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1.
Correcting Estimators of θ and Tajima's D for Ascertainment Biases Caused by the Single-Nucleotide Polymorphism Discovery Process
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Most single-nucleotide polymorphism (SNP) data suffer from an ascertainment bias caused by the process of SNP discovery followed by SNP genotyping. The final genotyped data are biased toward an excess of common alleles compared to directly sequenced data, making standard genetic methods of analysis inapplicable to this type of data. We here derive corrected estimators of the fundamental population genetic parameter θ = 4Neμ (Ne, effective population size; μ, mutation rate) on the basis of the average number of pairwise differences and on the basis of the number of segregating sites. We also derive the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction. 相似文献
2.
Dragan Perovic Jutta Förster Pierre Devaux Djabbar Hariri Morgane Guilleroux Kostya Kanyuka Rebecca Lyons Jens Weyen David Feuerhelm Ute Kastirr Pierre Sourdille Marion Röder Frank Ordon 《Molecular breeding : new strategies in plant improvement》2009,23(4):641-653
Monogenically-inherited resistance to Soil-borne cereal mosaic virus (SBCMV) in hexaploid bread wheat cultivars ‘Tremie’ and ‘Claire’ was mapped on chromosome 5D. The two closest flanking markers
identified in the Claire-derived mapping population, Xgwm469-5D and E37M49, are linked to the resistance locus at distances of 1 and 9 cm, respectively. Xgwm469-5D co-segregated with the SBCMV resistance in the Tremie-derived population and with the recently identified Sbm1 locus in the cv. Cadenza. This suggested that Tremie and Claire carry a resistance gene allelic to Sbm1, or one closely linked to it. The diagnostic value of Xgwm469-5D was assessed using a collection of SBCMV resistant and susceptible cultivars. Importantly, all susceptible genotypes carried
a null allele of Xgwm469-5D, whereas resistant genotypes presumably related to either Claire and Tremie or Cadenza revealed a 152 or 154 bp allele of
Xgwm469-5D, respectively. Therefore, Xgwm469-5D is well suited for marker assisted selection for SBCMV resistance. 相似文献
3.
In human populations, a null allele having several nucleotide differences from the wild-type allele is segregating at the
FUT2 locus (the ABO-Secretor locus) encoding α(1,2)fucosyltransferase. To estimate the age of the most recent common ancestor
(MRCA) of these two alleles, we sequenced FUT2 homologues from chimpanzee, gorilla, orangutan, and green monkey. Since we did not detect acceleration or any heterogeneity
in the substitution rate at this locus among these species, the age of the MRCA was estimated to be around 3 MYA, assuming
the divergence time of human and chimpanzee to be 5 MYA. We developed a simple test to examine whether or not the old age
of the MRCA of the FUT2 is consistent with that expected for two divergent neutral alleles sampled from a random mating population. An application
of the test to the data at FUT2 indicated that the age of the MRCA is too old to be explained by the simple neutral assumptions, although our test depends
on accurate estimation of the divergence time of human and chimpanzee in units of twice the human population size. Various
possibilities including balancing selection are discussed to explain this old age of the MRCA.
Received: 9 May 1999 / Accepted: 20 September 1999 相似文献
4.
The maize landraces in the North East Himalayan (NEH) region in India, especially in the Sikkim state, are morphologically
highly diverse. The present study provides details of phenotypic and molecular characterization of a set of 48 selected maize
landrace accessions, including the ‘Sikkim Primitives’ which have a unique habit of prolificacy (5–9 ears on a single stalk).
Multi-location phenotypic evaluation of these 48 accessions revealed significant genetic variability for grain yield and its
components, leading to identification of several promising accessions. Cluster analysis and PCA using nine morpho-agronomic
characters clearly separated ‘Sikkim Primitives’ from the rest of the accessions. PCA revealed two principal components describing
90% of the total variation, with hundred kernel weight, ear length, ear diameter, number of kernels per ear and flowering
behaviour forming the most discriminatory traits. The accessions were genotyped using 42 microsatellite or simple sequence
repeat (SSR) markers using a ‘population bulk DNA fingerprinting strategy’, with allele resolution using an automated DNA
Sequencer. The study revealed a high mean number of alleles per SSR locus (13.0) and high Polymorphism Information Content
(PIC) value of 0.60. The analysis also led to identification of 163 private/unique alleles, differentiating 44 out of 48 accessions.
Six highly frequent SSR alleles were detected at different loci (phi014, phi062, phi090, umc1266, umc1367 and umc2250) with individual frequencies ≥0.75. Some of these SSR loci were reported to tag specific genes/QTL for some important traits,
indicating that chromosomal regions harboring these SSR alleles were not selectively neutral. Cluster analysis using Rogers’
genetic distance also revealed distinct genetic identity of the ‘Sikkim Primitives’ from the rest of the accessions in India,
including Sikkim. Mantel’s test revealed significant and positive correlation between the phenotypic and molecular genetic
dissimilarity matrices. The study was the first to portray the patterns of phenotypic and molecular diversity in the maize
landraces from the NEH region in India. 相似文献
5.
C. Channuntapipat M. Sedgley G. Collins 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(6-7):1115-1122
Partial genomic and cDNA sequences of the RNase alleles S1, S7, S8 and Sf were obtained from Prunus dulcis cvs ’Ne Plus Ultra’, ’Ferragnes’ and ’Nonpareil’ 15–1, and IRTA Selection 12–2. Total DNA was extracted from leaves, and cDNA
was prepared from total RNA extracted from styles. The partial cDNA sequences of the S1 allele from ’Ferragnes’, and the S7 and S8 alleles from ’Nonpareil’ 15–1, matched those reported in the literature for the alleles Sb, Sc and Sd respectively. The sequences of the S1, S7, S8 and Sf alleles found in genomic DNA contained introns of 562, 1,530, 2,208 and 689 bp respectively. The exon/intron splice junction
sites of all alleles followed the GT/AG consensus sequence rule, and the sequences were found to be highly conserved.
Received: 18 October 2000 / Accepted: 8 March 2001 相似文献
6.
Associative overdominance: Evaluating the effects of inbreeding and linkage disequilibrium 总被引:1,自引:0,他引:1
E. Zouros 《Genetica》1993,89(1-3):35-46
Expressions are obtained for the expected phenotypic values of homozygous and heterozygous genotypes for a neutral marker
locus linked to a locus segregating for a recessive deleterious gene. The phenotypic values are functions of the allele frequencies
at the marker locus, the inbreeding coefficient and the degree of association of the deleterious gene with the marker alleles.
The analysis is extended to more than two alleles at the marker locus. Either linkage disequilibrium or inbreeding alone can
produce an apparent superiority of heterozygotes for the marker locus (unless specified otherwise, the terms ‘homozygote’
and ‘heterozygote’ will refer to the marker locus). The effect of linkage disequilibrium on the difference between the heterozygote
and homozygote values can be positive (associative overdominance) or negative (associative underdominance), depending on the
frequencies of the marker alleles and the degree of their association with the deleterious gene. Inbreeding has always a positive
effect. In general, the expected value of a homozygote is a positive function of its allele frequency. When the various homozygous
genotypes are combined into one class and the various heterozygous genotypes into another, the phenotypic difference of the
two classes is a function of the evenness of the allelic frequency distribution. Inbreeding is a more likely explanation of
associative overdominance if the frequency of the deleterious gene is low, but its effect on the character high. Conversely,
linkage disequilibrium is more likely if the frequency is high and the effect low. The degrees of association between marker
alleles and the deleterious gene can, in principle, be estimated from the observed phenotypic scores and used to calculate
expected multi-locus genotype scores. This could provide the basis for statistical tests of the associative overdominance
hypothesis as an explanation of observed correlations between multi-locus heterozygosity and phenotypic traits. 相似文献
7.
Potenko VV 《Biochemical genetics》2007,45(3-4):291-304
Genetic variation and differentiation of 12 populations of Picea jezoensis from the Russian Far East were studied using 20 allozyme loci. The mean number of alleles per locus was 2.63, the percent
of polymorphic loci was 88.1%, the observed heterozygosity was 0.181, and the mean value of expected heterozygosity amounted
to 0.189. The values of expected heterozygosity of the northern and central mainland populations were higher than in the southern
part of the natural range. A significant bias of Hardy–Weinberg heterozygosity to equilibrium heterozygosity (Heq) suggests that most of the mainland populations have recently experienced a severe expansion in population size while populations
from Kamchatka Peninsula have undergone a reduction in population size. Unbiased Nei’s genetic distance values were low within
and between the mainland and Sakhalin Island populations (DN=0.008). The largest values (DN=0.063) were found between the mainland/Sakhalin and Kamchatka Peninsula populations. Based on genetic distance, P. jezoensis and P. kamtschatkensis could be considered as distinct taxa, but P. ajanensis, P. microsperma, and P. komarovii do not warrant taxonomic recognition. 相似文献
8.
Riaz S Tenscher AC Ramming DW Walker MA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,122(6):1059-1073
A limited genetic mapping strategy based on simple sequence repeat (SSR) marker data was used with five grape populations
segregating for powdery mildew (Erysiphe necator) resistance in an effort to develop genetic markers from multiple sources and enable the pyramiding of resistance loci. Three
populations derived their resistance from Muscadinia rotundifolia ‘Magnolia’. The first population (06708) had 97 progeny and was screened with 137 SSR markers from seven chromosomes (4,
7, 9, 12, 13, 15, and 18) that have been reported to be associated with powdery or downy mildew resistance. A genetic map
was constructed using the pseudo-testcross strategy and QTL analysis was carried out. Only markers from chromosome 13 and
18 were mapped in the second (04327) and third (06712) populations, which had 47 and 80 progeny, respectively. Significant
QTLs for powdery mildew resistance with overlapping genomic regions were identified for different tissue types (leaf, stem,
rachis, and berry) on chromosome 18, which distinguishes the resistance in ‘Magnolia’ from that present in other accessions
of M. rotundifolia and controlled by the Run1 gene on chromosome 12. The ‘Magnolia’ resistance locus was termed as Run2.1. Powdery mildew resistance was also mapped in a fourth population (08391), which had 255 progeny and resistance from M. rotundifolia ‘Trayshed’. A locus accounting for 50% of the phenotypic variation mapped to chromosome 18 and was named Run2.2. This locus overlapped the region found in the ‘Magnolia’-based populations, but the allele sizes of the flanking markers
were different. ‘Trayshed’ and ‘Magnolia’ shared at least one allele for 68% of the tested markers, but alleles of the other
32% of the markers were not shared indicating that the two M. rotundifolia selections were very different. The last population, 08306 with 42 progeny, derived its resistance from a selection Vitis romanetii C166-043. Genetic mapping discovered a major powdery mildew resistance locus termed Ren4 on chromosome 18, which explained 70% of the phenotypic variation in the same region of chromosome 18 found in the two M. rotundifolia resistant accessions. The mapping results indicate that powdery mildew resistance genes from different backgrounds reside
on chromosome 18, and that genetic markers can be used as a powerful tool to pyramid these loci and other powdery mildew resistance
loci into a single line. 相似文献
9.
Tomoyuki Kado Asako Matsumoto Tokuko Ujino-Ihara Yoshihiko Tsumura 《Tree Genetics & Genomes》2008,4(1):133-141
Sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) are the most important timber species in Japan. To quantify and compare the level of nucleotide variation in these species,
we investigated their variation at ten nuclear loci. Average values of nucleotide diversity at synonymous sites (π
SYN) found in sugi and hinoki were 0.0038 and 0.0069, respectively. However, although the average value of nucleotide diversity
was higher in hinoki than in sugi, their average values of haplotype diversity were similar. Deviations from the standard
neutral model were detected at two loci in hinoki using Tajima’s D, Fay and Wu’s H, and Strobeck’s S statistics, which seem to be due to its historical population structure. Levels of divergence between the two species at
synonymous sites of the ten genes ranged from 0.121 to 0.566 (0.28 on average). These values positively correlated with their
guanine + cytosine contents at third-codon positions of synonymous sites (%GC3s). 相似文献
10.
Hilde Nybom Artur Mikiciński Larisa Garkava-Gustavsson Jasna Sehic Mariusz Lewandowski Piotr Sobiczewski 《Trees - Structure and Function》2012,26(1):199-213
Fire blight (Erwinia amylovora) causes serious damage to pome fruit orchards, and identification of germplasm with heritable disease resistance is therefore
crucial. Two dominant SCAR (sequence characterised amplified region) marker alleles (AE10-375 and GE-8019), flanking a previously
identified QTL (quantitative trait locus) for resistance to fire blight on ‘Fiesta’ linkage group 7 in apple cultivars related
to ‘Cox’s Orange Pippin’, were screened on 205 apple cultivars. Both marker alleles were present in 22% of the cultivars,
indicating presence of the QTL allele for tolerance, and both were lacking in 25%, indicating homozygosity for absence of
the QTL tolerance allele. However, 33% had only the marker allele AE10-375, while 20% had only GE-8019, suggesting that some
cultivars with the dominant alleles for both of the flanking markers can carry these on separate chromosomes and may lack
the QTL allele for tolerance. In 2009 and 2010, terminal shoots of greenhouse-grown grafted trees of 21 cultivars (only 20
in 2010) were inoculated with Erwinia amylovora. ‘Idared’ (susceptible) and ‘Enterprise’ (tolerant) were included as controls. Disease severity for each cultivar was expressed
as percentage of necrosis in relation to entire length of shoot, and the ranking of cultivars in 2009 and 2010 was compared
with a Spearman rank correlation test, P < 0.01. A relationship between presence of both flanking marker alleles for tolerance and level of fire blight tolerance
was confirmed with a Mann–Whitney U-test, P < 0.01 in 2009, and P < 0.05 in 2010. A PCO (principal coordinate) analysis based on band profiles obtained with 12 SSR (simple sequence repeat)
loci produced three loose clusters, two of which contained known offspring of ‘Cox’s Orange Pippin’, and one with cultivars
that were either unrelated or had an unknown origin. Cases where DNA markers did not predict level of fire blight damage as
expected, were, however, as common among descendants of ‘Cox’s Orange Pippin’ as among apparently unrelated cultivars. Obviously
the ‘Fiesta’ LG 7 QTL has some predictive value, both for known ‘Cox’ relatives and others, but more efficient markers would
be desirable for marker-assisted selection. 相似文献
11.
W. E. Van de Weg 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(8):1092-1096
Phytophthora fragariae var. fragariae is the causal agent of red stele (red core) root rot in strawberry (Fragaria spp.). The inheritance of resistance to one isolate of this fungus was studied in 12 segregating populations of F.×ananassa derived from crosses between four resistant cultivars (‘Climax’, ‘Redgauntlet’, ‘Siletz’, and ‘Sparkle’) and three susceptible
cultivars (‘Blakemore’, ‘Glasa’, and ‘Senga’ Sengana’). The analysis clearly supports the hypothesis of a single segregating
dominant resistance gene. It is proposed that this gene be designated Rpf2.
Received 12 November 1996 / Accepted: 22 November 1996 相似文献
12.
Allan M. Crawford Steven M. Kappes Korena A. Paterson Mauricio J. deGotari Ken G. Dodds Brad A. Freking Roger T. Stone Craig W. Beattie 《Journal of molecular evolution》1998,46(2):256-260
Previous studies suggest the median allele length of microsatellites is longest in the species from which the markers were
derived, suggesting that an ascertainment bias was operating. We have examined whether the size distribution of microsatellite
alleles between sheep and cattle is source dependent using a set of 472 microsatellites that can be amplified in both species.
For those markers that were polymorphic in both species we report a significantly greater number of markers (P < 0.001) with longer median allele sizes in sheep, regardless of microsatellite origin. This finding suggests that any ascertainment
bias operating during microsatellite selection is only a minor contributor to the variation observed.
Received: 6 January 1997 / Accepted: 19 May 1997 相似文献
13.
14.
The frequencies of alleles of killer cell immunoglobulin-like receptor genes, KIR3DL3 and KIR3DL2, and the carrier frequency of KIR2DL4 alleles have been determined from a population of African Americans (n = 100) by DNA sequencing of the coding regions. Fifty alleles of KIR3DL3 were observed with the most frequent, KIR3DL3*00901 (13%). KIR3DL2 was also diverse; 32 alleles with KIR3DL2*00103 the most frequent (17%). For KIR2DL4, of the 18 alleles observed, one allele, KIR2DL4*00103, was found in 64 of the 100 individuals. Thirty-six novel alleles encoding a total of 28 unique receptors are described.
Pairwise comparisons among all of the alleles at each locus suggest a predominance of synonymous substitutions. The variation
at all three framework loci fits a neutral model of evolution. 相似文献
15.
P. B. Cregan J. Mudge E. W. Fickus D. Danesh R. Denny N. D. Young 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(5):811-818
The soybean cyst nematode (SCN) (Heterodera glycines Inchinoe) is the most economically significant soybean pest. The principal strategy to reduce or eliminate damage from this
pest is the use of resistant cultivars. Identifying resistant segregants in a breeding program is a difficult and expensive
process which is complicated by the oligogenic nature of the resistance and genetic variability in the pathogen. Fortunately,
resistance at one SCN-resistance locus, rhg1, is generally accepted as a necessity for the development of resistant genotypes using any source of resistance and when challenged
by any SCN race. Thus, the development of SCN resistant cultivars would be expedited if an effective and rapid system were
available to identify breeding lines carrying a resistance allele at the rhg1 locus. In this study we report two simple sequence repeat (SSR) or microsatellite loci that cosegregate and map 0.4 cM from
rhg1. Allelic variation at the first of these loci, BARC-Satt309, distinguished most, if not all, SCN-susceptible genotypes from
those carrying resistance at rhg1 derived from the important SCN-resistance sources ’Peking’, PI 437654, and PI 90763. BARC-Satt309 was also effective in distinguishing
SCN resistance sources PI 88788 and PI 209332 from many, but not all, susceptible genotypes. BARC-Satt309 cannot be used in
marker-assisted selection in populations developed from typical southern US cultivars crossed with the important resistance
sources PI 88788 or PI 209332 because these genotypes all carry the identical allele at the BARC-Satt309 locus. A second SSR
locus, BARC-Sat_168, was developed from a bacterial artificial chromosome (BAC) clone that was identified using the primers
to BARC-Satt309. BARC-Sat_168 distinguished PI 88788 and PI 209332 from southern US cultivars such as ’Lee’, ’Bragg’ and ’Essex’.
Both BARC-Satt309 and BARC-Sat_168 were used to assay lines from SCN-susceptible×SCN-resistant crosses and proved to be highly
effective in identifying lines carrying rhg1 resistance from those carrying the allele for SCN susceptibility at the rhg1 locus.
Received: 5 November 1998 / Accepted: 3 February 1999 相似文献
16.
V. Korzun M. S. Röder M. W. Ganal A. J. Worland C. N. Law 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(8):1104-1109
Two sets of single chromosome recombinant lines comparing 2D chromosomes from the wheat varieties ‘Ciano 67’ and ‘Mara’ with
the common 2D chromosome of ‘Cappelle-Desprez’ in a ‘Cappelle-Desprez’ background were used to detect a diagnostic wheat microsatellite
marker for the dwarfing gene Rht8. The genetic linkage maps place the wheat microsatellite marker WMS 261 0.6 cM distal to Rht8 on the short arm of chromosome 2D. By PCR analysis the WMS 261 alleles of ‘Mara’, ‘Cappelle-Desprez’ and ‘Ciano 67’ could
be distinguished by different fragment sizes of 192 bp, 174 bp and 165 bp, respectively. A screen of over 100 international
varieties of wheat showed that the three allelic variants were all widespread. It also demonstrated that a limited number
of varieties carried novel WMS 261 variants of over 200 bp. Following classification of the individual recombinant lines for
allelic variants at the WMS 261 locus it was possible to attribute a 7- to 8-cm reduction in plant height with the WMS 261-192-bp
allele compared to the WMS 261-174-bp allele in the set of recombinant lines comparing 2D chromosomes of ‘Mara’ and ‘Cappelle-Desprez’.
A height reduction of around 3 cm was detected between the WMS 261-174-bp allele and the WMS 261-165-bp allele in the recombinant
lines comparing 2D chromosomes of ‘Cappelle-Desprez’ and ‘Ciano 67’.
Received: 17 October 1997 / Accepted: 12 November 1997 相似文献
17.
Eleven polymorphic microsatellite marker loci were developed from a Leisler’s bat (Nyctalus leisleri) genomic enriched library. Assessment of the usefulness of these markers for population genetics studies of Leisler’s bats
was carried out by screening 100 specimens sampled from eight locations in Ireland and two in Northeastern France. Both moderately
and highly polymorphic marker loci were identified. Five to 28 alleles were found to be segregating per locus with observed
heterozygosities values ranging from 28.4 to 94%. Initial evaluation indicates that these microsatellites will be useful for
genetic based studies aiming, for instance, at parentage and population structure of Leisler’s bats. 相似文献
18.
19.
Kelly JK 《Genetica》2008,132(2):187-198
The rare-alleles model of quantitative variation posits that a common allele (the ‘wild-type’) and one or more rare alleles
segregate at each locus affecting a quantitative trait; a scenario predicted by several distinct evolutionary hypotheses.
Single locus arguments suggest that artificial selection should substantially increase the genetic variance (Vg) if the rare-alleles
model is accurate. This paper tests the ‘ΔVg prediction’ using a large artificial selection experiment on flower size of Mimulus guttatus. Vg for flower size does evolve, increasing with selection for larger flower while decreasing in the other direction. These
data are consistent with a model in which flower size variation is caused by rare, partially dominant alleles. However, this
explanation becomes increasingly tenuous when considered with other data (correlated responses to selection and the effects
of inbreeding). A combination of modern (marker-based mapping) and classical (biometric) techniques will likely to be required
to determine the distribution of allele frequencies at loci influencing quantitative traits. 相似文献
20.
Michael D. Sabath 《Biochemical genetics》1981,19(3-4):347-353
The marine toad, Bufo marinus, was introduced to Australia from Hawaii in 1935. From 1935 to 1974, the toad population expanded exponentially to occupy 584,000 km2, and now has a continuous distribution from Cape York to Tweed River on the eastern coast of the continent. Genetic analysis of the population indicates a difference in allele frequency at the sorbitol dehydrogenase locus. There are two alleles segregating at the locus (NAD-Sdha and NAD-Sdhb). The NAD-Sdhaa homozygote is common in the two southern populations, but uncommon in northern populations. The north-south difference has been established in less than 25 generations. 相似文献