis to confirm inheritability between parent and offspring. Among the 13 founders, there were 7 PSY alleles, 7 HYb alleles, 11 ZEP alleles, 5 NCED alleles, and 4 alleles for the eQTL that control the transcription levels of PDS and ZDS among the ancestral species, indicating that some founders acquired those alleles from them. The carotenoid composition data of 263 breeding pedigrees in juice sac tissues revealed that the phenotypic variance of carotenoid composition was similar to that in the 13 founders, whereas the mean of total carotenoid content increased. This increase in total carotenoid content correlated with the increase in either or both β-cryptoxanthin and violaxanthin in juice sac tissues. Bayesian statistical analysis between allelic composition of target genes and carotenoid composition in 263 breeding pedigrees indicated that PSY-a and ZEP-e alleles at PSY and ZEP loci had strong positive effects on increasing the total carotenoid content, including β-cryptoxanthin and violaxanthin, in juice sac tissues. Moreover, the pyramiding of these alleles also increased the β-cryptoxanthin content. Interestingly, the offset interaction between the alleles with increasing and decreasing effects on carotenoid content and the epistatic interaction among carotenoid metabolic genes were observed and these interactions complexed carotenoid profiles in breeding population. These results revealed that allele composition would highly influence the carotenoid composition in citrus fruits. The allelic genotype information for the examined carotenoid metabolic genes in major citrus varieties and the trio-tagged SNPs to discriminate the optimum alleles (PSY-a and ZEP-e) from the rest would promise citrus breeders carotenoid enrichment in fruit via molecular breeding.
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Manela, Citra, Taufik Hidayat, Rika Susanti, and Noverika Windasari. "Genetic Analysis of TPOX, CSF1PO, D3S1358, D8S1179, vWA, D5S818, and TH01 Short Tandem Repeats Loci in Nias Population, Indonesia." Open Access Macedonian Journal of Medical Sciences 10, A (May 27, 2022): 1089–92. http://dx.doi.org/10.3889/oamjms.2022.9853.
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BACKGROUND: Nias is an island located off the western coast of Sumatra, Indonesia. Nias is situated above the Eurasian and Indo-Australian subduction zone plates. This makes it prone to earthquakes and tsunamis. Genetic analysis and genetic variation of short tandem repeats (STR) locus are not widely known. These data are valuable for individual identification and paternity testing. METHODS: Seven STR loci (TPOX, CSF1PO, D3S1358, D8S1179, vWA, D5S818, and TH01) were analyzed using 25 healthy and unrelated persons Nias population. Allele frequency, power of discrimination (PD), expected heterozygosity, and probability of exclusion (PE) were calculated. RESULTS: We found 40 alleles. The allele with highest frequency was alleles 9 at the TH01 loci. While the lowest frequency were allele 9 at the CSF1PO loci, allele 12 at the TPOX loci, alleles 17 and 18 at the D8S1179 loci, and alleles 16 and 20 at the vWA loci. The highest Expected Heterozygosity, PD, and PE at the D8S1179 loci. The highest number of alleles is also at D8S1179 loci. All loci followed the Hardy–Weinberg equilibrium (p > 0.05). The PD values for all tested loci ranged from 80.6 to 94.5%. CONCLUSION: We report the allele frequencies and forensic statistical parameters of seven STR loci (TPOX, CSF1PO, D3S1358, D8S1179, vWA, D5S818, and TH01) in the Nias population, which can be used as a forensic database reference for Nias populations.
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Dotlačil, L., E. Gregová, J. Hermuth, Z. Stehno, and J. Kraic. "Diversity of HMW-Glu Alleles and Evaluation of their Effects on some Characters in Winter Wheat Landraces and Old Cultivars." Czech Journal of Genetics and Plant Breeding 38, No. 3-4 (August 1, 2012): 109–16. http://dx.doi.org/10.17221/6244-cjgpb.
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Earliness, morphological and agronomic characters and grain quality were studied in 123 European landraces and old cultivars of winter wheat in three-year field experiments. Simultaneously, HMW Glu-alleles were identified in these cultivars by means of SDS-PAGE. Within this set of cultivars 224 Glu-lines (with occurrence over 5% in the cultivar) were identified carrying 3 different allelic combinations at 1A, 10 combinations at 1B and 3 combinations at 1D chromosomes, respectively. Relatively rare were alleles 2* at 1A and 3+12 at 1D as well as alleles 8, 6, 9, 7, 13+16 and 17+ 18 at 1B. Allele 20 at 1B was identified only in cultivars from DNK, CHE and EST. Allele 2* at 1A locus was found mainly in cultivars from Eastern, South-Eastern and Central Europe. Allelic combination 17+18 at 1B was also characteristic of cultivars from Central Europe. However, the gluten patterns themselves were not a sufficient tool for geographic characterisation of cultivars. The composition of Glu-alleles influenced the earliness of cultivars (alleles 2* at 1A, 17+ 18 and 6 at 1B and 3+12 at 1D). Spike length was positively affected by allele 1 at 1A and number of spikelets per spike by alleles 2+12 et 1D chromosome. Allele 2* was also associated with lower grain weight per spike. Crude protein content was decreased in cultivars where GS at 1A locus was absent (0). The value of gluten index was considerably higher (59.2) in cultivars bearing allelic combination 5+10 at 1D. A number of alleles affected the values of SDS micro-sedimentation test.
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Freeth, Allan L., John B. Gibson, and Ann V. Wilks. "Transcription analysis of alcohol dehydrogenase null alleles from natural populations of Drosophila melanogaster." Genome 30, no. 1 (February 1, 1988): 25–30. http://dx.doi.org/10.1139/g88-005.
Full textAbstract:
Southern analysis of 19 Adh null activity alleles isolated from Tasmanian populations of Drosophila melanogaster have shown that there are no detectable insertions or deletions in an 11.8-kb region that contains the gene. Northern blot analyses of the null alleles have shown that they all produce a transcript about 100 bases longer than that produced by the normal allele and they accumulate a precursor of 1800 bases. The amount of the major transcript produced by the null alleles is about 10% of that produced by normal alleles. The molecular properties of the null alleles suggest that they share a common origin.Key words: alcoahol dehydrogenase, null alleles, mRNA, Drosophila melanogaster.
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Suprovich, T., Т. Karchevska, R. Kolinchuk, and V. Mizyk. "DETERMINATION OF ALLELES OF BOLA-DRB3.2 GENE ASSOCIATED WITH NECROBACTERIOSIS OF THE COWS OF UKRAINIAN BLACK-AND-WHITE DAIRY CATTLE." Animal Breeding and Genetics 51 (March 28, 2018): 205–13. http://dx.doi.org/10.31073/abg.51.28.
Full textAbstract:
The main objective of research "BoLA and disease" is the need to develop approaches and obtain reliable criteria which would allow to judge about animal genetic predisposition to the disease and about change of its immunological status in the development of pathological process. Genes of class II of main histocompatibility complex have the greatest association to diseases. Now 54 alleles of BoLA-DRB3.2 have been described by PCR-RFLP. The high level of allelic diversity of the gene is caused by necessity of tying a wide range of foreign antigens, which leads to the possibility of its use as a marker for various diseases of cattle. This article presents the results of detecting alleles of BoLA-DRB3.2 gene, which have the expressed relationship with the disease of Ukrainian Black-and-White Dairy cows on necrobacteriosis and can be used as DNA markers of this disease. Diagnosis of necrobacteriosis was set at the basis of clinical, pathological and epizootic data and laboratory results. The blood samples were taken from 114 cows, 43 of which had the disease. Spectrum of alleles of exon 2 of BoLA-DRB3 gene was studied by PCR. 54 alleles were determined in total. Alleles, which have a close relationship with susceptibility or resistance to necrobacteriosis and can be used as DNA markers, were established on indicators of frequency and relative risk (RR) with test on Pearson criterion (χ2). 32 alleles were determined in the experimental group of animals. There were seven alleles with a frequency greater than 5%. The most often determined allele of BoLA-DRB3.2 was *24. It is present in 18% of the animals. And often determined alleles were *22 (7,9%) and *28 (7,5%). Limit higher than 5% was for alleles *08 and * 09 (6,1%), *03 and *16 (5,3%). The lowest frequency of detection was for alleles *06, *25, *31 and *41 (0,4%). Alleles of BoLA-DRB3.2*24 (16,9%), *22 (10,6%), *28 (8,5%), *03 (7,7%), *08 and *10 (6,3%) were often determined in the group of healthy cows. Alleles *06, *14, *19, *25 and *51 weren’t determined in this group. The animals with necrobacteriosis had often alleles *24 (19,8%), *16 (12,8%), *23 (8,1%), *8, *10 and *28 (5,8%). Alleles *01, *11, *21, *31 and *41 weren’t in general. In the three experimental groups 8 alleles were determined with a frequency of over 5% (all herd, healthy and diseased animals respectively). There are four alleles among them presented in all three samples: *08, *10, *24 and *28. Two "informative" alleles (*03 and *22) were found in every the 20th animal simultaneously in two groups of cows – healthy animals and in the total sample. Also two "informative" alleles *16 and *23 were simultaneously in the diseased cows and in the total sample. 11 alleles have significant association with susceptibility or resistance to necrobacteriosis on criterion of relative risk. There are 4 alleles *16 (24,1%), * 18 (5,25%), *25 (5,04%) and *23 (4,41%), indicating the relationship with disease (RR ≥ 2). Four alleles of BoLA-DRB3.2 are significant on criterion χ2 and have a sufficient test of validity for the studied biological objects. Allele *16 shows a very high level test of validity P = 0,999 (χ2 = 16,6). Three alleles *03 (4,93), *23 (4,86) and *22 (4,03) have a minimum acceptable test of validity for χ2 for P = 0,95. 8 alleles: *3 (-7,7), *21 (- ,44), *36 (-3,87), *22 (-3,57), *12 (-3,18), *1 and *11 (-3,13) and *26 (- 2,51) indicate neсrobaсteriosis resistance (RR ≤ -2). Allele would be associated with the disease if the condition performed RR ≥ 2 і χ2> 3,8. There are two such alleles: *16 (RR = 24,1; χ2 = 16,6), *23 (RR = 4,41; χ2 = 4,86). Also "negative" alleles on risk of disease manifest are *18 (5,25) and *25 (5,08), but with insufficient validity of Pearson criterion (respectively 2,45 and 1,66). Allele would be associated with the resistance to disease if the condition performed RR ≤ -2 і χ2> 3,8. There are 2 alleles associated with resistance to necrobacteriosis: *03 (RR = -7,7; χ2 = 4,93) and *22 (RR = -3,57; χ2 = 4,03). Also six alleles (* 01, * 11, * 12, * 21, * 26 and * 36) detected resistance to neсrobacteriosis on high level of relative risk, but with insufficient validity. It should be noted, that allele BoLA-DRB3.2*22, which proved to be a "positive" marker of resistance to necrobacteriosis, has a strong correlation with resistance to mastitis in cows of Ukrainian Black-and-White Dairy (RR = -2,52; χ2 = 5,02) and Ukrainian Red-and-White Dairy breeds (RR = -4,66; χ2 = 11,11) in previous studies. The study of the distribution of alleles of exon 2 of BoLA-DRB3 gene at the Ukrainian Black-and-White Dairy cows, which were healthy and diseased by necrobacteriosis, revealed the alleles which had a close relationship with penchant to this disease (* 16 and * 23) and two alleles associated with resistance (* 03 and * 22). Given the fact that the research was conducted directly on animal blood DNA the detected alleles BoLA-DRB3 should be used as DNA markers in the analysis of susceptibility or resistance to necrobacteriosis of cows.
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Eagles, H. A., Karen Cane, Haydn Kuchel, G. J. Hollamby, Neil Vallance, R. F. Eastwood, N. N. Gororo, and P. J. Martin. "Photoperiod and vernalization gene effects in southern Australian wheat." Crop and Pasture Science 61, no. 9 (2010): 721. http://dx.doi.org/10.1071/cp10121.
Full textAbstract:
Photoperiod and vernalization genes are important for the optimal adaptation of wheat to different environments. Diagnostic markers are now available for Vrn-A1, Vrn-B1, Vrn-D1 and Ppd-D1, with all four genes variable in southern Australian wheat-breeding programs. To estimate the effects of these genes on days to heading we used data from 128 field experiments spanning 24 years. From an analysis of 1085 homozygous cultivars and breeding lines, allelic variation for these four genes accounted for ~45% of the genotypic variance for days to heading. In the presence of the photoperiod-insensitive allele of Ppd-D1, differences between the winter genotype and genotypes with a spring allele at one of the genes ranged from 3.5 days for Vrn-B1 to 4.9 days for Vrn-D1. Smaller differences occurred between genotypes with a spring allele at one of the Vrn genes and those with spring alleles at two of the three genes. The shortest time to heading occurred for genotypes with spring alleles at both Vrn-A1 and Vrn-D1. Differences between the photoperiod-sensitive and insensitive alleles of Ppd-D1 depended on the genotype of the vernalization genes, being greatest when three spring alleles were present (11.8 days) and least when the only spring allele was at Vrn-B1 (3.7 days). Because of these epistatic interactions, for the practical purposes of using these genes for cross prediction and marker-assisted selection we concluded that using combinations of alleles of genes simultaneously would be preferable to summing effects of individual genes. The spring alleles of the vernalization genes responded differently to the accumulation of vernalizing temperatures, with the common spring allele of Vrn-A1 showing the least response, and the spring allele of Vrn-D1 showing a response that was similar to, but less than, a winter genotype.
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Trent, C., W. B. Wood, and H. R. Horvitz. "A novel dominant transformer allele of the sex-determining gene her-1 of Caenorhabditis elegans." Genetics 120, no. 1 (September 1, 1988): 145–57. http://dx.doi.org/10.1093/genetics/120.1.145.
Full textAbstract:
Abstract We have characterized a novel dominant allele of the sex-determining gene her-1 of Caenorhabditis elegans. This allele, called n695, results in the incomplete transformation of XX animals into phenotypic males. Previously characterized recessive her-1 alleles transform XO animals into phenotypic hermaphrodites. We have identified five new recessive her-1 mutations as intragenic suppressors of n695. Three of these suppressors are weak, temperature-sensitive alleles. We show that the recessive her-1 mutations are loss-of-function alleles, and that the her-1(n695) mutation results in a gain-of-function at the her-1 locus. The existence of dominant and recessive alleles that cause opposite phenotypic transformations demonstrates that the her-1 gene acts to control sexual identity in C. elegans.
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Clifford, R. J., and T. Schüpbach. "Coordinately and differentially mutable activities of torpedo, the Drosophila melanogaster homolog of the vertebrate EGF receptor gene." Genetics 123, no. 4 (December 1, 1989): 771–87. http://dx.doi.org/10.1093/genetics/123.4.771.
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Abstract The torpedo (top) locus of Drosophila encodes the fruitfly homolog of the vertebrate epidermal growth factor receptor gene and the neu proto-oncogene. We have isolated 13 top alleles in a screen for mutations failing to complement the female sterility of top, a recessive maternal effect allele that disrupts the establishment of the dorsoventral pattern of the egg shell and embryo. Several alleles recovered in this screen are zygotic lethal mutations; genetic analysis of these alleles has demonstrated that top is allelic to the embryonic lethal locus faint little ball. The 13 mutations recovered in our screens and 19 previously isolated top alleles have been genetically characterized through complementation tests with a series of hypomorphic and amorphic alleles. Nearly every top allele fails to complement the maternal effect sterility of top. Complementation tests show that the gene is required not only for oogenesis and embryogenesis, but also for pupal viability, for the growth of certain imaginal discs and for the patterning of specific ectodermal derivatives of the imaginal discs. Complementation analysis further demonstrates that the top lesions can be divided into general phenotypic categories: alleles affecting all gene activities in a coordinate manner, alleles preferentially affecting embryogenesis, alleles preferentially retaining oogenesis activity and alleles differentially affecting the development of specific imaginal disc derivatives. Correlations observed between the various developmental defects produced by top lesions suggest that the gene possesses several differentially, though not independently, mutable activities.
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Dowla, Mirza A. N. N. U., Shahidul Islam, Katia Stefanova, Graham O’ Hara, Wujun Ma, and Ian Edwards. "Phenology and Dwarfing Gene Interaction Effects on the Adaptation of Selected Wheat (Triticum aestivum L.) Advanced Lines across Diverse Water-Limited Environments of Western Australia." Agriculture 10, no. 10 (October 13, 2020): 470. http://dx.doi.org/10.3390/agriculture10100470.
Full textAbstract:
Photoperiod, vernalization, and plant height controlling genes are major developmental genes in wheat that govern environmental adaptation and hence, knowledge on the interaction effects among different alleles of these genes is crucial in breeding cultivars for target environments. The interaction effects among these genes were studied in nineteen Australian advanced lines from diverse germplasm pools and four commercial checks. Diagnostic markers for the Vrn-A1 locus revealed the presence of the spring allele Vrn-A1a in 10 lines and Vrn-A1c in one line. The dominant alleles of Vrn-B1a and Vrn-D1a were identified in 19 and 8 lines, respectively. The most common photoperiod-insensitive allele of Ppd-D1a was identified in 19 lines and three and four copy photoperiod-insensitive alleles (Ppd-B1a and Ppd-B1c) were present in five and one lines, respectively. All the lines were photoperiod-sensitive for the Ppd-A1 locus. All lines were semi-dwarf, having either of the two dwarfing alleles; 14 lines had the Rht-B1b (Rht-1) and the remaining had the Rht-D1b (Rht-2) dwarfing allele. The presence of the photoperiod-insensitive allele Ppd-D1a along with one or two spring alleles at the Vrn1 loci resulted in an earlier heading and better yield. Dwarfing genes were found to modify the heading time—the Rht-D1b allele advanced heading by three days and also showed superior effects on yield-contributing traits, indicating its beneficial role in yield under rain-fed conditions along with an appropriate combination of photoperiod and vernalization alleles. This study also identified the adaptability value of these allelic combinations for higher grain yield and protein content across the different the water-limited environments.
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Jarvi, Susan, Kiara Bianchi, Margaret Farias, Kimberly Wiegand, Sarah Skinner, Ashley Asano, and Christopher Czerwonka. "Major histocompatibility complex class II gene diversity and tolerance to avian malaria in Hawaiian honeycreepers (Drepanidinae) (99.15)." Journal of Immunology 186, no. 1_Supplement (April 1, 2011): 99.15. http://dx.doi.org/10.4049/jimmunol.186.supp.99.15.
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Abstract Susceptibility to avian malaria differs both within and between species of Hawaiian honeycreepers. Due to their critical function in adaptive immunity, proteins encoded by Mhc genes may be key in the development of tolerance to Plasmodium relictum in low elevation populations of `amakihi (Hemignathus virens). To evaluate gene copy number, 263 Mhc class II peptide-binding region clones were sequenced from a captive family of `amakihi. Phylogenetic analysis suggests a minimum of 10 Mhc class II genes with detection of 35 unique alleles. Species comparisons (total 503 clones, eight birds/species) reveal that Mhc diversity is highest in `amakihi [d = 0.085(0.015)] with 98 distinct alleles detected (average 13.5/bird), followed by `apapane (Himatione sanguinea) [d = 0.068(0.012)] with 66 distinct alleles detected (average 11/bird) and in a highly susceptible species, the i`iwi (Vestiaria coccinea) diversity appears lowest with d = 0.057(0.011) and 66 distinct alleles detected (average 10.6/bird). Within `amakihi, Mhc sequences from birds from low elevation (56 distinct alleles, average 14.25 alleles/bird) and high elevation (50 distinct alleles, average 12.75 alleles/bird) subpopulations appear distinct with detection of only one shared allele. Microarray-based population level analysis (~1,000 individuals) of Mhc diversity in `amakihi detected at least one allele with a significantly higher frequency in low elevation populations than mid or high elevation subpopulations.
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Sui, Xinxia, Linhai Wang, Xianchun Xia, Zhenlin Wang, and Zhonghu He. "Development of an allele-specific marker for Glu-B3 alleles in common wheat and establishment of a multiplex PCR assay." Crop and Pasture Science 61, no. 12 (2010): 978. http://dx.doi.org/10.1071/cp10241.
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Low-molecular-weight glutenin subunits (LMW-GS) have significant effects on the processing quality of end-use products of common wheat. It is more efficient to discriminate LMW-GS alleles with PCR-based molecular markers than with SDS-PAGE. In the present study, we developed an allele-specific PCR marker, designated Glu-B3abefg, which can be used to discriminate protein alleles Glu-B3a, b, e, f, and g simultaneously. Based on ten previously developed allele-specific STS markers, three multiplex PCRs, viz. Glu-B3c + Glu-B3d, Glu-B3b + Glu-B3g, and Glu-B3h + Glu-B3i, were established. Six Glu-B3 alleles (b, c, d, g, h, and i) could be discriminated using the three multiplex PCRs. Results of tests on 158 wheat varieties and lines using Glu-B3abefg and the three multiplex PCRs were consistent with those using the ten STS markers separately. The new allele-specific marker and three multiplex PCRs represent an efficient way to undertake marker-assisted selection of Glu-B3 alleles.
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Eagles, H. A., J. Hyles, Jayne Wilson, Karen Cane, K. L. Forrest, M. J. Hayden, K. Ramm, and Ben Trevaskis. "A linked SNP marker to genotype Fr-B2 in wheat." Crop and Pasture Science 69, no. 9 (2018): 859. http://dx.doi.org/10.1071/cp18248.
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Fr-B2 is a complex locus on chromosome 5B that affects frost tolerance, days to heading, grain yield and probably other traits of commercial importance in wheat (Triticum aestivum L.). It interacts epistatically with other major genes, especially VRN1. There are two known alleles of Fr-B2: an intact, wild-type allele, and an allele with a large deletion. Published methods for identifying these alleles are slow and expensive, making the development of a high-throughput, co-dominant SNP (single-nucleotide polymorphism) marker highly desirable, especially for commercial wheat breeding. A diverse panel of cultivars and breeding lines was characterised for SNPs and alleles of Fr-B2. Four SNP markers co-segregated as a haplotype block with Fr-B2 across unrelated cultivars and related backcrosses differing for alleles of Fr-B2. A robust KASP (Kompetitive allele-specific PCR) assay was developed for one of the SNPs, KASP_IWB26333, which should facilitate the inclusion of Fr-B2 on genotyping platforms for breeding and research.
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Vissinga, C. S., P. Charmley, and P. Concannon. "Influence of coding region polymorphism on the peripheral expression of a human TCR V beta gene." Journal of Immunology 152, no. 3 (February 1, 1994): 1222–27. http://dx.doi.org/10.4049/jimmunol.152.3.1222.
Full textAbstract:
Abstract A number of human TCR V beta gene segments are reported to be polymorphic, with alleles differing by one or a small number of amino acid substitutions. In the absence of detailed structural information regarding the interaction of specific positions in the TCR with Ag or MHC, the significance of such variation is difficult to assess. In this report the relative use of the two common alleles of the human V beta 6.7 gene, 6.7a and 6.7b, which differ by two non-conservative amino acid substitutions, and the use of two common alleles of the V beta 12.2 gene, which differ by only silent substitutions, were measured in PBL derived from individuals heterozygous for these alleles. Equal use of V beta 12.2 alleles was observed, consistent with the inability of selection mechanisms to discriminate between the products of these alleles that are indistinguishable at the amino acid level. However, statistically significant skewing in the use of V beta 6.7 alleles was observed in 15 of 16 individuals studied. Expression levels for each allele ranged from 16 to 84% of the total V beta 6.7 signal in heterozygous individuals, with either the 6.7a or the 6.7b allele predominant in different individuals. Based on segregation studies in families, it seems unlikely that other unidentified polymorphism in the TCR beta locus, such as in the V beta 6.7 promoter, was responsible for the differential allele expression. Family studies provided no evidence for an association between specific HLA haplotypes and V beta 6.7 allele use. These results indicate that even modest allelic variation in human TCR V beta coding regions can have a significant impact on the expression of human V beta genes in the peripheral repertoire.