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1.
Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations 总被引:4,自引:0,他引:4
M. Lorieux B. Goffinet X. Perrier D. González de León C. Lanaud 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,90(1):73-80
A maximum-likelihood approach is used in order to estimate recombination fractions between markers showing segregation distortion in backcross populations. It is assumed that the distortions are induced by viability differences between gametes or zygotes due to one or more selected genes. We show that Bailey's (1949) estimate stays consistent and efficient under more general assumptions than those defined by its author. This estimate should therefore be used instead of the classical maximum-likelihood estimate. The question of detection of linkage is also discussed. We show that the order of markers on linkage groups may be affected by segregation distortion. 相似文献
2.
Background
Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), expressed sequence tags (ESTs) were analyzed in silico to identify SNPs and InDels in this study, aiming to develop more molecular markers in cotton.Results
A total of 1,349 EST-based SNP and InDel markers were developed by comparing ESTs between Gossypium hirsutum and G. barbadense, mining G. hirsutum unigenes, and analyzing 3′ untranslated region (3′UTR) sequences. The marker polymorphisms were investigated using the two parents of the mapping population based on the single-strand conformation polymorphism (SSCP) analysis. Of all the markers, 137 (10.16%) were polymorphic, and revealed 142 loci. Linkage analysis using a BC1 population mapped 133 loci on the 26 chromosomes. Statistical analysis of base variations in SNPs showed that base transitions accounted for 55.78% of the total base variations and gene ontology indicated that cotton genes varied greatly in harboring SNPs ranging from 1.00 to 24.00 SNPs per gene. Sanger sequencing of three randomly selected SNP markers revealed discrepancy between the in silico predicted sequences and the actual sequencing results.Conclusions
In silico analysis is a double-edged blade to develop EST-SNP/InDel markers. On the one hand, the designed markers can be well used in tetraploid cotton genetic mapping. And it plays a certain role in revealing transition preference and SNP frequency of cotton genes. On the other hand, the developmental efficiency of markers and polymorphism of designed primers are comparatively low.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1046) contains supplementary material, which is available to authorized users. 相似文献3.
Recombinant inbred lines for genetic mapping in tomato 总被引:11,自引:5,他引:6
Paran I. Goldman I. Tanksley S. D. Zamir D. 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,90(3-4):542-548
A cross between the cultivated tomato Lycopersicon esculentum and a related wild species L. cheesmanii yielded 97 recombinant inbred lines (RILs) which were used to construct a genetic map consisting of 132 molecular markers. Significant deviation from the expected 1:1 ratio between the two homozygous classes was found in 73% of the markers. In 98% of the deviating markers, L. esculentum alleles were present in greater frequency than the L. cheesmanii alleles. For most of the markers with skewed segregation, the direction of the deviation was maintained from F2 to F7 generations. The average heterozygosity in the population was 15%. This value is significantly greater than the 1.5% heterozygosity expected for RILs in the F7 generation. On average, recombination between linked markers was twice as high in the RILs than in the F2 population used to derive them. The utility of RILs for the mapping of qualitative and quantitative traits is discussed. 相似文献
4.
A model is presented which allows estimation of linkage from dihybrid F2 populations with distorted single gene segregation by applying the maximum-likelihood method. For different selection processes operating on one locus at either the gametic or the zygotic level, it can be demonstrated that, if the deficit is previously taken into account, testing for free recombination can be carried out without prior knowledge of the causes of this deficit. In the presence of linkage, the expected frequencies of two phenotypic classes depend on whether gametic or zygotic selection is operating. The remaining two classes can be utilized for the estimation of linkage as their frequency ratio is independent of these selection types. The application of this procedure to situations with coupling, incomplete penetrance, gametic and zygotic selection is discussed. 相似文献
5.
V. H. Beaumont J. Mantet T. R. Rocheford J. M. Widholm 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1996,93(4):606-612
The F2 generations from two maize crosses were used to compare the ability of RAPD and RFLP marker systems to create a genetic linkage map. Both RFLPs and RAPDs were shown to provide Mendelian-type markers. Most of the RFLPs (80%) could be placed with a good level of certainty (LOD>4) on the genetic linkage map. However, because of their dominant nature, only between 37% and 59% of the RAPDs could be placed with such a LOD score. The use of combined data from RFLPs and RAPDs increases the level of information provided by RAPDs and allows the creation of a combined RFLP/RAPD genetic linkage map. Thus, the RAPD technique was found to be a powerful method to provide improved probes coverage on a previously created RFLP map and to locate markers linked to chromosomal regions of interest. 相似文献
6.
Dideoxy polymorphism scanning,a gene-based method for marker development for genetic linkage mapping
David Rotter Scott E. Warnke Faith C. Belanger 《Molecular breeding : new strategies in plant improvement》2007,19(3):267-274
One of the fastest growing areas of biotechnology research today is marker-assisted breeding of crops. As a prerequisite to
marker assisted breeding, genetic linkage maps are currently being developed for many species. For many purposes gene-based
markers are the marker type of choice. The biggest problem in genetic linkage mapping using gene-based markers is the identification
of polymorphisms between the parents of the population. To improve the efficiency of marker generation, we have developed
a simple, and reasonable-cost method of polymorphism detection termed dideoxy polymorphism scanning. Since most of the time
required to develop a gene-based linkage map is spent in identification of useful polymorphisms, this method will significantly
shorten the time required for map generation and therefore reduce the overall cost. 相似文献
7.
High output genetic mapping of polyploids using PCR-generated markers 总被引:16,自引:0,他引:16
Bruno W. S. Sobral Rhonda J. Honeycutt 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1993,86(1):105-112
Summary The polymerase chain reaction (PCR) with arbitrarily selected primers has been established as an efficient method to generate fingerprints that are useful in genetic mapping and genomic fingerprinting. To further increase the productivity of mapping and fingerprinting efforts, we have altered existing protocols to include the use of the Stoffel fragment, which is derived from genetically engineered Taq polymerase. We also optimized the thermal profile of the reaction to increase the number of useful primers. In mapping of the genome of Saccharum spontaneum SES 208, a polyploid wild relative of sugarcane, these modifications allowed for an increase of 30% in the number of loci screened per primer, and an 80% increase in the number of polymorphisms per primer. Furthermore, the enzyme cost per reaction was decreased approximately 1.6-fold. Finally, there was an increase from about 70% to about 97% in the number of primers that were useful (i.e., gave a reproducible fingerprint) using our protocol. We have placed some of these markers into linkage groups. 相似文献
8.
We present a multipoint algorithm for mapping quantitative trait loci (QTLs) using dominant markers. The algorithm is designed
for outbred populations and is particularly suited for large families. The algorithm works with either codominant or dominant
markers, either of which may be interspersed within the same linkage map. Concurrently, the algorithm also partitions dominance
variance at the QTL. Computer simulations show that with large families, QTL mapping with dominant markers can be almost as
powerful as with bi-allelic, codominant markers. Yet despite this, other situations show a large standard deviation in the
estimate of the QTL position, thus making QTL mapping with dominant markers in outbred populations a useful detection tool,
albeit limited in its resolution.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
9.
Effects of missing marker and segregation distortion on QTL mapping in F2 populations 总被引:1,自引:0,他引:1
Luyan Zhang Shiquan Wang Huihui Li Qiming Deng Aiping Zheng Shuangcheng Li Ping Li Zhonglai Li Jiankang Wang 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,121(6):1071-1082
Missing marker and segregation distortion are commonly encountered in actual quantitative trait locus (QTL) mapping populations.
Our objective in this study was to investigate the impact of the two factors on QTL mapping through computer simulations.
Results indicate that detection power decreases with increasing levels of missing markers, and the false discovery rate increases.
Missing markers have greater effects on smaller effect QTL and smaller size populations. The effect of missing markers can
be quantified by a population with a reduced size similar to the marker missing rate. As for segregation distortion, if the
distorted marker is not closely linked with any QTL, it will not have significant impact on QTL mapping; otherwise, the impact
of the distortion will depend on the degree of dominance of QTL, frequencies of the three marker types, the linkage distance
between the distorted marker and QTL, and the mapping population size. Sometimes, the distortion can result in a higher genetic
variance than that of non-distortion, and therefore benefits the detection of linked QTL. A formula of the ratio of genetic
variance explained by QTL under distortion and non-distortion was given in this study, so as to easily determine whether the
segregation distortion marker (SDM) increases or decreases the QTL detection power. The effect of SDM decreases rapidly as
its linkage relationship with QTL becomes looser. In general, distorted markers will not have a great effect on the position
and effect estimations of QTL, and their effects can be ignored in large-size mapping populations. 相似文献
10.
Characterization of zygotic and nucellar seedlings from sour orange-like citrus rootstock candidates using RAPD and EST-SSR markers 总被引:1,自引:0,他引:1
Madhugiri Nageswara Rao Jaya R. Soneji Chunxian Chen Shu Huang Fred G. Gmitter Jr. 《Tree Genetics & Genomes》2008,4(1):113-124
A series of crosses designed for introgression of mandarin (Citrus reticulata Blanco) and pummelo (C. maxima Merr.) germplasm, to develop an alternative rootstock to sour orange (C. aurantium L.), were carried out. It is necessary to identify those hybrids that yield nucellar seedlings for rootstock propagation.
Rootstocks can be developed through traditional plant breeding methods; however, the ability to screen and select for economically
important traits (such as production of true nucellar seedlings) in an efficient fashion is limited by the difficulties of
screening techniques based on whole plant performance. To address these problems, we have used randomly amplified polymorphic
DNA (RAPD) and fluorescently labeled expressed sequence tag simple sequence repeat (EST-SSR) molecular markers. A total of
204 individual seedlings obtained from 34 hybrid parental plants were successfully characterized using five RAPD primers.
Ten hybrid parents and their progenies, found to be genetically similar among themselves, were selected for more scrutiny
using eight EST-SSR primer pairs. The degrees of genetic similarity (nucellars) among progeny seedlings were determined and
compared with that of their parents. The mean genetic similarity varied from 67–99% among the selected rootstock candidates
screened. The genetic similarity relationship identified using RAPD and EST-SSR molecular markers was highly concordant (p = 0.001). Two elite rootstock candidates (B6R5T56; B6R11T129) that seem to be ideal for future mandarin and pummelo derived
rootstock breeding programs have been identified. Our results indicate that either RAPD or EST-SSR analyses could be equally
successful in identifying true nucellars among the progenies obtained from introgression crosses of mandarin and pummelo,
thus improving the accuracy of early selection in a citrus rootstock breeding program. 相似文献
11.
Modeling segregation distortion for viability selection I. Reconstruction of linkage maps with distorted markers 总被引:1,自引:0,他引:1
Zhu C Wang C Zhang YM 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,114(2):295-305
Molecular markers have been widely used to map quantitative trait loci (QTL). The QTL mapping partly relies on accurate linkage
maps. The non-Mendelian segregation of markers, which affects not only the estimation of genetic distance between two markers
but also the order of markers on a same linkage group, is usually observed in QTL analysis. However, these distorted markers
are often ignored in the real data analysis of QTL mapping so that some important information may be lost. In this paper,
we developed a multipoint approach via Hidden Markov chain model to reconstruct the linkage maps given a specified gene order
while simultaneously making use of distorted, dominant and missing markers in an F2 population. The new method was compared with the methods in the MapManager and Mapmaker programs, respectively, and verified
by a series of Monte Carlo simulation experiments along with a working example. Results showed that the adjusted linkage maps
can be used for further QTL or segregation distortion locus (SDL) analysis unless there are strong evidences to prove that
all markers show normal Mendelian segregation. 相似文献
12.
T. Debener L. Mattiesch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(5):891-899
A segregating population of diploid rose hybrids (2n = 2x = 14) was used to construct the first linkage maps of the rose genome.
A total of 305 RAPD and AFLP markers were analysed in a population of 60 F1 plants based on a so-called ”double-pseudotestcross” design. Of these markers 278 could be located on the 14 linkage groups
of the two maps, covering total map lengths of 326 and 370 cM, respectively. The average distances between markers in the
maps for 93/1–117 and 93/1–119 is 2.4 and 2.6 cM, respectively. In addition to the molecular markers, genes controlling two
phenotypic characters, petal number (double versus single flowers) and flower colour (pink versus white), were mapped on linkage
groups 3 and 2, respectively. The markers closest to the gene for double flowers, Blfo, and to the gene for pink flower colour, Blfa, cosegregated without recombinants. The maps provide a tool for further genetic analyses of horticulturally important genes
as, for example, resistance genes and a starting point for marker-assisted breeding in roses.
Received: 22 September 1998 / Accepted: 12 March 1999 相似文献
13.
Quantitative genetic variance associated with chromosomal markers in segregating populations 总被引:1,自引:0,他引:1
J. C. M. Dekkers M. R. Dentine 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1991,81(2):212-220
Summary Use of chromosomal markers can accelerate genetic progress for quantitative traits in pedigree selection programs by providing early information on Mendelian segregation effects for individual progeny. Potential effectiveness of selection using markers is determined by the amount of additive genetic variance traced from parents to progeny by the markers. Theoretical equations for the amount of additive genetic variance associated with a marker were derived at the individual level and for a segregating population in joint linkage equilibrium. Factors considered were the number of quantitative trait loci linked to the marker, their individual effects, and recombination rates with the marker. Subsequently, the expected amount of genetic variance associated with a marker in a segregating population was derived. In pedigree selection programs in segregating populations, a considerable fraction of the genetic variance on a chromosome is expected to be associated with a marker located on that chromosome. For an average chromosome in the bovine, this fraction is approximately 40% of the Mendelian segregation variance contributed by the chromosome. The effects of interference and position of the marker on this expectation are relative small. Length of the chromosome has a large effect on the expected variance. Effectiveness of MAS is, however, greatly reduced by lack of polymorphism at the marker and inaccuracy of estimation of chromosome substitution effects. The size of the expected amount of genetic variance associated with a chromosomal marker indicates that, even when the marker is not the active locus, large chromosome substitution effects are not uncommon in segregating populations. 相似文献
14.
Wei-Ren Wu Wei-Ming Li 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1996,93(7):1156-1160
In this paper, the theory of joint mapping of quantitative trait loci is extended to F2 populations. Two independent regression equations, related to the additive and dominance effects respectively, are derived. Therefore, there are three alternative strategies for mapping QTLs, called additive-based mapping (ABM), dominance-based mapping (DBM) and additive-dominance-based mapping (ADBM). Simulation results have shown that ADBM is the most appropriate in most situations. 相似文献
15.
Cato S.A. Corbett G.E. Richardson T.E. 《Molecular breeding : new strategies in plant improvement》1999,5(3):275-281
Efficient construction of reasonable density genetic linkage maps is an essential component of QTL detection programmes. The
AFLP technique has been used to produce genetic linkage maps in a range of species. We have developed protocols to generate
reproducible AFLP profiles in Pinus radiata and have evaluated the inheritance and informativeness of AFLP markers in this
important timber species. The large genome size of P. radiata necessitated increased levels of selection at both the pre-amplification
and selective amplification steps of the AFLP protocol to generate reproducible AFLP profiles. Once optimised ca. 41.3 scorable
AFLP bands were resolvable through denaturing gels, of which 48.4% were polymorphic in a screen of eight unrelated trees.
This level of polymorphism is ca. three times higher than with RAPD markers. The total number of bands and the number of polymorphismic
bands per PCR were ca. halved when AFLPs were electrophoresed on non-denaturing gels and stained with ethidium bromide. Using
the protocols developed, AFLP is an efficient method for generating the DNA markers required for genetic linkage map construction
in P. radiata.
This revised version was published online in June 2006 with corrections to the Cover Date. 相似文献
16.
A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross 总被引:4,自引:0,他引:4
D. C. Jarrell M. L. Roose S. N. Traugh R. S. Kupper 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1992,84(1-2):49-56
Summary Isozymes and restriction fragment length polymorphisms were used as markers in the construction of a genetic map of the citrus nuclear genome. The map was based on the segregation of 8 isozyme, 1 protein, and 37 RFLP loci in 60 progeny of a cross of two intergeneric hybrids, Sacaton citrumelo (Citrus paradisi Macf. x Poncirus trifoliata (L.) Raf.) and Troyer citrange (C. sinensis (L.) Osbeck x P. trifoliata), often used as rootstocks. The map contains 38 of 46 studied loci distributed on ten linkage groups. A genome size of 1,700 cM was estimated from partial linkage data. Approximately 35% of the genome should be within 10 cM and 58% within 20 cM of the mapped markers. Eight loci in three linkage groups and 1 unlinked locus deviated significantly from Mendelian segregation. 相似文献
17.
Hiroyuki Shibaike 《Journal of plant research》1998,111(3):383-388
With the advent of molecular genetic mapping, it is possible to study the genetic basis of natural heritable variation in
new ways. Here, three potential uses of molecular genetic mapping in plant ecology and evolutionary biology are discussed;
(1) accurate estimation of genetic parameters, (2) understanding speciation and/or adaptation, and (3) investigating whole
genome organization. Basic methods for mapping genes and important mapping strategies are outlined. Recent studies are introduced
to illustrate progress so far in applying the new methods in ecological and evolutionary research. 相似文献
18.
In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum 总被引:1,自引:0,他引:1
Manli Li Nana Yuyama Le Luo Mariko Hirata Hongwei Cai 《Molecular breeding : new strategies in plant improvement》2009,24(1):41-47
In order to develop simple sequence repeat (SSR) markers for sorghum, a total of 2,113 primer pairs were designed from 81,342
public genomic sequence contigs of sorghum [methyl-filtered sequences downloaded from SAMI (Sorghum Assembled Genomic Island)].
After screening eight sorghum lines, 1,758 primers amplifying polymorphisms were identified. Of these 1,710 SSR markers were
predominantly polymorphic in the eight lines and could detect from two to eight alleles. In addition, 1,692 of the markers
were mapped on to the ten sorghum chromosomes by in silico mapping. The number of markers per chromosome ranged from 107 to
285. These SSR markers will provide an ideal marker system to help with gene targeting, gene cloning, quantitative trait locus
mapping, and marker-assisted selection in sorghum species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
19.
S. J. Knapp J. L. Holloway W. C. Bridges B. H. Liu 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(1):74-81
The development of efficient methods for amplifying random DNA sequences by the polymerase chain reaction has created the basis for mapping virtually unlimited numbers of mixed-phase dominant DNA markers in one population. Although dominant markers can be efficiently mapped using many different kinds of matings, recombination frequencies and locus orders are often mis-estimated from repulsion F2 matings. The major problem with these matings, apart from excessive sampling errors of recombination frequency () estimates, is the bias of the maximum-likelihood estimator (MLE) of (
ML).
when the observed frequency of double-recessive phenotypes is 0 and the observed frequency of double-dominant phenotypes is less than 2/3 — the bias for those samples is — . We used simulation to estimate the mean bias of
ML. Mean bias is a function of n and and decreases as n increases. Valid maps of dominant markers can be built by using sub-sets of markers linked in coupling, thereby creating male and feamle coupling maps, as long as the maps are fairly dense (about 5 cM) — the sampling errors of increase as increases for coupling linkages and are equal to those for backcross matings when =0. The use of F2 matings for mapping dominant markers is not necessarily proscribed because they yield twice as many useful markers as a backcross population, albeit in two maps, for the same number of DNA extractions and PCR assays; however, dominant markers can be more effeciently exploited by using doubled-haploid, recombinant-inbred, or other inbred populations. 相似文献
20.
The objective of this study was to obtain an overview of the genetic relationships within Perinereis aibuhitensis using Inter-Simple Sequence Repeat (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) markers that were derived from related populations residing in the Chinese coasts. The percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at the species level. The analysis of molecular variance revealed that 81.22% (ISSR) and 76.29% (SRAP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Nei's genetic differentiation (Gst) (0.2568/0.2876). The gene flow number (Nm) was 1.4470/1.2385, which indicated that there was limited gene exchange between populations. The phylogenetic tree of the ten P. aibuhitensis populations was separated into four major clusters using the neighbor-joining (NJ) method. These results provide a simple and useful basis for P. aibuhitensis germplasm research and aquaculture breeding. 相似文献