gerud1.0: a computer program for the reconstruction of parental genotypes from progeny arrays using multilocus DNA data

We have no standard computer algorithm for the reconstruction of parental genotypes from the data generated by molecular studies of progeny arrays. Here I present a computer program that uses the multilocus genotypes of parents and offspring to reconstruct the genotypes of unknown parents contributing gametes to a progeny array for which one parent is known a priori. A second program performs simulations to assess the reliability of the algorithm under various scenarios. These programs will aid scientists engaged in parentage analyses, particularly in species with large clutches.     

Methods to predict transgressive segregation in barley and other self-pollinated crops

Most of agronomically important characters are biometric traits. An improvement of these traits in cultivated plants by deriving segregants superior to parents, which could be developed as cultivars, is a main goal in breeding of self-pollinated crops. Two problems need to be solved: when will the progeny be better than its parents and how can a genetic potential of a given pair of parental genotypes be predicted? In this paper, transgressive segregation in homozygous barley populations is shortly reviewed. Various approaches to choosing parental forms are shown, and a theoretical method for predicting the frequency of transgressive segregants in a homozygous population is presented. Additionally, relationships between parental diversity estimated with molecular markers and the progeny performance are discussed. Although the prediction of transgressive segregation is still a problem, it seems promising to apply an approach measuring the performance of the parental genotypes and estimating their genetic distance by molecular markers.     

IS ORGANELLE DNA STRICTLY MATERNALLY INHERITED? POWER ANALYSIS OF A BINOMIAL DISTRIBUTION

Although numerous exceptions are well known, organelle DNA is often exclusively or predominantly maternally inherited. In such cases, maternal inheritance is often documented by the study of progeny derived from crosses between parents with distinguishable organelle genotypes. These studies generally detect a single type of progeny, those containing organelles derived from only one of the parents; no progeny containing organelles derived either from the opposite parent or from both parents are found. However, in most cases the number of progeny examined is quite small. I present a simple binomial model of organelle inheritance to determine the power of such experiments to distinguish between the hypothesis of strict maternal inheritance and a more complex hypothesis involving the presence of both organelle types within a progeny array. Extremely large sample sizes of progeny are required to distinguish these two hypotheses with reasonable confidence when organelle transmission is not strictly maternal. As a result, studies involving simple progeny testing may be misleading. Larger samples, more complex breeding designs, or more sensitive molecular methods are required to document adequately strict maternal inheritance of organelles.     

Determining the minimum sample size required to obtain sufficient progeny with a desired genotype at two quantitative trait loci

In this paper we determine the minimum progeny sample size n needed to obtain, with probability , at least m individuals of a desired two-locus genotype affecting quantitative traits. The two quantitative trait loci (QTLs) of interest may be linked or independent, with or without epistatic interaction between them. Parental genotypes may be known or unknown, and gene action at either locus may range from additive to overdominance. To reduce the required sample size, mating patterns that will produce a high proportion of desired progeny are suggested for different progeny genotypes and dominance levels. Based on the assumption of normally distributed quantitative trait expression, individuals can be classified into a genotype or genotypic group according to their phenotypic expressions. This technique is used to select both parents and progeny with unknown genotypes. Choice of parental classification criteria for a given quantitative trait affects classification accuracy, and hence the probability of obtaining progeny of the desired genotype. The complexity of this probability depends on the dominance level at each locus, the recombination fraction, and the awareness of parental genotypes. The procedure can be expanded to deal with more than two loci.BU-1168-MB in the Biometrics Unit Technical Report Series, 337 Warren Hall, Cornell University, Ithaca, NY 14853, USAFormerly known as S.-F. Shyu     

Assigning Linkage Haplotypes from Parent and Progeny Genotypes

Given the genotypes of parents and progeny, their haplotypes over several or many linked loci can be easily assigned by listing the allele type at each locus along the haplotype known to be from each parent. Only a small number (5-10) of progeny per family is usually needed to assign the parental and progeny haplotypes. Any gaps left in the haplotypes may be filled in from the assigned haplotypes of relatives. The process is facilitated by having multiple alleles at the loci and by using more linked loci in the haplotype and with more progeny from the mating. Crossover haplotypes in the progeny can be identified by their being unique or uncommon, and the crossover point can often be detected if the locus linkage map order is known. The haplotyping method applies to outbreeding populations in plants, animals and man, as well as to traditional experimental crosses of inbred lines. The method also applies to half-sib families, whether the genotypes of the mates are known or unknown. The haplotyping procedure is already used in linkage analysis but does not seem to have been published. It should be useful in teaching and in genetic applications of haplotypes.     

Informative missingness in genetic association studies: case-parent designs

We consider the effect of informative missingness on association tests that use parental genotypes as controls and that allow for missing parental data. Parental data can be informatively missing when the probability of a parent being available for study is related to that parent's genotype; when this occurs, the distribution of genotypes among observed parents is not representative of the distribution of genotypes among the missing parents. Many previously proposed procedures that allow for missing parental data assume that these distributions are the same. We propose association tests that behave well when parental data are informatively missing, under the assumption that, for a given trio of paternal, maternal, and affected offspring genotypes, the genotypes of the parents and the sex of the missing parents, but not the genotype of the affected offspring, can affect parental missingness. (This same assumption is required for validity of an analysis that ignores incomplete parent-offspring trios.) We use simulations to compare our approach with previously proposed procedures, and we show that if even small amounts of informative missingness are not taken into account, they can have large, deleterious effects on the performance of tests.     

Ecological constraints limit the fitness of fungal hybrids in the Heterobasidion annosum species complex

The ability of two closely related species to maintain species boundaries in spite of retained interfertility between them is a documented driving force of speciation. Experimental evidence to support possible interspecific postzygotic isolation mechanisms for organisms belonging to the kingdom Fungi is still missing. Here we report on the outcome of a series of controlled comparative inoculation experiments of parental wild genotypes and F(1) hybrid genotypes between closely related and interfertile taxa within the Heterobasidion annosum fungal species complex. Results indicated that these fungal hybrids are not genetically unfit but can fare as well as parental genotypes when inoculated on substrates favorable to both parents. However, when placed in substrates favoring one of the parents, hybrids are less competitive than the parental genotypes specialized on that substrate. Furthermore, in some but not all fungus x plant combinations, a clear asymmetry in fitness was observed between hybrids carrying identical nuclear genomes but different cytoplasms. This work provides some of the first experimental evidence of ecologically driven postzygotic reinforcement of isolation between closely related fungal species characterized by marked host specificity. Host specialization is one of the most striking traits of a large number of symbiotic and parasitic fungi; thus, we suggest the ecological mechanism proven here to reinforce isolation among Heterobasidion spp. may be generally valid for host-specialized fungi. The validity of this generalization is supported by the low number of known fungal hybrids and by their distinctive feature of being found in substrates different from those colonized by parental species.     

Inbreeding effective population size and parentage analysis without parents

An important use of genetic parentage analysis is the ability to directly calculate the number of offspring produced by each parent (k(i)) and hence effective population size, N(e). But what if parental genotypes are not available? In theory, given enough markers, it should be possible to reconstruct parental genotypes based entirely on a sample of progeny, and if so the vector of parental k(i) values. However, this would provide information only about parents that actually contributed offspring to the sample. How would ignoring the 'null' parents (those that produced no offspring) affect an estimate of N(e)? The surprising answer is that null parents have no effect at all. We show that: (i) The standard formula for inbreeding N(e) can be rewritten so that it is a function only of sample size and ∑(k(2)(i)); it is not necessary to know the total number of parents (N). This same relationship does not hold for variance N(e). (ii) This novel formula provides an unbiased estimate of N(e) even if only a subset of progeny is available, provided the parental contributions are accurately determined, in which case precision is also high compared to other single-sample estimators of N(e). (iii) It is not necessary to actually reconstruct parental genotypes; from a matrix of pairwise relationships (as can be estimated by some current software programs), it is possible to construct the vector of k(i) values and estimate N(e). The new method based on parentage analysis without parents (PwoP) can potentially be useful as a single-sample estimator of contemporary N(e), provided that either (i) relationships can be accurately determined, or (ii) ∑(k(2)(i)) can be estimated directly.     

Ecological Constraints Limit the Fitness of Fungal Hybrids in the Heterobasidion annosum Species Complex

The ability of two closely related species to maintain species boundaries in spite of retained interfertility between them is a documented driving force of speciation. Experimental evidence to support possible interspecific postzygotic isolation mechanisms for organisms belonging to the kingdom Fungi is still missing. Here we report on the outcome of a series of controlled comparative inoculation experiments of parental wild genotypes and F₁ hybrid genotypes between closely related and interfertile taxa within the Heterobasidion annosum fungal species complex. Results indicated that these fungal hybrids are not genetically unfit but can fare as well as parental genotypes when inoculated on substrates favorable to both parents. However, when placed in substrates favoring one of the parents, hybrids are less competitive than the parental genotypes specialized on that substrate. Furthermore, in some but not all fungus × plant combinations, a clear asymmetry in fitness was observed between hybrids carrying identical nuclear genomes but different cytoplasms. This work provides some of the first experimental evidence of ecologically driven postzygotic reinforcement of isolation between closely related fungal species characterized by marked host specificity. Host specialization is one of the most striking traits of a large number of symbiotic and parasitic fungi; thus, we suggest the ecological mechanism proven here to reinforce isolation among Heterobasidion spp. may be generally valid for host-specialized fungi. The validity of this generalization is supported by the low number of known fungal hybrids and by their distinctive feature of being found in substrates different from those colonized by parental species.     

<Emphasis Type="Italic">In silico</Emphasis> genotyping of the maize nested association mapping population

Nested Association Mapping (NAM) has been proposed as a means to combine the power of linkage mapping with the resolution of association mapping. It is enabled through sequencing or array genotyping of parental inbred lines while using low-cost, low-density genotyping technologies for their segregating progenies. For purposes of data analyses of NAM populations, parental genotypes at a large number of Single Nucleotide Polymorphic (SNP) loci need to be projected to their segregating progeny. Herein we demonstrate how approximately 0.5 million SNPs that have been genotyped in 26 parental lines of the publicly available maize NAM population can be projected onto their segregating progeny using only 1,106 SNP loci that have been genotyped in both the parents and their 5,000 progeny. The challenge is to estimate both the genotype and genetic location of the parental SNP genotypes in segregating progeny. Both challenges were met by estimating their expected genotypic values conditional on observed flanking markers through the use of both physical and linkage maps. About 90%, of 500,000 genotyped SNPs from the maize HapMap project, were assigned linkage map positions using linear interpolation between the maize Accessioned Gold Path (AGP) and NAM linkage maps. Of these, almost 70% provided high probability estimates of genotypes in almost 5,000 recombinant inbred lines.     

THE SIGNIFICANCE OF OUTCROSSING IN AN INTIMATE PLANT-HERBIVORE RELATIONSHIP. I. DOES OUTCROSSING PROVIDE AN ESCAPE FROM HERBIVORES ADAPTED TO THE PARENT PLANT?

Sexual reproduction may be advantageous for hosts that are preyed on or parasitized by enemies that are highly adapted to them. Sexual reproduction can create rare genotypes that may escape predation by virtue of rarity and can create variable progeny that may escape predation if enemies are specialized to only one genotype of host. Populations of the herbivorous thrips, Apterothrips apteris, have been shown to be adapted to individual Erigeron glaucus clones. Here, we show that thrips adapted to the parental clone could better use plant progeny of the “home” clone produced through selfing than progeny derived from selfing of other clones. Thus, despite recombination, progeny produced by selfing presented a resource that was similar to the parental phenotype with respect to use by adapted thrips. We also show that E. glaucus susceptibility to thrips has a genetic basis and then ask whether outcrossing provides a means for E. glaucus clones to escape attack by adapted thrips. When we compared the success of thrips on progeny produced by selfing or outcrossing of the home clone, we found that the merits or disadvantages associated with outcrossing were dependent on the susceptibility to infestation of the parental clones. Selfing by clones characterized by low infestations of thrips appeared to preserve resistant genotypes; all outcrossed progeny had, on average, higher infestation levels than selfed progeny. In contrast, outcrossed progeny of clones characterized by high infestations of thrips had either the same thrips density as progeny from selfing, when the pollen donor was a highly infested clone, or lower density, when the pollen donor was a low infestation clone. The advantages of outcrossing were caused by the alleles contributed to progeny rather than to progeny variability or rarity.     

The mixed mating system of Impatiens capensis and infection by a foliar rust pathogen: patterns of resistance and fitness consequences

Outcrossing by hosts may offer protection from natural enemies adapted to parental genotypes by creating diverse progeny that differ from their parents through genetic recombination. However, past experimental work addressing the relationship between mating system and disease in offspring has given conflicting results, suggesting that outcrossing might also cause the dissolution of resistant genotypes. To determine if selfed progeny are more susceptible to disease caused by the heteroecious rust, Puccinia recondita, or if selfing preserves existing resistant genotypes, we used a factorial design to compare levels of infection of selfed and outcrossed progeny of Impatiens capensis, a woodland annual with a mixed mating system. We compared the level of host infection when exposed to three pathogen sources in the field: the sympatric rust population, and two allopatric rust populations. Outcrossed progeny exposed to sympatric rust had higher infection scores than selfed progeny exposed to the same rust, suggesting that outcrossing breaks up resistant genotypes. In addition, there was a trend for the rust to be more infective on sympatric rather than allopatric hosts. We also examined whether rust infection differentially alters the fitness of selfed and outcrossed progeny. Outcrossed plants that escaped infection had higher fitness, as measured by fruit production, than selfed plants, but there was no difference in fitness between infected selfed and infected outcrossed plants. Thus, outcrossing was advantageous in the absence of disease, but there was no fitness difference between selfed and outcrossed progeny in the presence of disease. In sum, our results indicate that interactions with pathogens can eliminate or reverse the advantage of outcrossing.     

Ignoring intermarker linkage disequilibrium induces false-positive evidence of linkage for consanguineous pedigrees when genotype data is missing for any pedigree member

Missing genotype data can increase false-positive evidence for linkage when either parametric or nonparametric analysis is carried out ignoring intermarker linkage disequilibrium (LD). Previously it was demonstrated by Huang et al. [1] that no bias occurs in this situation for affected sib-pairs with unrelated parents when either both parents are genotyped or genotype data is available for two additional unaffected siblings when parental genotypes are missing. However, this is not the case for autosomal recessive consanguineous pedigrees, where missing genotype data for any pedigree member within a consanguinity loop can increase false-positive evidence of linkage. False-positive evidence for linkage is further increased when cryptic consanguinity is present. The amount of false-positive evidence for linkage, and which family members aid in its reduction, is highly dependent on which family members are genotyped. When parental genotype data is available, the false-positive evidence for linkage is usually not as strong as when parental genotype data is unavailable. For a pedigree with an affected proband whose first-cousin parents have been genotyped, further reduction in the false-positive evidence of linkage can be obtained by including genotype data from additional affected siblings of the proband or genotype data from the proband's sibling-grandparents. For the situation, when parental genotypes are unavailable, false-positive evidence for linkage can be reduced by including genotype data from either unaffected siblings of the proband or the proband's married-in-grandparents in the analysis.     

Isolation and characterization of polymorphic microsatellite loci for parentage analysis in a rhacophorid tree frog (Chirixalus eiffingeri) with unusual parental care

Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.     

Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n=3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n=5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the within-animal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.     

Parental effects in Lychnis flos-cuculi. II: Selection on time of emergence and seedling performance in the field

Selection on the timing of seedling emergence was investigated in an experimental population of Lychnis flos-cuculi, a perennial hay-meadow species. Seeds obtained from a full diallel cross of 8 genotypes from a field population were sown along an environment gradient that included the parental site. Significant directional selection for early emergence was found and the intensity of selection varied among sites. Emergence time varied significantly among progeny families of different maternal and paternal genotypes. These differences could be attributed to parental effects whereas narrow-sense heritabilities were close to zero. Survivorship until autumn differed among progeny of paternal families. Survivorship of maternal progeny varied among sites. Whereas differences in survival and plant size among individuals from different emergence cohorts persisted over the winter, the significance of these differences among progeny from different parental genotypes disappeared. It is suggested that a response to selection on emergence time might be low since (1) the narrow sense heritability was low, (2) parental genotypes differed in their effect on offspring emergence time when used as female parent or as pollen donor and (3) there was a family x site interaction for survival. Families with relatively early emerging seedlings also had a significantly higher seed weight, emergence percentage, and plant weight although the strength of these among-family correlations varied among sites. It is therefore not likely that simultaneous selection on emergence time and either of these traits would retard a response to selection on emergence time.     

The transmission/disequilibrium test and parental-genotype reconstruction: the reconstruction-combined transmission/ disequilibrium test

Spielman and Ewens recently proposed a method for testing a marker for linkage with a disease, which combines data from families with and without information on parental genotypes. For some families without parental-genotype information, it may be possible to reconstruct missing parental genotypes from the genotypes of their offspring. The treatment of such a reconstructed family as if parental genotypes have been typed, however, can introduce bias. In the present study, a new method is presented that employs parental-genotype reconstruction and corrects for the biases resulting from reconstruction. The results of an application of this method to a real data set and of a simulation study suggest that this approach may increase the power to detect linkage.     

Accuracy and precision of methods to estimate the number of parents contributing to a half-sib progeny array

Molecular technologies have made feasible large-scale studies of genetic parentage in nature by permitting the genotypic examination of hundreds or thousands of progeny. One common goal of such studies is to estimate the true number of unshared parents who contributed to a large half-sib progeny array. Here we introduce computer programs designed to count the number of gametotypes contributed by unshared parents to each such progeny array, as well as assess the accuracy and precision of various estimators for the true number of unshared parents via computer simulation. These simulations indicate that under most biological conditions (1) a traditional approach (the multilocus MINIMUM METHOD) that merely counts the number of distinct haplotypes in offspring and divides by 2L, where L is the number of loci assayed, often vastly underestimates the true number of unshared parents who contributed to a half-sib progeny array; (2) a recently developed HAPLOTYPES estimator is a considerable improvement over the MINIMUM METHOD when parental numbers are high; and (3) the accuracy and precision of the HAPLOTYPES estimator increase as marker polymorphism and sample size increase, or as reproductive skew and the number of parents contributing to the progeny array decrease. Generally, HAPLOTYPES-based estimates of parental numbers in large half-sib cohorts should improve the characterization of organismal reproductive strategies and mating systems from genetic data.     

Predicting parental genotypes and gene segregation for tetrasomic inheritance

Recent genome mapping projects in tetraploid plant species require a method for analysing the segregation patterns of molecular marker loci in these species. The present study presents a theoretical model and a statistical analysis for predicting the genotypes of a pair of tetraploid parents at a codominant (for example, RFLPs, microsatellites) or dominant (for example, AFLPs, RAPDs) molecular marker locus based on their and their progeny’s phenotypes scored at that locus (gel-band patterns). The theory allows for null alleles and for any degree of double-reduction to be modelled. A simulation study was performed to investigate the properties of the theoretical model. This showed that in many circumstances both the parental genotypes can be correctly identified with a probability of nearly 1, even when the molecular data were complicated by null alleles or double-reduction. Configurations where the parental genotype cannot be identified are discussed. The power to detect double-reduction varies considerably, depending on the proportion of identical alleles carried and shared by the parents, and the number of null alleles. Incorrect deductions of the occurrence of double-reduction were rare. The method was applied to data on a microsatellite locus segregating in the parents and 74 offspring of a tetraploid potato cross. Twentyfour parental configurations were consistent with the parental gel pattern, but only one of these was compatible with all the phenotypic data on the offspring. The feasibility for extending the present model to predict segregation of several linked loci, and particularly the linkage phase, is briefly discussed. Received: 7 June 1999 / Accepted: 28 September 1999     

Trisomy 21 Down syndrome

Summary The lymphocyte chromosomes of trisomy 21 Down syndrome patients and their parents in a random series of 374 families were analyzed, the objective being the identification of parental mosaicism. The numbers of parents in whom at least two trisomy 21 cells were detected were seven mothers and three fathers, a frequency of 2.7% of families. Confirmation of mosaicism was by identification of parental transmission of the extra chromosome to the progeny, by repeat chromosome analysis, and/or by the presence of more than one affected child. If to these are added six others in whom only one trisomic cell was detected, but with no other supporting evidence, the frequency could be as high as 4.3%. Differences in parental age at the birth of Down syndrome progeny may be accounted for by differences in frequencies of mosaicism in germ cells and somatic tissue. Mosaicism was found more frequently in the mothers than in the fathers, but more data are required for confirmation of a real difference.