The calculation of recombination frequencies in crosses of allogamous plant species with applications to linkage mapping

SummaryThe recombination frequency (r) between two loci defined by conventional or molecular markers can be estimated by solving proper Maximum Likelihood equations. These are based on expected and observed marker class frequencies in the progeny of a cross, and are specific for each allelic configuration of the parents(1). In a cross between two diploid parents up to four different alleles, besides a null allele, can be detected at one locus. This defines in each parent, considering a locus A, nine basic allelic configurations based on two allelic marker fragments(Ai/Aj), one single marker allele and a null allele (Ai/AO), or just null alleles (AO/AO). With respect to two loci the consideration of all possible diploid allelic configurations in the parents of a cross allows the detection of 21 different expected marker class distributions producing estimates of r in the progeny. General formulas for calculating the ML equations and the corresponding information functions have been developed for the 21 marker class distributions. Simplified formulas have been also derived and the relative efficiency of the information functions compared. As expected, in the majority of cases, allelic marker configurations give more precise estimates of linkage values than single marker configurations. A method for the construction of linkage maps based on two point estimates, linkage subgroups and allelic bridges is presented. The method is an improvementon an original proposal by Ritter et al.(1990).

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Abstract 12291: Contribution of Rare Mutations in Mendelian Hypercholesterolemia Genes to Risk for Premature Coronary Artery Disease in the Population

Circulation ◽

10.1161/circ.130.suppl_2.12291 ◽

2014 ◽

Vol 130 (suppl_2) ◽

Author(s):

Hong-Hee Won ◽

Ron Do ◽

Keyword(s):

Coronary Artery Disease ◽

Coronary Artery ◽

Null Allele ◽

Coronary Revascularization ◽

Null Alleles ◽

Premature Coronary Artery Disease ◽

Rare Mutations ◽

Increased Risk ◽

Artery Disease ◽

Cad Risk

Introduction: Low-density lipoprotein cholesterol (LDL-C) is a causal risk factor for coronary artery disease (CAD). Rare mutations in at least 6 genes lead to Mendelian forms of high or reduced LDL-C; three ( APOB, LDLR, PCSK9 ) act in a dominant pattern whereas three ( ABCG5, ABCG8, LDLRAP1 ) in a recessive pattern. We address to what extent rare mutations in Mendelian LDL-C genes contribute to early CAD risk in the population. Methods: We sequenced the exons of the 6 genes in 9,329 early CAD cases (myocardial infarction, angiographic CAD, or coronary revascularization in men≤50 and women≤60) and 10,245 controls from 9 studies using targeted and whole exome next-generation sequencing. We tested 3 sets: ‘Null alleles’ (nonsense, splice-site, or frameshift); ‘Deleterious (7/7)’ (null and missense annotated as damaging by 7 algorithms); and ‘Deleterious (6/7)’ (null and missense annotated as damaging by at least 6 algorithms). Given the rarity of deleterious mutations, we aggregated these mutations in each gene and tested for an excess or deficit in cases vs . controls. Results: Counts of mutations are provided in Table. Null mutations in LDLR , carried by 1:500 participants, confered a 8-fold increase in CAD risk (P=8х10 -7 ) whereas heterozygosity for a null mutation in ABCG5 (1:650 frequency) was associated with a 3-fold increased risk (P=5х10 -3 ). ‘Deleterious (7/7)’ mutations in LDLR , carried by 1:100 participants, confered a 4-fold increased risk (P=8х10 -17 ) whereas heterozygosity for a ‘Deleterious (7/7)’ mutation in ABCG5 (1:250 frequency) was associated with a 2-fold increased risk (P=2х10 -3 ). Heterozygous null allele carriers at LDLR and ABCG5 had increased LDL-C (P<0.001). Conclusions: Of early CAD cases, 2-3% carry a rare, deleterious mutation at LDLR or ABCG5 associated with increased risk. Although previously reported to cause recessive sitosterolemia, we find that heterozygosity for a null allele at ABCG5 is associated with markedly higher early CAD risk.

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Abstract 495: GSTM1 Deficiency Exacerbates Hypertension in the Remnant Model of Chronic Kidney Disease

Hypertension ◽

10.1161/hyp.62.suppl_1.a495 ◽

2013 ◽

Vol 62 (suppl_1) ◽

Author(s):

Sylvia Cechova ◽

Rosa Chan ◽

Beverly Koller ◽

Thu H Le

Keyword(s):

Oxidative Stress ◽

Chronic Kidney Disease ◽

Kidney Disease ◽

Null Allele ◽

Null Alleles ◽

Hypertensive Nephrosclerosis ◽

Baseline Systolic Blood Pressure ◽

Glutathione S Transferases ◽

Targeting Strategy ◽

Multiple Chronic Diseases

There is a general consensus that oxidative stress is a factor in the progression of chronic kidney disease (CKD). Hence, genetic variants that affect the capacity to handle oxidative stress may influence the outcomes of CKD. One important class of enzymes that has evolved to combat the damaging effects of reactive oxygen species is the glutathione-S-transferases. In particular, the μ class isoform 1 (GSTM1) has emerged as a potential modifier of multiple chronic diseases in humans. Approximately 30%-50% of humans are completely deficient of the GSTM1 enzyme because of homozygous inheritance of the GSTM1 null allele, GSTM1(0). We have identified the GSTM1 gene as a modifier of disease progression in hypertensive nephrosclerosis (HN). In an ancillary study of the African American (AA) Study of Hypertension and Kidney Disease (AASK) Trial, we reported that participants carrying one ( 1/0 ) or two ( 0/0 ) null alleles had 1.7- and 2-fold higher risk of the composite outcome of a 50% decline in the glomerular filtration rate (GFR), dialysis, or death relative to those with two active alleles. Here, the objective of our study was to determine the consequence of deletion of Gstm1 on the course of chronic kidney disease induced by reduction of renal mass (RRM) model in mice. We generated Gstm1-/- (KO) mice on the 129S6 background through conventional gene targeting strategy. By radiotelemetry, Gstm1 KO mice displayed a modest but significantly higher baseline systolic blood pressure (SBP) compared to their wild type (WT, Gtsm1 +/+ ) littermates: KO (n = 5): 138.8 ± 1.3; WT (n = 5): 132.1 ± 1.1, p < 0.01. Baseline urinary isoprostane (ng/100 mg of body weight) was significantly higher in KO mice than WT mice (15.1 ± 2.9; WT: 8.0 ± 0.8, p < 0.04). Four weeks after sub-total nephrectomy, Gstm1 KO mice developed significantly more severe hypertension than WT mice. The average SBP over a 2 week recording by radiotelemetry was 154.0 ± 3.2 mm Hg in KO mice (n = 5), and 142.3 ± 4.2 in WT mice (n = 3), p < 0.01. The effects of deletion of Gstm1 on kidney function and histopathology are under investigation. In conclusion, loss of GSMT1 increases oxidative stress and exaggerates hypertension in the murine model of chronic kidney disease.

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Molecular genetics of cryptopleurine resistance in Saccharomyces cerevisiae: expression of a ribosomal protein gene family.

Genetics ◽

10.1093/genetics/135.3.719 ◽

1993 ◽

Vol 135 (3) ◽

pp. 719-730

Author(s):

A G Paulovich ◽

J R Thompson ◽

J C Larkin ◽

Z Li ◽

J L Woolford

Keyword(s):

Saccharomyces Cerevisiae ◽

Ribosomal Protein ◽

Gene Fusion ◽

Null Allele ◽

Ribosomal Subunit ◽

Null Alleles ◽

Protein Synthesis Inhibitor ◽

Lacz Gene ◽

Ribosomal Subunits ◽

Cry1 Gene

Abstract The Saccharomyces cerevisiae CRY1 gene encodes the 40S ribosomal subunit protein rp59 and confers sensitivity to the protein synthesis inhibitor cryptopleurine. A yeast strain containing the cry1-delta 1::URA3 null allele is viable, cryptopleurine sensitive (CryS), and expresses rp59 mRNA, suggesting that there is a second functional CRY gene. The CRY2 gene has been isolated from a yeast genomic library cloned in bacteriophage lambda, using a CRY1 DNA probe. The DNA sequence of the CRY2 gene contains an open reading frame encoding ribosomal protein 59 that differs at five residues from rp59 encoded by the CRY1 gene. The CRY2 gene was mapped to the left arm of chromosome X, centromere-proximal to cdc6 and immediately adjacent to ribosomal protein genes RPS24A and RPL46. Ribosomal protein 59 is an essential protein; upon sporulation of a diploid doubly heterozygous for cry1-delta 2::TRP1 cry2-delta 1::LEU2 null alleles, no spore clones containing both null alleles were recovered. Several results indicate that CRY2 is expressed, but at lower levels than CRY1: (1) Introduction of CRY2 on high copy plasmids into CryR yeast of genotype cry1 CRY2 confers a CryS phenotype. Transformation of these CryR yeast with CRY2 on a low copy CEN plasmid does not confer a CryS phenotype. (2) Haploids containing the cry1-delta 2::TRP1 null allele have a deficit of 40S ribosomal subunits, but cry2-delta 1::LEU2 strains have wild-type amounts of 40S ribosomal subunits. (3) CRY2 mRNA is present at lower levels than CRY1 mRNA. (4) Higher levels of beta-galactosidase are expressed from a CRY1-lacZ gene fusion than from a CRY2-lacZ gene fusion. Mutations that alter or eliminate the last amino acid of rp59 encoded by either CRY1 or CRY2 result in resistance to cryptopleurine. Because CRY2 (and cry2) is expressed at lower levels than CRY1 (and cry1), the CryR phenotype of cry2 mutants is only expressed in strains containing a cry1-delta null allele.

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Expression of Functional CD32 Molecules on Human NK Cells Is Determined by an Allelic Polymorphism of the FcγRIIC Gene

Blood ◽

10.1182/blood.v91.7.2369.2369_2369_2380 ◽

1998 ◽

Vol 91 (7) ◽

pp. 2369-2380 ◽

Cited By ~ 2

Author(s):

Diana Metes ◽

Linda K. Ernst ◽

William H. Chambers ◽

Andrei Sulica ◽

Ronald B. Herberman ◽

...

Keyword(s):

Nk Cells ◽

Null Allele ◽

Nk Cell ◽

Full Length ◽

Null Alleles ◽

Soluble Form ◽

Allelic Polymorphism ◽

Reading Frame ◽

Normal Individuals ◽

Alternatively Spliced

Human natural killer (NK) cells were thought to express only FcγRIIIA (CD16), but recent reports have indicated that NK cells also express a second type of FcγR, ie, FcγRII (CD32). We have isolated, cloned, and sequenced full-length cDNAs of FcγRII from NK cells derived from several normal individuals that may represent four different products of the FcγRIIC gene. One transcript (IIc1) is identical with the already described FcγRIIc form. The other three (IIc2-IIc4) appear to represent unique, alternatively spliced products of the same gene, and include a possible soluble form. Analyses of the full-length clones have revealed an allelic polymorphism in the first extracellular exon, resulting in either a functional open reading frame isoform or a null allele. Stable transfection experiments enabled us to determine a unique binding pattern of anti-CD32 monoclonal antibodies to FcγRIIc. Further analyses of NK-cell preparations revealed heterogeneity in CD32 expression, ranging from donors lacking CD32 expression to donors expressing high levels of CD32 that were capable of triggering cytotoxicity. Differences in expression were correlated with the presence or absence of null alleles. These data show that certain individuals express high levels of functional FcγRIIc isoforms on their NK cells.

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Transcriptional profiling of Ovis aries identifies Ovar-DQA1 allele frequency differences between nematode-resistant and susceptible selection lines

Physiological Genomics ◽

10.1152/physiolgenomics.00273.2006 ◽

2007 ◽

Vol 30 (3) ◽

pp. 253-261 ◽

Cited By ~ 22

Author(s):

Orla M. Keane ◽

Ken G. Dodds ◽

Allan M. Crawford ◽

John C. McEwan

Keyword(s):

Linkage Disequilibrium ◽

Null Allele ◽

Intestinal Parasites ◽

Transcriptional Profiling ◽

Radical Scavenging ◽

Gastrointestinal Nematodes ◽

Ovis Aries ◽

Differentially Expressed ◽

Null Alleles ◽

Transcription Profiles

Gastrointestinal nematodes are a major cause of disease in grazing livestock; however, individual animals differ in their response to infection. To identify genes whose expression correlates with resistance status, transcriptional profiling of resistant and susceptible sheep was undertaken. Transcription profiles were taken at three time points during the growth of lambs. The number of genes differentially expressed increased as animals were exposed to longer nematode challenge. Almost 300 genes, with a variety of functions, were differentially expressed overall, although genes more highly expressed in resistant animals typically had major histocompatibility complex (MHC) II, free radical scavenging or smooth muscle-specific functions. The Ovar-DQA1 gene was 8.4-fold more highly expressed in resistant animals. This was due in part to a higher frequency of DQA1 null alleles in susceptible animals. The null allele of DQA1 was also associated with susceptibility in a separate selection flock, presenting the hypothesis that failure to present parasite antigens to immune cells led to nematode susceptibility. To test this hypothesis, commercial rams from three breeds were genotyped for the null allele of DQA1. The homozygous null allele was associated with susceptibility in only one of the three breeds tested indicating that the null allele does not cause susceptibility to intestinal parasites per se but is probably in linkage disequilibrium with additional polymorphisms in the MHC region. A combination of these polymorphisms may contribute to susceptibility in some populations. The extent of linkage disequilibrium between polymorphisms may vary from breed to breed or population to population.

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Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

10.7287/peerj.preprints.2559v1 ◽

2016 ◽

Author(s):

Nathan K Truelove ◽

Loong Fai Ho ◽

Richard F Preziosi ◽

Stephen J. Box

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Null Allele ◽

Florida Keys ◽

Illumina Miseq ◽

Allele Frequencies ◽

Null Alleles ◽

Queen Conch ◽

Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

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Allotype Reagents Distinguish Donor and Recipient Antibodies after Hematopoietic Transplantation.

Blood ◽

10.1182/blood.v108.11.2906.2906 ◽

2006 ◽

Vol 108 (11) ◽

pp. 2906-2906

Author(s):

Julie R. Boiko ◽

Bita Sahaf ◽

David B. Miklos

Keyword(s):

Monoclonal Antibodies ◽

B Cell ◽

Allele Frequency ◽

Null Allele ◽

Competitive Inhibition ◽

Null Alleles ◽

Wild Type ◽

Cell Engraftment ◽

Human Sera ◽

Null Allele Frequency

Abstract Allogeneic immune responses provide beneficial graft-versus-leukemia (GVL) and detrimental graft-versus-host disease (GVHD). To characterize allogeneic B cells and their antibodies in relation to GVHD and GVL, antigen specific assays are required to distinguish donor and recipient antibodies. Inherited polymorphisms in heavy chain constant regions of immunoglobulin can be recognized by allotype specific monoclonal antibodies. We hypothesize that B cell reconstitution differs after myeloablative and nonmyeloablative (NMA) HCT with clinical implications. To test this, we developed allotype ELISAs to quantify donor and recipient antibody responses for specific infectious and allogeneic antigens. Human sera were screened by ELISA coating monoclonal antibodies specific for human allotypes (IgG1m(f), m(z), m(a), IgG2m(n), and IgG3m(g1)) at titers providing shared dynamic ranges. Pre-transplant sera from 48 patients and their donors were serially diluted, and allotype-specific immunoglobulin was detected by alkaline phosphatase-conjugated polyclonal anti-human IgG. Allotype-null sera clearly segregated from wild-type sera with 10-fold absorbency differences. Each null phenotype was confirmed by total IgG and isotype-specific quantification. Overall, IgG1m(f) was null in 8 of 96 sera (null allele frequency 29%), and IgG2m(n) was null in 23 of 96 (null allele frequency 48%). Six patients were null for both, and overall 17 of 48 donor/recipient transplant pairs were informative for either allotype. Nulls for the remaining three allotypes were infrequently recognized limiting their clinical utility. Additionally, we measured monoclonal IgG1 purified from 5 multiple myeloma patients identifying three null alleles, one wild-type, and a single intermediate polymorphism. Labeled conjugation of the wild-type monoclonal IgG1 enables competitive inhibition analysis of null allotype improving null allotype sensitivity for engraftment less than 5%. Sera were collected monthly from all HCT patients informative for allotype antibody. Three NMA HCT patients who underwent total lymphoid irradiation and anti-thymoglobulin (TLI/ATG) conditioning have donors that are null for IgG2m(n) and are being prospectively assessed for recipient antibody loss. Their recipient allotype-specific IgG persists at pretransplant recipient levels in all three patients measured six months after NMA HCT, and the lead patient expresses 100% pretransplant recipient allotype antibody ten months after HCT. Conversely, a single NMA patient null for IgG2m(n) with a wild-type donor has no detectable IgG2m(n) donor antibodies four months after HCT despite having 100% donor peripheral B cell engraftment measured 30 days after NMA HCT. In contrast, an informative patient undergoing myeloablative HCT developed 25% IgG2m(n) donor specific antibodies 3 months post-transplant, and 50% at 7 months. Others have reported donor allotype specific antibody achieves full engraftment by 6 months after myeloablative HCT (Van Tol et al. Blood 1996). Our ongoing preliminary studies suggest NMA HCT patients experience delayed donor antibody onset and prolonged recipient antibodies as compared to patients undergoing myeloablative HCT. In order to confirm this, we are measuring antigen-specific donor allotype antibody reconstitution for infectious antigens (EBV and tetanus) and allogeneic H-Y antigens.

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Linkage mapping of sex-specific differences

Genetics Research ◽

10.1017/s0016672301005389 ◽

2002 ◽

Vol 79 (1) ◽

pp. 85-96 ◽

Cited By ~ 35

Author(s):

RONGLING WU ◽

CHANG-XING MA ◽

S. S. WU ◽

ZHAO-BANG ZENG

Keyword(s):

Molecular Markers ◽

Numerical Analysis ◽

Gene Mapping ◽

Meiotic Recombination ◽

Linkage Mapping ◽

Recombination Fraction ◽

Linkage Maps ◽

Information Functions ◽

Marker Loci ◽

Asymptotic Variances

Most current linkage analyses assume identical fractions of meiotic recombination between homologous marker loci of the two sexes. This assumption is not realistic, because considerable sex-related differences have been observed in recombination fraction. In this paper, a general EM-based algorithm is presented to estimate sex-specific recombination fractions for a mixed set of molecular markers segregating differently in a full-sib family derived from two heterozygous parents. The asymptotic variances of the estimates of linkage specifically for each of the parents are evaluated using a numerical analysis based on information functions. This approach will have important implications for precise gene mapping based on sex-specific linkage maps.

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A Robust Statistical Method to Detect Null Alleles in Microsatellite and SNP Datasets in Both Panmictic and Inbred Populations

Statistical Applications in Genetics and Molecular Biology ◽

10.2202/1544-6115.1620 ◽

2011 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Philippe Girard

Keyword(s):

Mating Systems ◽

Null Allele ◽

A Priori ◽

Detection Methods ◽

Null Alleles ◽

Robust Statistical Method ◽

Wide Range ◽

Fixation Indices ◽

Inbreeding Level ◽

Inbred Populations

Null alleles are common technical artifacts in genetic-based analysis. Powerful methods enabling their detection in either panmictic or inbred populations have been proposed. However, none of these methods appears unbiased in both types of mating systems, necessitating a priori knowledge of the inbreeding level of the population under study. To counter this problem, I propose to use the software FDist2 to detect the atypical fixation indices that characterize markers with null alleles. The rational behind this approach and the parameter settings are explained. The power of the method for various sample sizes, degrees of inbreeding and null allele frequencies is evaluated using simulated microsatellite and SNP datasets and then compared to two other null allele detection methods. The results clearly show the robustness of the method proposed here as well as its greater accuracy in both panmictic and inbred populations for both types of marker. By allowing a proper detection of null alleles for a wide range of mating systems and markers, this new method is particularly appealing for numerous genetic studies using co-dominant loci.

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