Estimation of the marker gene frequency and linkage disequilibrium from conditional marker data.

A method is proposed to calculate the maximum likelihood estimate of gene frequency and linkage disequilibrium from disease-codominant marker conditional data. The method is illustrated using data on sickle-cell anemia and Duchenne muscular dystrophy and linked polymorphic restriction endonuclease cleavage sites.     

A composite-conditional-likelihood approach for gene mapping based on linkage disequilibrium in windows of marker loci

A composite-conditional-likelihood (CCL) approach is proposed to map the position of a trait-influencing mutation (TIM) using the ancestral recombination graph (ARG) and importance sampling to reconstruct the genealogy of DNA sequences with respect to windows of marker loci and predict the linkage disequilibrium pattern observed in a sample of cases and controls. The method is designed to fine-map the location of a disease mutation, not as an association study. The CCL function proposed for the position of the TIM is a weighted product of conditional likelihood functions for windows of a given number of marker loci that encompass the TIM locus, given the sample configuration at the marker loci in those windows. A rare recessive allele is assumed for the TIM and single nucleotide polymorphisms (SNPs) are considered as markers. The method is applied to a range of simulated data sets. Not only do the CCL profiles converge more rapidly with smaller window sizes as the number of simulated histories of the sampled sequences increases, but the maximum-likelihood estimates for the position of the TIM remain as satisfactory, while requiring significantly less computing time. The simulations also suggest that non-random samples, more precisely, a non-proportional number of controls versus the number of cases, has little effect on the estimation procedure as well as sample size and marker density beyond some threshold values. Moreover, when compared with some other recent methods under the same assumptions, the CCL approach proves to be competitive.     

AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group ditsribution

We exploited the AFLP technique to saturate a RFLP linkage map derived from a maize mapping population. By using two restriction enzyme, EcoRI and PstI, differing in methylation sensitivity, both in combination with MseI, we detected 1568 bands of which 340 where polymorphic. These were added to the exitsing RFLP marker data to study the effects of incorporation of AFLPs produced by different restriction-enzyme combinations upon genetic maps. Addition of the AFLP data resulted in greater genome coverage, both through linking previously separate groups and the extension of other groups. The increase of the total map length was mainly caused by the addition of markers to telomeric regions, where RFLP markers were poorly represented. The percentage of informative loci was significantly different between the EcoRI and PstI assays. There was also evidence that PstI AFLP markers were more randomly distributed across chromosomes and chromosome regions, while EcoRI AFLP markers clustered mainly at centomeric regions. The more-random ditsribution of PstI AFLP markers on the genetic map reported here may reflect a preferential localisation of the markers in the hypomethylated telomeric regions of the chromosomes. Received: 22 December 1998 / Accepted: 25 March 1999     

The posterior probability of linkage allowing for linkage disequilibrium and a new estimate of disequilibrium between a trait and a marker

The posterior probability of linkage (PPL) statistic has been developed as a method for the rigorous accumulation of evidence for or against linkage allowing for both intra- and inter-sample heterogeneity. To date, the method has assumed linkage equilibrium between alleles at the trait locus and the marker locus. We now generalize the PPL to allow for linkage disequilibrium (LD), by incorporating variable phase probabilities into the underlying linkage likelihood. This enables us to recover the marginal posterior density of the recombination fraction, integrating out nuisance parameters of the trait model, including the locus heterogeneity (admixture) parameter, as well as a vector of LD parameters. The marginal posterior density can then be updated across data subsets or new data as they become available, while allowing parameters of the trait model to vary between data sets. The method applies immediately to general pedigree structures and to markers with multiple alleles. In the case of SNPs, the likelihood is parameterized in terms of the standard single LD parameter D'; and it therefore affords a mechanism for estimation of D' between the marker and the trait, again, without fixing the parameters of the trait model and allowing for updating across data sets. It is even possible to allow for a different associated allele in different populations, while accumulating information regarding the strength of LD. While a computationally efficient implementation for multi-allelic markers is still in progress, we have implemented a version of this new LD-PPL for SNPs and evaluated its performance in nuclear families. Our simulations show that LD-PPLs tend to be larger than PPLs (stronger evidence in favor of linkage/LD) with increased LD level, under a variety of generating models; while in the absence of linkage and LD, LD-PPLs tend to be smaller than PPLs (stronger evidence against linkage). The estimate of D' also behaves well even in relatively small, heterogeneous samples.     

Mendelian inheritance, linkage and genotypic disequilibrium in microsatellite loci isolated from Hymenaea courbaril (Leguminosae)

The Neotropical tree Hymenaea courbaril, locally known as Jatobá, is a valuable source of lumber and also produces comestible and medicinal fruit. We characterized Mendelian inheritance, linkage and genotypic disequilibrium at nine microsatellite loci isolated from H. courbaril, in order to determine if they would provide accurate estimates of population genetic parameters of this important Amazon species. The study was made on 250 open-pollinated offspring originated from 14 seed trees. Only one of nine loci presented significant deviation from the expected Mendelian segregation (1:1). Genotypic disequilibrium between pairwise loci was investigated based on samples from 55 adult and 56 juvenile trees. No genetic linkage between any paired loci was observed. After Bonferroni's corrections for multiple tests, we found no evidence of genotypic disequilibrium between pairs of loci. We conclude that this set of loci can be used for genetic diversity/ structure, mating system, gene flow, and parentage analyses in H. courbaril populations.     

A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker

Quantitative trait transmission/disequilibrium tests (quantitative TDTs) are commonly used in family-based genetic association studies of quantitative traits. Despite the availability of various quantitative TDTs, some users are not aware of the properties of these tests and the relationships between them. This review aims at outlining the broad features of the various quantitative TDT procedures carried out in the frequently used QTDT and FBAT packages. Specifically, we discuss the “Rabinowitz” and the “Monks-Kaplan” procedures, as well as the various “Abecasis” and “Allison” regression-based procedures. We focus on the models assumed in these tests and the relationships between them. Moreover, we discuss what hypotheses are tested by the various quantitative TDTs, what testing procedures are best suited to various forms of data, and whether the regression-based tests overcome population stratification problems. Finally, we comment on power considerations in the choice of the test to be used. We hope this brief review will shed light on the similarities and differences of the various quantitative TDTs.     

AFLP分子标记及其应用(综述)

本文简述ＡＦＬＰ分子标记的原理、方法与特点,并综述其在植物遗传多态性及系统发育学研究、基因定位及高密度遗传图谱（或物理图谱）构建和品种鉴定及抗性育种特征性状的分子标记中的应用现状和前景。     

Lipoprotein(a): its inheritance and molecular basis of its atherothrombotic role

Lipoprotein(a) or Lp(a), is a member of the plasma lipoproteins with general properties of LDL but with a protein moiety represented by apoB100 disulfide linked to apolipoprotein(a) or apo(a). Apo(a) is polymorphic in size; at present a total of 11 isoforms have been reported, but more are likely to be identified in view of the fact that at least 19 alleles of the apo(a) gene have recently been reported. There are remarkable variations in the plasma Lp(a) levels; but uncertainties still exist about the factors responsible for this variability. High plasma Lp(a) levels have been associated with an increased incidence of cardiovascular disease, mainly based on epidemiological evidence. Both atherogenic and thrombogenic potentials have been suggested; the first attributable to the LDL-like properties of Lp(a) and the other to the plasminogen-like characteristics of apo(a). From the mechanistic viewpoint in vitro studies suggest that the thrombogenic action may occur at the level of the endothelium whereas Lp(a) that localizes in the sub-endothelial intima is expected to undergo complexation with matrix components and favor the formation of the atherosclerotique plaque. How Lp(a) polymorphism relates to the postulated cardiovascular pathogenicity of this lipoprotein remains to be established.     

Human fibronectin gene (FN1) RFLPs: Mapping and linkage disequilibrium analysis

We report a mapping and linkage disequilibrium analysis of six restriction fragment length polymorphisms (RFLPs) of the human fibronectin gene. The polymerase chain reaction conditions are described for four of the RFLPs.     

Inferring linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations

Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.     

An RFLP for glycoprotein A (MN) is in linkage disequilibrium with MN and Ss

Using a cDNA for glycophorin A (MN), we screened 10 unrelated Caucasians using 22 restriction enzymes for RFLPs. A common StuI RFLP was identified and shown to be in marked linkage disequilibrium with both the MN and Ss blood-group antigens in a larger group of unrelated Caucasians. This provides a DNA marker for a locus that has been of major importance in genetic and population studies. The demonstrated disequilibrium will prove useful in localizing the gene for glycophorin B and in studies of genetic and physical distances on human chromosomes.     

Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

Cinnamyl alcohol dehydrogenase (CAD) is involved in the biosynthesis of lignin, a component of plant cell wall which negatively impacts paper pulp processing and biomass fermentation to ethanol. Transgenic poplars with depressed CAD activity show structural alterations of lignin. Natural CAD mutants have been identified in several plants; however, no natural CAD mutants have been identified in poplar. We surveyed the natural genetic variation in CAD4, a gene coding for CAD, in 360 poplar trees from Western Europe. We measured linkage disequilibrium (LD) between single-nucleotide polymorphisms (SNPs), performed neutrality tests and estimated diversity indexes, and investigated their dependence from sample size. We identified 45 SNPs, six of which caused an amino acid substitution. Our results suggest a short span of LD in Populus nigra CAD4 gene. We identified carriers of different nonsynonymous SNPs in CAD4; those subjects are candidate to be used in classical breeding programs to obtain carriers of different combinations of functional polymorphisms. We showed that use of small sample size might lead to biased estimates of LD, neutrality tests, and diversity indexes.     

Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations.

Positional cloning of gene(s) underlying a complex trait requires a high-resolution linkage map between the trait locus and genetic marker loci. Recent research has shown that this may be achieved through appropriately modeling and screening linkage disequilibrium between the candidate marker locus and the major trait locus. A quantitative genetics model was developed in the present study to estimate the coefficient of linkage disequilibrium between a polymorphic genetic marker locus and a locus underlying a quantitative trait as well as the relevant genetic parameters using the sample from randomly mating populations. Asymptotic covariances of the maximum-likelihood estimates of the parameters were formulated. Convergence of the EM-based statistical algorithm for calculating the maximum-likelihood estimates was confirmed and its utility to analyze practical data was exploited by use of extensive Monte-Carlo simulations. Appropriateness of calculating the asymptotic covariance matrix in the present model was investigated for three different approaches. Numerical analyses based on simulation data indicated that accurate estimation of the genetic parameters may be achieved if a sample size of 500 is used and if segregation at the trait locus explains not less than a quarter of phenotypic variation of the trait, but the study reveals difficulties in predicting the asymptotic variances of these maximum-likelihood estimates. A comparison was made between the statistical powers of the maximum-likelihood analysis and the previously proposed regression analysis for detecting the disequilibrium.     

Development and characterization of a codominant marker linked to root-knot nematode resistance, and its application to peach rootstock breeding

 The presence of a codominant AFLP marker, EAA/MCAT10, correlates with the primary source of resistance to root-knot nematodes (Meloidogyne incognita and M. javanica) in rootstock cultivars of peach [Prunus persica (L.) Batsch]. Two allelic DNA fragments of this AFLP marker were cloned, sequenced and converted to sequence tagged sites (STS). Four nucleotide differences (i.e. one addition and three substitutions) were observed between the two clones. Furthermore, there was a diagnostic Sau3 AI cleavage site (GATC) in the large fragment that was absent from the small fragment (GTTC at this site). The applicability of this STS marker system to peach germplasm improvement was evaluated: genomic DNAs of cross parents (i.e. ‘Lovell’ and ‘Nemared’), four F₁ hybrids (K62-67, K62-68, P101-40 and P101-41) and two F₂ populations (from K62-68 and P101-41), as well as DNA from a test panel of 18 rootstock cultivars or selections, were PCR-amplified with the Mij3F/Mij1R primer pair and then digested with Sau3 AI. The banding patterns showed that the EAA/MCAT10 STS markers can clearly distinguish the three genotypes – homozygous resistant, heterozygous resistant and homozygous susceptible – in the ‘Lovell’בNemared’ cross. In addition, results from the rootstock survey were consistent with each rootstock’s phenotypic response to nematode infection, except for ‘Okinawa’, ‘Flordaguard’ and ‘Yunnan’ where root-knot resistance may have arisen independently. Therefore, the EAA/MCAT10 STS markers will be a useful tool to initiate marker assisted selection studies in peach rootstock breeding for root-knot nematode resistance. Received: 4 January 1999 / Accepted: 4 January 1999     

Development and mapping of a codominant SCAR marker linked to the andromonoecious gene of melon

Monoecy is an important goal for melon breeding because of the agronomic advantages it provides to parental lines in that they do not require hand emasculation to develop monoecious F₁ hybrids, the latter producing fruits of higher quality. Monoecious phenotype is conferred by the dominant allele of the andromonoecious (a) gene, whereas recessive homozygous plants are andromonoecious. A bulked segregant analysis (BSA) approach performed in a set of 38 double-haploid lines has allowed us to identify an AFLP marker linked to the a gene at 3.3 cM. Following cloning and sequencing of the AFLP fragment, specific PCR primers were designed and used in the amplification of a codominant SCAR marker. Using a backcrossed mapping population of 530 plants, the SCAR marker could be mapped near the a locus (5.5 cM). Size difference between the two allelic SCAR fragments is 42 bp and might be due to a deletion/insertion. The SCAR marker is closest to the a gene identified to date, and can be useful in breeding programs, using marker-assisted selection procedures to screen for sexual types in melon.     

A haplotype and linkage disequilibrium analysis of the hereditary hemochromatosis gene region

Hereditary hemochromatosis is a recessive disease of iron metabolism widely distributed among people of European descent. Most patients have inherited the causative mutation from a single ancestor. In the course of cloning the hemochromatosis gene, genotypes were generated for these samples at 43 microsatellite repeat markers that span the 6.5-Mb hemochromatosis gene region. The data used to reconstruct the ancestral haplotype across the hemochromatosis gene region are presented in this paper. Portions of the ancestral haplotype were present on 85% of patient chromosomes in this sample and ranged in size from approximately 500 kb to greater than 6.5 Mb. Only one marker, D6S2239, was identical by descent on all of the patient chromosomes containing the ancestral mutation. In contrast, only 3 of the 128 control chromosomes, or 2.3%, carried the ancestral mutation and the surrounding ancestral haplotype. To test new methods for gene finding using linkage disequilibrium we analyzed the genotypic data with a multilocus maximum likelihood method (DISMULT) and a single point method (DISLAMB), both written to analyze data generated from multi-allelic markers. The maximum value from DISLAMB analysis occurred at marker D6S2239, which is less than 20 kb from the hemochromatosis gene HFE, consistent with the haplotype analysis. The peak of the multi-point analysis was 700 kb from HFE, possibly due to the nonuniform recombination rates within this large region. The recombination rate appears to be lower than expected centromeric of the HFE gene. Received: 10 June 1997 / Accepted: 4 December 1997     

A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.)

A genetic linkage map was constructed for an F₁ genotype of auto-tetraploid alfalfa (Medicago sativa L.) using two backcross populations of 101 individuals each and 82 single-dose restriction fragments segregating in each population. The percentages of marker loci deviating from Mendelian ratios were considerably less than reported for inbred diploid mapping populations (4–9% compared to 18–54%), probably due to the greater buffering capacity of autotetraploids against the effects of deleterious recessive alleles. Four homologous coupling-phase cosegregation groups were detected for seven of the eight linkage groups of diploid alfalfa and aligned using probes in common. No cosegregation groups were found for linkage group 7 due to the lack of polymorphisms in this cross. A composite map was generated by integrating the four homologous cosegregation groups and consisted of 88 loci on seven linkage groups covering 443 cM. The locus map-orders and distances were in general agreement with those found in diploid alfalfa. The mapping population segregates for winterhardiness, fall dormancy, and freezing tolerance; and the map will be used to locate genomic regions affecting these traits. Received: 9 December 1998 / Accepted: 22 June 1999