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1.
A chromosomal region originating from Malus floribunda 821 confers Vf scab resistance to many isolates of Venturia inaequalis. Twelve DNA markers located in this region were used to scan the equivalent of 31 cM in 98 Malus accessions. This allowed a molecular diagnosis of a source of resistance in apple germplasm with the aid of pedigree information, and in the context of a limited marker survey representing other chromosomes. At least five marker alleles were present in all scab-resistant breeding selections or varieties arising from M. floribunda. The validity of findings based on RAPD markers was confirmed with SCAR assays and Southern-hybridisation experiments. The order of markers determined in previous mapping studies was confirmed and sets of recombinants identified that establish reliable fine-mapping orders within 0.7 cM of the resistance locus. None of the marker alleles were present in the accessions that are either susceptible or possess weak polygenic resistance to scab. The presence of some alleles corresponding to those present at least 5.3 cM from Vf in M. floribunda was detected in some accessions. Other major sources of scab resistance do not appear to possess alleles in common with the Vf region, which will simplify future allelism tests. The results are discussed in the context of the introgression of resistance loci together with marker-assisted selection. The use of breeding pedigrees to assist in fine-scale mapping and map-based cloning is discussed. Received: 16 February 1999 / Accepted: 11 March 1999  相似文献   

2.
This paper investigates marker-assisted introgression of a major gene into an outbred line, where identification of the introgressed gene is incomplete because marker alleles are not unique to the base populations (the same marker allele can occur in both donor and recipient population). Those markers are used to identify the introgressed allele as well as the background genotype. The effect of using those markers, as if they were completely informative on the retention of the introgressed allele, was examined over five generations of backcrossing by using a single marker or a marker bracket for different starting frequencies of the marker alleles. Results were calculated by using both a deterministic approach, where selection is only for the desired allele, and by a stochastic approach, where selection is also on background genotype. When marker allele frequencies in donor and recipient population diverged from 1 and 0 (using a diallelic marker), the ability to retain the desired allele rapidly declined. Marker brackets performed notably better than single markers. If selection on background marker genotype was applied, the desired allele could be lost even more quickly than expected at random because the chance that the allele, which is common in the donor line, is present on the locus identifying the introgressed allele and is surrounded by alleles common in the recipient line on the background marker loci, will descend from the donor line (double recombination has taken place), is a lot smaller than the chance that this allele will stem from the recipient line (in which the allele occurs in low frequency). Marker brackets again performed better. Preselection against marker homozygotes (producing uninformative gametes) gave a slightly better retention of the introgressed allele.  相似文献   

3.
The S incompatibility system of apple was confirmed through the application of the gene Got-1 for glutamate oxaloacetate transaminase as a marker for the S locus. The 11S alleles proposed by Kobel et al. (1939) were confirmed through anomalous segregations for Got-1 observed in 14 semi-compatible crosses and regular segregations observed in 2 fully compatible crosses. The S allele genotypes of Idared (S 3 S 7), Cox (S 5 S 9) and Fiesta (S 3 S 5) were determined and found to fall within the original series. By associating parental incompatibility genotypes with the segregation of Got-1 alleles, we were able to deduce the coupling of S and Got-1 alleles in 9 varieties.  相似文献   

4.
Analysis of two cherry progenies from semi-compatible crosses for the esterase enzyme system showed extremely distorted segregation ratios for Est-5. Analysis of two progenies from compatible crosses for esterase and for stylar ribonuclease proved that Est-5 is linked with the incompatibility locus S. The recombination fraction is 4%. About a fifth of some 50 cultivars or selections genotyped for Est-5 were heterozygous. The various heterozygotes could provide ’testers’ for the presence in cultivars of unknown genotype of 8 of the 11 known S alleles. A seedling suitable for testing S 9 has been identified and crosses have been made to raise testers for S 10 and S 11 . Isoenzyme analysis of the four progenies for glutamate oxaloacetate transaminase, and of one of them for isocitrate dehydrogenase, showed no evidence for the linkage of Got-1 or Idh-2 with S, contrary to a previous report. Estimation of linkage with S in semi-compatible crosses is discussed. Received: 16 April 1999 / Accepted: 22 June 1999  相似文献   

5.
Adaptation to local conditions within demes balanced by migration can maintain polymorphisms for variants that reduce fitness in certain ecological contexts. Here, we address the effects of such polymorphisms on the rate of introgression of neutral marker genes, possibly genetically linked to targets of selection. Barriers to neutral gene flow are expected to increase with linkage to targets of local selection and with differences between demes in the frequencies of locally adapted alleles. This expectation is borne out under purifying and disruptive selection, regimes that promote monomorphism within demes. In contrast, overdominance within demes induces minimal barriers to neutral introgression even in the face of very large differences between demes in the frequencies of locally adapted alleles. Further, segregation distortion, a phenomenon observed in a number of interspecific hybrids, can in fact promote transmission by migrants to future generations at rates exceeding those of residents.  相似文献   

6.
This article reports the marker-assisted introgression of favorable alleles at three quantitative trait loci (QTL) for earliness and grain yield among maize elite lines. The QTL were originally detected in 1992 by means of ANOVA in a population of 96 recombinant inbred lines (RILs). Introgression started from a selected RIL, which was crossed three times to one of the original parents and then self-fertilized, leading to BC(3)S(1) progenies. Markers were used to assist both foreground and background selection at each generation. At the end of the program, the effect of introgression was assessed phenotypically in agronomic trials, and QTL detection was performed by composite interval mapping among BC(3)S(1) progenies. The marker-assisted introgression proved successful at the genotypic level, as analyzed by precision graphical genotypes, although no emphasis was put on the reduction of linkage drag around QTL. Also, QTL positions were generally sustained in the introgression background. For earliness, the magnitude and sign of the QTL effects were in good agreement with those expected from initial RIL analyses. Conversely, for yield, important discrepancies were observed in the magnitude and sign of the QTL effects observed after introgression, when compared to those expected from initial RIL analyses. These discrepancies are probably due to important genotype-by-environment interactions.  相似文献   

7.
Summary Selective genotyping is the term used when the determination of linkage between marker loci and quantitative trait loci (QTL) affecting some particular trait is carried out by genotyping only individuals from the high and low phenotypic tails of the entire sample population. Selective genotyping can markedly decrease the number of individuals genotyped for a given power at the expense of an increase in the number of individuals phenotyped. The optimum proportion of individuals genotyped from the point of view of minimizing costs for a given experimental power depends strongly on the cost of completely genotyping an individual for all of the markers included in the experiment (including the costs of obtaining a DNA sample) relative to the cost of rearing and trait evaluation of an individual. However, in single trait studies, it will almost never be useful to genotype more than the upper and lower 25% of a population. It is shown that the observed difference in quantitative trait values associated with alternative marker genotypes in the selected population can be much greater than the actual gene effect at the quantitative trait locus when the entire population is considered. An expression and a figure is provided for converting observed differences under selective genotyping to actual gene effects.  相似文献   

8.
Detection of hybridization and introgression in wild populations that have been supplemented by hatchery fish is necessary during development of conservation and management strategies. Initially, allozyme data and more recently highly polymorphic microsatellite markers have been used to obtain this information. We used both markers to assess the effectiveness of four assignment methods (Structure, NewHybrids, Baps and GeneClass) to detect hatchery introgression in wild stocked populations. Simulations of hybrid genotypes from real parental data revealed that the number and type of markers used with Structure, NewHybrids and Baps can identify as admixed most first and second generation hybrids as well as first generation backcrosses. In wild populations, introgression rates estimated from different markers and methods were correlated. However, slight disagreements were observed at both population and individual levels. Overall, the fully Bayesian (Structure, NewHybrids and Baps) performed better than partially Bayesian (GeneClass) assignment tests. In wild collections, Baps analyses were limited because of the lack of a native baseline. In all cases, the efficiency of methods was reduced as introgression increased.  相似文献   

9.
If marker alleles that identify a gene for introgression are not completely unique to the different base populations, the trait allele can be lost quickly during the process of backcrossing. This study considers ways to deal with incompletely informative markers in order to retain the desired allele. Selection was based on the probability of the presence of the desired (introgressed) trait allele, which was calculated for each marker genotype, using a single marker or a diallelic or triallelic marker bracket. The percentage of individuals retaining the introgressed allele was calculated over five generations of backcrossing, for selected fractions between 0 and 1, for marker alleles that could occur in both base populations. The best results were obtained with a rather large selected fraction, when all individuals, heterozygous and homozygous for the most desirable allele at the marker loci, were selected. Additional selection against marker homozygotes (which might have the highest probability of carrying the desired-trait allele, but produce uninformative gametes) altered the optimum selected fraction, making the selected fraction more consistently inversely related to a better retention of the desired-trait allele. A marker bracket was found to give a better retention of the desired-trait allele than a single marker and triallelic markers were better than diallelic markers, giving a retention of almost 50%. The earlier that preselection of parents (on informativeness) took place the better the overall result; preselection should occur preferably in the base populations. Preselection could make marker alleles unique to alternative base populations and markers would effectively become fully informative. Selection in the base populations might not be possible or not desirable, for example, because of the available number of individuals. This is unlikely to be a problem when parents are paired up to exclude any common marker alleles.  相似文献   

10.
Seven DNA variants that polymorphic genetic marker D16S752 reveals in Croatian population are reported in this paper. The marker is a GATA tetranucleotide repeat linked to human E-cadherin gene (CDH1). Prior studies involving this marker revealed only four DNA allele variants. The reported DNA variants contribute to the collection of hypervariable DNA polymorphisms data useful in the field of anthropological and population genetic and forensic medicine.  相似文献   

11.
China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China(400) and other regions in Asia(670). Among the six major rice groups(aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroup...  相似文献   

12.
Summary Methods are presented for determining linkage between a marker locus and a nearby locus affecting a quantitative trait (quantitative trait locus=QTL), based on changes in the marker allele frequencies in selection lines derived from the F-2 of a cross between inbred lines, or in the high and low phenotypic classes of an F-2 or BC population. The power of such trait-based (TB) analyses was evaluated and compared with that of methods for determining linkage based on the mean quantitative trait value of marker genotypes in F-2 or BC populations [marker-based (MB) analyses]. TB analyses can be utilized for marker-QTL linkage determination in situations where the MB analysis is not applicable, including analysis of polygenic resistance traits where only a part of the population survives exposure to the Stressor and analysis of marker-allele frequency changes in selection lines. TB analyses may be a useful alternative to MB analyses when interest is centered on a single quantitative trait only and costs of scoring for markers are high compared with costs of raising and obtaining quantitative trait information on F-2 or BC individuals. In this case, a TB analysis will enable equivalent power to be obtained with fewer individuals scored for the marker, but more individuals scored for the quantitative trait. MB analyses remain the method of choice when more than one quantitative trait is to be analyzed in a given population.Contribution from the ARO, Bet Dagan, Israel. No. 1698-E, 1986 series  相似文献   

13.
Summary As compared to classical, fixed sample size techniques, simulation studies showed that a proposed sequential sampling procedure can provide a substantial decrease (up to 50%, in some cases) in the mean sample size required for the detection of linkage between marker loci and quantitative trait loci. Sequential sampling with truncation set at the required sample size for the non-sequential test, produced a modest further decrease in mean sample size, accompanied by a modest increase in error probabilities. Sequential sampling with observations taken in groups produced a noticeable increase in mean sample size, with a considerable decrease in error probabilities, as compared to straightforward sequential sampling. It is concluded that sequential sampling has a particularly useful application to experiments aimed at investigating the genetics of differences between lines or strains that differ in some single outstanding trait.  相似文献   

14.
Summary The genetic variance among F2-derived lines of backcrosses (BCgF2-derived lines) depends on the backcross generation (g), the number of F1 plants crossed and selfed in generations 1 through g, and the number of BCgF2-derived lines evaluated. Additive genetic variance decreases linearly with backcrossing when one BCF1 plant per generation is crossed and selfed. The relationship is curvilinear if more than one BCF1 plant is used; as the number of BCF1 plants increases, additive genetic variance among BC1F2-derived lines approaches that among BC0F2-derived lines. The effect of population size on genetic variance is due both to fixation of alleles in previous generations and to sampling of genotypes in the population being evaluated. Dominance and repulsion linkage can cause small increases in genetic variance from BC0 to BC1.Joint contribution of USDA-ARS and Journal Paper No. J-11095 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 2471  相似文献   

15.
In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.  相似文献   

16.
The segregation of several isozyme marker genes has been studied in F2 inbred families from hybrids between self-sterile and five self-fertile inbred lines (nos. 2, 3, 4, 5, and 8) as well as from interline hybrids. Self-pollination of F1 hybrids between self-sterile forms and lines 5 and 8 gave an F2 segregation ratio of 1 heterozygote:1 homozygote for the gene Prx7 (chromosome 1R) against the allele from the line. This is interpreted as a result of tight linkage of the Prx7 gene with the S1 gene in chromosome 1R (recombination at a level of 0–1%). The self-pollination of such hybrids with lines 2,3 and 4 gave normal segregation for the Prx7 gene (1:2:1). This means that these lines carry a self-fertility allele which is not on chromosome 1R. Interline hybrids 5×2, 5×3 and 5×4 had self-fertility alleles for the two S genes and in inbred F2 progenies gave the expected deviating segregation for the Prx7 gene in a ratio of 2:3:1. The segregation of interline hybrid 5×8 was normal, 1:2:1, as expected. Highly-deviating segregation in an inbred F2 family of a hybrid with line 5 has also been obtained for another gene from chromosome 1R — Pgi2 (recombination with the S1 locus of 16.7%). By using the same method it has been estimated that line 4 has a self-fertility allele of the S2 locus from chromosome 2R and that the genes -Glu and Est4/11 are linked with it (recombination 16.7% and 17.5–20% respectively). Lines 2 and 3 have a self-fertility allele of the S5 locus from chromosome 5R which is linked with the Est5-7 gene complex (recombination at a level of 28.8–36.0%).  相似文献   

17.

Background

One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of genetic variation present in the tomato genome. Like many self-pollinated crops, cultivated tomato accessions show a low molecular but high phenotypic diversity. Here we describe the whole-genome resequencing of eight accessions (four cherry-type and four large fruited lines) chosen to represent a large range of intra-specific variability and the identification and annotation of novel polymorphisms.

Results

The eight genomes were sequenced using the GAII Illumina platform. Comparison of the sequences with the reference genome yielded more than 4 million single nucleotide polymorphisms (SNPs). This number varied from 80,000 to 1.5 million according to the accessions. Almost 128,000 InDels were detected. The distribution of SNPs and InDels across and within chromosomes was highly heterogeneous revealing introgressions from wild species and the mosaic structure of the genomes of the cherry tomato accessions. In-depth annotation of the polymorphisms identified more than 16,000 unique non-synonymous SNPs. In addition 1,686 putative copy-number variations (CNVs) were identified.

Conclusions

This study represents the first whole genome resequencing experiment in cultivated tomato. Substantial genetic differences exist between the sequenced tomato accessions and the reference sequence. The heterogeneous distribution of the polymorphisms may be related to introgressions that occurred during domestication or breeding. The annotated SNPs, InDels and CNVs identified in this resequencing study will serve as useful genetic tools, and as candidate polymorphisms in the search for phenotype-altering DNA variations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-791) contains supplementary material, which is available to authorized users.  相似文献   

18.
Blackmold, caused by the fungus Alternaria alternata, is a major ripe fruit disease of processing tomatoes. Previously, we found blackmold resistance in a wild tomato (Lycopersicon cheesmanii) and quantitative trait loci (QTL) for resistance were mapped in an interspecific population. Five QTLs were selected for introgression from L. cheesmanii into cultivated tomato using marker-assisted selection (MAS). Restriction fragment length polymorphism and PCR-based markers flanking, and within, the chromosomal regions containing QTLs were used for MAS during backcross and selfing generations. BC1 plants heterozygous at the QTLs, and subsequent BC1S1 and BC1S2 lines possessing different homozygous combinations of alleles at the target QTLs, were identified using DNA markers. Field experiments were conducted in 1998 (with 80 marker-selected BC1S2 lines) and 1999 (with 151 marker-selected BC1S2 and BC1S3 lines) at three California locations. Blackmold resistance was assessed during both years, and horticultural traits were evaluated in 1999. The BC1S2 and BC1S3 lines containing L. cheesmanii alleles at the QTLs were associated with a large genetic variance for resistance to blackmold and moderate heritability, suggesting that significant genetic gain may be achieved by selection in this genetic material. L. cheesmanii alleles at three of the five introgressed QTLs showed a significant, positive effect on blackmold resistance. A QTL on chromosome 2 had the largest positive effect on blackmold resistance, alone and in combination with other QTLs, and was also associated with earliness, a positive horticultural trait. The other four QTLs were associated primarily with negative horticultural traits. Fine mapping QTLs using near isogenic lines could help determine if such trait associations are due to linkage drag or pleiotropy.  相似文献   

19.
Summary While Lycopersicon esculentum and Solanum lycopersicoides have been successfully hybridized, attempts at further direct gene introgression have been unsuccessful due to the presence of incompatibility barriers. A systematic study of the initial hybridization and subsequent backcrosses has identified multiple barriers to introgression. These barriers are expressed as pollen tube inhibition in the upper style and lower pistil, and failures in syngamy, zygote development, and sporogenesis. Upper style cross-incompatibility barriers were successfully avoided by bud pollinations using a stigma complementation procedure to allow pollen germination on otherwise unreceptive stigmas. The inhibition of pollen tube growth was observed in the lower pistil. A combination of environmental, plant, and genetic manipulations facilitated consistent pollen tube growth to the ovule micropyles in all crosses attempted. Failures at syngamy and early zygote formation proved to be the most difficult barriers to overcome — these were particularly severe in crosses to F1 hybrid plants. Progeny were obtained in all crossing combinations attempted except in the initial hybridization with S. lycopersicoides as the pistillate parent. Although the strong pre-zygotic barriers were overcome in this cross, further progress was restricted by post-zygotic failures. The capability to overcome pre-zygotic barriers and to excise and culture very young embryos has allowed plantlet recovery from male sterile F1 plants. Partially pollen-fertile F1 plants were recovered when relatively large F1 populations were generated from different S. lycopersicoides accessions. In general, barriers to introgression diminished with increased backcrossing, though exceptions were noted. Progeny from the second backcross to L. esculentum possessed adequate fertility to set self-seed under field conditions. Although all backcross progeny were developed from only a few F1 individuals, considerable genetic variability was recovered for fruit and vegetative characteristics. Potentially useful levels of disease resistance, particularly to Botrytis cinerea, were also recovered.  相似文献   

20.
《遗传学报》2020,47(10):637-649
The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice (Oryza sativa L.). In this study, we focus on two types of genomic footprints, introgression and differentiation, in a population of more than 1200 Chinese rice accessions. We found that a Xian/indica and a temperate Geng/japonica accession respectively contained an average of 19.3-Mb and 6.8-Mb alien introgressed chromosomal segments, of which many contained functional sequence variants, quantitative trait loci, or genes controlling flowering, grain, and resistance traits. Notably, we found most introgressions, including the known heterotic loci Hd3a and TAC1, were distributed differentially between the female and male parents of three-line indica hybrid rice, indicating their potential contribution to heterosis. We also found many differentiated regions between subgroups within a subpopulation contained agronomically important loci, such as DTH7, Hd1 for heading date, and qCT7 for cold tolerance, providing new candidates for studying local adaptation or heterosis. Tracing these footprints allows us to better understand the genetic exchange or differentiation underlying agronomic traits in modern Chinese rice cultivars. These findings also provide potential targets for rice genetic research and breeding.  相似文献   

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