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1.
Jihad M Abdallah Bruno Goffinet Christine Cierco-Ayrolles Miguel Pérez-Enciso 《遗传、选种与进化》2003,35(6):513-532
Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance. 相似文献
2.
Local adaptation is important in evolutionary processes and speciation. We used multiple
tests to identify several candidate genes that may be involved in local adaptation from
1026 loci in 14 natural populations of Cryptomeria japonica, the most
economically important forestry tree in Japan. We also studied the relationships between
genotypes and environmental variables to obtain information on the selective pressures
acting on individual populations. Outlier loci were mapped onto a linkage map, and the
positions of loci associated with specific environmental variables are considered. The
outlier loci were not randomly distributed on the linkage map; linkage group 11 was
identified as a genomic island of divergence. Three loci in this region were also
associated with environmental variables such as mean annual temperature, daily maximum
temperature, maximum snow depth, and so on. Outlier loci identified with high significance
levels will be essential for conservation purposes and for future work on molecular
breeding. 相似文献
3.
Detection of QTL affecting harvest traits in a commercial Atlantic salmon population 总被引:1,自引:0,他引:1
R. D. Houston S. C. Bishop A. Hamilton D. R. Guy A. E. Tinch J. B. Taggart A. Derayat B. J. McAndrew C. S. Haley 《Animal genetics》2009,40(5):753-755
Genetic variation in performance and quality traits measured at harvest has previously been demonstrated in Atlantic salmon aquaculture populations. To map major loci underlying this variation, we utilized data from 10 families from a commercial breeding programme. Significant QTL were detected affecting harvest weight and length traits on linkage group 1, and affecting waste weight on linkage group 5. In total, 11 of the 29 linkage groups examined showed at least suggestive evidence for a QTL. These data suggest that major loci affecting economically important harvest characteristics are segregating in commercial salmon populations. 相似文献
4.
XianHu Zheng YouYi Kuang WeiHua Lv DingChen Cao XiaoFeng Zhang Chao Li CuiYun Lu XiaoWen Sun 《中国科学:生命科学英文版》2013,56(4):351-359
The ability to detect and identify quantitative trait loci (QTLs) in a single population is often limited. Analyzing multiple populations in QTL analysis improves the power of detecting QTLs and provides a better understanding of their functional allelic variation and distribution. In this study, a consensus map of the common carp was constructed, based on four populations, to compare the distribution and variation of QTLs. The consensus map spans 2371.6 cM across the 42 linkage groups and comprises 257 microsatellites and 421 SNPs, with a mean marker interval of 3.7 cM/marker. Sixty-seven QTLs affecting four growth traits from the four populations were mapped to the consensus map. Only one QTL was common to three populations, and nine QTLs were detected in two populations. However, no QTL was common to all four populations. The results of the QTL comparison suggest that the QTLs are responsible for the phenotypic variability observed for these traits in a broad array of common carp germplasms. The study also reveals the different genetic performances between major and minor genes in different populations. 相似文献
5.
Rogers J Garcia R Shelledy W Kaplan J Arya A Johnson Z Bergstrom M Novakowski L Nair P Vinson A Newman D Heckman G Cameron J 《Genomics》2006,87(1):30-38
Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate species in biomedical research. To create new opportunities for genetic and genomic studies using rhesus monkeys, we constructed a genetic linkage map of the rhesus genome. This map consists of 241 microsatellite loci, all previously mapped in the human genome. These polymorphisms were genotyped in five pedigrees of rhesus monkeys totaling 865 animals. The resulting linkage map covers 2048 cM including all 20 rhesus autosomes, with average spacing between markers of 9.3 cM. Average heterozygosity among those markers is 0.73. This linkage map provides new comparative information concerning locus order and interlocus distances in humans and rhesus monkeys. The map will facilitate whole-genome linkage screens to locate quantitative trait loci (QTLs) that influence individual variation in phenotypic traits related to basic primate anatomy, physiology, and behavior, as well as QTLs relevant to risk factors for human disease. 相似文献
6.
True and false positive peaks in genomewide scans: applications of length-biased sampling to linkage mapping. 总被引:11,自引:6,他引:5
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J D Terwilliger W D Shannon G M Lathrop J P Nolan L R Goldin G A Chase D E Weeks 《American journal of human genetics》1997,61(2):430-438
Disease-susceptibility loci are now being mapped via genomewide scans in which a linkage statistic is computed at each of a large number of markers. Such disease-susceptibility loci may be identified via a peak in the test statistic when the latter is plotted against the genetic map. In this paper we establish, by appealing to renewal theory, that true positive peaks are expected to be longer than false positive peaks. These results are verified by a realistic simulation of a genomewide linkage study based on the affected-sib-pair design. Since longer peaks are more likely to contain a gene of interest than are shorter peaks, these differences may aid in linkage mapping, justifying assignment of lower priority to shorter peaks. However, since these differences are generally small, statistics based on both peak length and height may not be much more powerful than those based on height alone. The results presented here also provide a theoretical framework for methods that use the length of shared haplotypes in populations to map disease genes. 相似文献
7.
Manli Li Nana Yuyama Mariko Hirata Yunwen Wang Jianguo Han Hongwei Cai 《Molecular breeding : new strategies in plant improvement》2010,26(3):467-476
Japanese lawngrass (Zoysia japonica) and Manila grass (Z. matrella) are the two most important and commonly used Zoysia species. A consensus based SSR linkage map was developed for the genus by combining maps from each species. This used previously
constructed maps for two Z. japonica populations and a new map from Z. matrella. The new SSR linkage map for Z. matrella was based on 86 F2 individuals and contained 213 loci and covered a map distance of 1,351.2 cM in 32 linkage groups. Comparison of the three
linkage maps constructed from populations with different genetic backgrounds indicated that most markers exhibited a consensus
order, although some intervals or regions displayed discrepancy in marker orders or positions. The integrated map comprises
507 loci with a mean interval of 4.1 cM, covering a map distance of 2,066.6 cM in 22 linkage groups. The SSR-based map will
allow marker-assisted selection and be useful for the mapping and cloning of economically important genes or quantitative
trait loci. 相似文献
8.
A consensus linkage map for swine chromosome 7 总被引:1,自引:0,他引:1
G A Rohrer L J Alexander C W Beattie P Wilkie G H Flickinger L B Schook A A Paszek L Andersson P Mariani L Marklund M Fredholm B Hoyheim A L Archibald V H Nielsen D Milan & M A M Groenen 《Animal genetics》1997,28(3):223-229
The First International Workshop on Swine Chromosome 7 (SSC7) was held in Minnesuing, Wisconsin, USA on 21–24 September 1995. The objective was to develop a comprehensive linkage map for porcine chromosome 7 by combining genotypic data from four swine reference populations. Contributions of genotypic data were made from the US Meat Animal Research Center, the University of Minnesota, the PiGMaP consortium and the Scandinavian consortium. Primers for selected sequence tagged site markers, to be genotyped across the reference populations, were exchanged to integrate individual maps of SSC7. Eighty-six loci were genotyped; these loci represented microsatellite, minisatellite, single-strand conformation polymorphism, restriction fragment length polymorphism, erythrocyte antigen and protein polymorphisms. Eighteen genes were mapped, including 12 markers within class I, class II and class III regions (four markers in each class) of the swine major histocompatibility complex. Forty-two markers were either genotyped on more than one population or were included in a haplotype system and used to develop skeletal linkage maps that spanned 147·6, 212·7 and 179·5 cM for the male, female and sex-average maps, respectively. A comprehensive linkage map was developed incorporating those markers with more than 30 informative meioses. The comprehensive map was slightly longer than the skeletal map, at 153·3, 215·3 and 183·8 cM, respectively, with only three intervals greater than 10 cM. These results significantly improve the genetic resolution of the porcine chromosome 7 map and represent an accurate approach for the merging of genetic maps produced in different reference populations. 相似文献
9.
Estimation of Recombination Frequencies and Construction of RFLP Linkage Maps in Plants from Crosses between Heterozygous Parents 总被引:22,自引:2,他引:20
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The construction of a restriction fragment length polymorphism (RFLP) linkage map is based on the estimation of recombination frequencies between genetic loci and on the determination of the linear order of loci in linkage groups. RFLP loci can be identified as segregations of singular or allelic DNA-restriction fragments. From crosses between heterozygous individuals several allele (fragment) configurations are possible, and this leads to a set of formulas for the evaluation of p, the recombination frequency between two loci. Tables and figures are presented illustrating a general outline of gene mapping using heterozygous populations. The method encompasses as special cases the mapping of loci from segregating populations of pure lines. Formulas for deriving the recombination frequencies and information functions are given for different fragment configurations. Information functions derived for relevant configurations are also compared. A procedure for map construction is presented, as it has been applied to RFLP mapping in an allogamous crop. 相似文献
10.
Doligez A Adam-Blondon AF Cipriani G Di Gaspero G Laucou V Merdinoglu D Meredith CP Riaz S Roux C This P 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,113(3):369-382
A grapevine (mainly Vitis vinifera L., 2n = 38) composite genetic map was constructed with CarthaGene using segregation data from five full-sib populations of 46, 95, 114, 139 and 153 individuals, to determine the relative position of a large set of molecular markers. This consensus map comprised 515 loci (502 SSRs and 13 other type PCR-based markers), amplified using 439 primer pairs (426 SSRs and 13 others) with 50.1% common markers shared by at least two crosses. Out of all loci, 257, 85, 74, 69 and 30 were mapped in 1, 2, 3, 4 and 5 individual mapping populations, respectively. Marker order was generally well conserved between maps of individual populations, with only a few significant differences in the recombination rate of marker pairs between two or more populations. The total length of the integrated map was 1,647 cM Kosambi covering 19 linkage groups, with a mean distance between neighbour loci of 3.3 cM. A framework-integrated map was also built, with marker order supported by a LOD of 2.0. It included 257 loci spanning 1,485 cM Kosambi with a mean inter-locus distance of 6.2 cM over 19 linkage groups. These integrated maps are the most comprehensive SSR-based maps available so far in grapevine and will serve either for choosing markers evenly scattered over the whole genome or for selecting markers that cover particular regions of interest. The framework map is also a useful starting point for the integration of the V. vinifera physical and genetic maps.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. 相似文献
11.
Freddy Bugge Christiansen 《Journal of genetics》1987,66(1):45-67
The balance between the creation of associations between alleles at different loci by immigration and the convergence to linkage equilibrium due to the recombination process is studied in a theoretical model. The geographical structure of the model is a stepping-stone chain of populations linking two genetically constant source populations. The model assumes an arbitrary number of autosomal loci and considers genetic variation (two alleles at each locus) that is not subject to natural selection. The gene frequencies at each locus will then show a linear cline through the stepping-stone chain of populations. The deviation from linkage equilibrium through the stepping-stone cline is characterized by an equation for linear measures that provide the linkage disequilibrium measures for a given set of loci in terms of the gene frequencies and the linkage disequilibria in the source populations and in terms of the linkage disequilibrium measures through the cline for lower numbers of loci. Numerical examples of this iterative solution are given, and it is shown that the build-up of the higher order Bennett-disequilibria through the cline is considerably more pronounced than the build-up of two-locus disequilibria. 相似文献
12.
Varshney RK Marcel TC Ramsay L Russell J Röder MS Stein N Waugh R Langridge P Niks RE Graner A 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,114(6):1091-1103
A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley. 相似文献
13.
Ulloa M Meredith WR Shappley ZW Kahler AL 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(2-3):200-208
An RFLP genetic linkage joinmap was constructed from four different mapping populations of cotton (Gossypium hirsutum L.). Genetic maps from two of the four populations have been previously reported. The third genetic map was constructed from
199 bulk-sampled plots of an F2.3 (HQ95–6×’MD51ne’) population. The map comprises 83 loci mapped to 24 linkage groups with an average distance between markers
of 10.0 centiMorgan (cM), covering 830.1 cM or approximately 18% of the genome. The fourth genetic map was developed from
155 bulk-sampled plots of an F2.3 (119– 5 sub-okra×’MD51ne’) population. This map comprises 56 loci mapped to 16 linkage groups with an average distance between
markers of 9.3 cM, covering 520.4 cM or approximately 11% of the cotton genome. A core of 104 cDNA probes was shared between
populations, yielding 111 RFLP loci. The constructed genetic linkage joinmap from the above four populations comprises 284
loci mapped to 47 linkage groups with the average distance between markers of 5.3 cM, covering 1,502.6 cM or approximately
31% of the total recombinational length of the cotton genome. The linkage groups contained from 2 to 54 loci each and ranged
in distance from 1.0 to 142.6 cM. The joinmap provided further knowledge of competitive chromosome arrangement, parental relationships,
gene order, and increased the potential to map genes for the improvement of the cotton crop. This is the first genetic linkage
joinmap assembled in G. hirsutum with a core of RFLP markers assayed on different genetic backgrounds of cotton populations (Acala, Delta, and Texas plain).
Research is ongoing for the identification of quantitative trait loci for agronomic, physiological and fiber quality traits
on these maps, and the identification of RFLP loci lineage for G. hirsutum from its diploid progenitors (the A and D genomes).
Received: 23 February 2001 / Accepted: 8 June 2001 相似文献
14.
Towards a saturated sorghum map using RFLP and AFLP markers 总被引:20,自引:3,他引:17
K. Boivin M. Deu J.-F. Rami G. Trouche P. Hamon 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(2):320-328
A near-saturated sorghum genetic linkage map was produced using RFLP, AFLP and morphological markers. First a composite,
essentially RFLP-based genetic linkage map was obtained from analyses of two recombinant inbred populations. This map includes
343 loci for 11 linkage groups spanning 1352 cM. Since this map was constructed with many previously mapped heterologous probes,
it offers a good basis for synteny studies. Separately, an AFLP map was obtained from the analysis of 168 bands revealed from
12 primer pair combinations. It includes 137 loci for 11 linkage groups spanning 849 cM. Taking into account the different
data sets, we constructed a combined genetic linkage map including 443 loci spanning 1899 cM. Two main features are to be
noted: (1) the distribution of AFLPs along the genome is not uniform; (2) an important stretching of the former core map is
induced after adding the AFLPs.
Received: 10 May 1998 / Accepted: 13 July 1998 相似文献
15.
A Study of Linkage Disequilibrium in British Populations of DROSOPHILA SUBOBSCURA 总被引:4,自引:4,他引:0
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Data have been obtained concerning the genetic content of samples of O chromosomes from three British populations, and J chromosomes from one population, of Drosophila subobscura. Some improvements to the genetic map of the O and J chromosomes have been made. Allele frequencies at the loci studied do not show much geographical variation, except where associations with geographically varying gene arrangements distort the picture. Striking nonrandom associations between alleles at three enzyme loci and closely linked O chromosome gene arrangements are present. Some historical explanation for these associations cannot at present be ruled out, but it is clear that a very high degree of genetic differentiation must exist between different gene arrangements in this species. There is no convincing direct evidence for linkage disequilibrium between pairs of enzyme loci, although there is a significant association between close linkage and a high value of the linkage disequilibrium measure. This suggests that there may be disequilibria between closely linked enzyme loci that are too small to be individually detectable. These results are in broad agreement with those reported by workers on other Drosophila species. At present there appears to be no evidence to support the concept that selection is sufficiently strong at individual enzyme loci to produce a high degree of nonrandom associations. (Franklin and Lewontin 1970). 相似文献
16.
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18.
Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes. 总被引:11,自引:0,他引:11
V Lefebvre S Pflieger A Thabuis C Caranta A Blattes J C Chauvet A M Daubèze A Palloix 《Génome》2002,45(5):839-854
Three populations composed of a total of 215 doubled haploid lines and 151 F2 individuals were used to design an intraspecific consensus map of pepper (Capsicum annuum L.). The individual maps varied from 685 to 1668 cM with 16 to 20 linkage groups (LGs). The alignment of the three individual maps permitted the arrangement of 12 consensus major linkage groups corresponding to the basic chromosome number of pepper and displaying a complex correspondence with the tomato map. The consensus map contained 100 known-function gene markers and 5 loci of agronomic interest (the disease-resistance loci L, pvr2, and Pvr4; the C locus, which determines capsaicin content; and the up locus, controlling the erect habit of the fruits). The locations of three other disease-resistance loci (Tsw, Me3, and Bs3) and the y locus, which determines the yellow fruit colour, were also found on this consensus map thanks to linked markers. Here we report on the first functional detailed map in pepper. The use of candidate gene sequences as genetic markers allowed us to localize four clusters of disease-resistance gene analogues and to establish syntenic relationships with other species. 相似文献
19.
J. Steven Brown Robert T. Sautter Cecile T. Olano James W. Borrone David N. Kuhn J. C. Motamayor Raymond J. Schnell 《Tropical plant biology》2008,1(2):120-130
In this paper, we report the construction of the first composite map of cacao from linkage data of one F2 and two F1 mapping populations with a high number of codominant markers in common. The combination of linkage information from all three maps results in the currently most precise estimates of marker locations and distances between markers, especially in densely marked areas. JoinMap®V4 software was used for all marker quality assessment and mapping. Individual (sub-composite) maps and the composite map contained 10 major linkage groups, corresponding to the number of cacao chromosomes. Homogeneity of marker placement was very high among sub-composite maps, the composite map, and the designated “reference” map. Care was exercised in the re-creation of sub-composite maps and the composite map to include only markers with acceptable mapping quality parameters. The composite map places more markers with higher precision than any individual map. This research clearly demonstrates for the first time a very high level of marker homogeneity among commercial cacao clones compared to other species. The observed homogeneity between different maps, including the composite one, is probably due to a narrow genetic base of commercial cacao clones. Markers linked to identified quantitative trait loci (QTLs) are more likely to retain linkage in other commercial clones, rendering the QTLs in cacao potentially more stable than in other species. 相似文献
20.
We have compared the efficiency of the lod score test which assumes heterogeneity (lod2) to the standard lod score test which assumes homogeneity (lod1) when three-point linkage analysis is used in successive map intervals. If it is assumed that a gene located midway between two linked marker loci is responsible for a proportion of disease cases, then the lod1 test loses power relative to the lod2 test, as the proportion of linked families decreases, as the flanking markers are more closely linked, and as more map intervals are tested. Moreover, when multipoint analysis is used, linkage for a disease gene is more likely to be incorrectly excluded from a complete and dense linkage map if true genetic heterogeneity is ignored. We thus conclude that, in general, the lod2 linkage test is more efficient for detecting a true linkage when a complete genetic marker map is screened for a heterogeneous disorder. 相似文献