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1.
C. Mae Culumber Steven R. Larson Kevin B. Jensen Thomas A. Jones 《Plant Systematics and Evolution》2011,294(3-4):207-225
Leymus is a genomically defined allopolyploid of genus Triticeae with two distinct subgenomes. Chloroplast DNA sequences of Eurasian and North American species are distinct and polyphyletic. However, phylogenies derived from chloroplast and nuclear DNA sequences are confounded by polyploidy and lack of polymorphism among many taxa. The AFLP technique can resolve phylogenetic relationships between closely related species, with a curvilinear relationship expected between the proportion of shared bands and nucleotide substitution rate (D), up to about 0.100 D. The objective of this study was to compare D and phylogenetic relationships among 16 Leymus taxa, based on chloroplast DNA sequences and multi-locus AFLP genotypes. Estimates of chloroplast D between taxa were 0.002 and 0.013 within and among continental regions, respectively. Estimates of AFLP D between taxa were 0.076 and 0.093 compared within and between continental regions, respectively, versus 0.024 within taxa. Bayesian and neighbor-joining cluster analyses effectively separated all AFLP genotypes by species, but showed that North American L. ambiguus is a hybrid species with nearly equal contributions from sympatric L. cinereus and L. salinus taxa. Two hierarchical AFLP clades, containing six North American taxa and four Eurasian taxa, had more than 98% bootstrap confidence with 0.071 and 0.055 D among taxa. Three other Eurasian taxa clustered with 79% and 89% confidence, with up to 0.79 D between taxa. These estimates provide benchmarks for phylogenetic comparisons of AFLP profiles, but three taxa could not be reliably grouped, which may reflect concurrent radiation of multiple lineages or lack of homologous AFLP characters caused by a high D. 相似文献
2.
Steven R. Larson Chantel Scheuring Parminder Kaur Paul F. Cliften Ivan W. Mott B. Shaun Bushman Jenifer J. Dong Yang Zhang Xiaojun Zhang Mahanz Kiani Yen-Hsuan Wu Yun-Hua Liu Hong-Bin Zhang N. Jerry Chatterton Richard R.-C. Wang 《Plant science》2009,177(5):427-438
Tall-caespitose basin wildrye (Leymus cinereus) and rhizomatous creeping wildrye (Leymus triticoides) are perennial Triticeae relatives of wheat and barley. Quantitative trait loci (QTLs) controlling rhizome proliferation were previously detected on homoeologous regions of LG3a and LG3b in two full-sib families derived from allotetraploid hybrids. Triticeae homoeologous group 3 aligns to rice chromosome 1, which contains the rice lax panicle and maize barrenstalk1 orthogene responsible for induction of axillary branch meristems, but this gene has not been mapped or sequenced in Triticeae. We developed bacterial artificial chromosome (BAC) libraries representing 6.1 haploid equivalents of the tetraploid Leymus genome (10.7 Mb). Overgo probes designed from the lax-barrenstalk1 orthogene hybridized to 12 Leymus BAC clones. Deduced amino-acid sequences from seven BAC clones were highly conserved with the rice, maize, and sorghum lax-barrenstalk1orthogenes. Gene specific primers designed from two of the most divergent BAC clones map to homoeologous regions of Leymus LG3a and LG3b and align with the lax-barrenstalk1 orthogene on rice 1L. Comparisons of genomic DNA sequences revealed two other conserved regions surrounding the Leymus LG3a, rice, and sorghum lax-barrenstalk1 ortholoci, and one of these regions was also present in maize and Leymus LG3b sequences. Comparisons of Leymus LG3a and LG3b lax-barrenstalk1 coding sequences and flanking genomic regions elucidate molecular differences between subgenomes. 相似文献
3.
Constructing dense genetic linkage maps 总被引:4,自引:0,他引:4
J. Jansen A. G. de Jong J. W. van Ooijen 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(6-7):1113-1122
This paper describes a novel combination of techniques for the construction of dense genetic linkage maps. The construction
of such maps is hampered by the occurrence of even small proportions of typing errors. Simulated annealing is used to obtain
the best map according to the optimality criterion: the likelihood or the total number of recombination events. Spatial sampling
of markers is used to obtain a framework map. The construction of a framework map is essential if the steps used for simulated
annealing are required to be simple. For missing-data imputation the Gibbs sampler is used. Map construction using simulated
annealing and missing-data imputation are used in an iterative way. In order to obtain some measure of precision of the genetic
linkage map obtained, the Metropolis-Hastings algorithm is used to obtain posterior intervals for the positions of markers.
The process of map construction is embedded in a framework of pre-mapping and post-mapping diagnostics. The techniques described
are illustrated using a practical application.
Received: 1 June 2000 / Accepted: 21 September 2000 相似文献
4.
We have generated a moderate resolution genetic map of mouse chromosomes 4 and 6 utilizing a (C57BL/6J x Mus spretus) F1 x Mus spretus backcross with RFLPs for 31 probes. The map for chromosome 4 covers 77 cM and details a large region of homology to human chromosome 1p. The map establishes the breakpoints in the mouse 4-human 1p region of homology to a 2-cM interval between Ifa and Jun in mouse and to the interval between JUN and ACADM in human. The map for mouse chromosome 6 spans a 65-cM region and contains a large region of homology to human 7q. These maps also provide chromosomal assignment and order for a number of previously unmapped probes. The maps should allow the rapid regional assignment of new markers to mouse chromosomes 4 and 6. In addition, knowledge of the gene order in mouse may prove useful in determining the gene order of the homologous regions in human. 相似文献
5.
Optimizing parental selection for genetic linkage maps. 总被引:49,自引:0,他引:49
Genetic linkage maps based on restriction fragment length polymorphisms are useful for many purposes; however, different populations are required to fulfill different objectives. Clones from the linkage map(s) are subsequently probed onto populations developed for special purposes such as gene tagging. Therefore, clones contained on the initial map(s) must be polymorphic on a wide range of genotypes to have maximum utility. The objectives of this research were to (i) calculate polymorphism information content values of 51 low-copy DNA clones and (ii) use the resulting values to choose potential mapping parents. Polymorphism information content was calculated using gene diversity by classifying restriction fragment patterns on a diverse set of 18 wheat genotypes. Combinations of potential parents were then compared by examining both the proportion of polymorphic clones and the likelihood that those mapped clones would give a polymorphism when used on other populations. Genotype pairs were identified that would map more highly informative DNA clones compared with a population derived from the most polymorphic potential parents. The methodologies used to characterize clones and rank potential parents should be applicable to other species and types of markers as well. 相似文献
6.
Leymus is a genus in the Triticeae tribe, Poaceae. The taxa of this genus are allopolyploid species which possess the Ns and Xm genomes. According to cytological, cytogenetic and molecular genetic analyses, some species of Hystrix and Elymus ought to be transferred to this genus. A world revision of the genus Leymus is needed. In this paper we summarize experimental results, provide a key to sections, species and varieties, and list all the taxa we recognize in Leymus with their synonyms. This synopsis is a new taxonomic system to be used for the revision of Leymus. 相似文献
7.
W. R. Gilks S. J. Welham J. Wang S. J. Clark G. J. King 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2012,125(7):1393-1402
This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8–12?cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many individuals were untyped. 相似文献
8.
9.
Jorgenson E Tang H Gadde M Province M Leppert M Kardia S Schork N Cooper R Rao DC Boerwinkle E Risch N 《American journal of human genetics》2005,76(2):276-290
Human genetic linkage maps are based on rates of recombination across the genome. These rates in humans vary by the sex of the parent from whom alleles are inherited, by chromosomal position, and by genomic features, such as GC content and repeat density. We have examined--for the first time, to our knowledge--racial/ethnic differences in genetic maps of humans. We constructed genetic maps based on 353 microsatellite markers in four racial/ethnic groups: whites, African Americans, Mexican Americans, and East Asians (Chinese and Japanese). These maps were generated using 9,291 subjects from 2,900 nuclear families who participated in the National Heart, Lung, and Blood Institute-funded Family Blood Pressure Program, the largest sample used for map construction to date. Although the maps for the different groups are generally similar, we did find regional and genomewide differences across ethnic groups, including a longer genomewide map for African Americans than for other populations. Some of this variation was explained by genotyping artifacts--namely, null alleles (i.e., alleles with null phenotypes) at a number of loci--and by ethnic differences in null-allele frequencies. In particular, null alleles appear to be the likely explanation for the excess map length in African Americans. We also found that nonrandom missing data biases map results. However, we found regions on chromosome 8p and telomeric segments with significant ethnic differences and a suggestive interval on chromosome 12q that were not due to genotype artifacts. The difference on chromosome 8p is likely due to a polymorphic inversion in the region. The results of our investigation have implications for inferences of possible genetic influences on human recombination as well as for future linkage studies, especially those involving populations of nonwhite ethnicity. 相似文献
10.
Salt Tolerance in the Triticeae: Leymus sabulosus 总被引:1,自引:0,他引:1
Elymus dahuhcus, Leymus giganteus, L. angustus, L. sabulosusand, to a lesser extent, L. triticoides, were found to tolerate200 mol m3 NaCl in solution culture. Elymus dahuricusdiffered from the Leymus species in its ion-uptake characteristics,showing a greater uptake of Cl and Na and a greater loss ofK from the shoots. In a more detailed experiment on Leymus sabulosusit was found that transpiration rates altered rapidly in responseto changes in external salinity whereas the accumulation ofNa and Cl in the leaves exhibited a lag of several days. Insalt stressed L. sabulosus Cl partially replaced the high levelsof nitrate found in the leaves of control plants. Glycinebetainelevels increased in the leaves from 8.0 mol m3 plantsap in the controls to 28 mol m3 plant sap at 250 molm3 NaCl. Key words: Salt stress, Transpiration, Solute accumulation, Leymus 相似文献
11.
Phylogenetic analyses of sequence data from two plastid genes (rbcL and ndhF) and two single-copy nuclear genes (DMC1 and EF-G) are used to elucidate the origin of the tetraploid, monotypic Hordelymus europaeus. Previous data have mostly shown an allopolyploid origin of Hordelymus, but very recently it was suggested that Hordelymus is autoploid. The present analysis, including representatives from all basic genome types accepted in the Triticeae, lends support to an alloploid origin. There is substantial support for the progenitor of Psathyrostachys as female genome donor of Hordelymus. Individual nuclear gene trees disagree about the male genome donor, but combined analysis of all data weakly supports the common progenitor of Pseudoroegneria and Henrardia as the male genome donor. 相似文献
12.
Two genetic linkage maps of tetraploid roses 总被引:11,自引:0,他引:11
S. Rajapakse D. H. Byrne L. Zhang N. Anderson K. Arumuganathan R. E. Ballard 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(4):575-583
A tetraploid F2 progeny segregating for resistance to black spot, growth habit, and absence of prickles on the stem and petioles was used
to construct genetic linkage maps of rose. The F1 of the progeny, 90–69, was created by crossing a black spot-resistant amphidiploid, 86–7, with a susceptible tetraploid,
82–1134. The F1 was open-pollinated to obtain 115 seedlings. AFLP and SSR markers were used to eliminate seedlings produced through cross-fertilization.
The remaining progeny set of 52 F2 plants was used to study the inheritance of 675 AFLPs, one isozyme, three morphological and six SSR markers. AFLP markers
were developed with three combinations of restriction enzymes, EcoRI/MseI, KpnI/MseI and PstI/MseI. Most of the markers appear to be in simplex or single-dose and segregated 3:1 in the progeny. One linkage map was constructed
for each parent using only the single-dose markers. The map of 86–7 consists of 171 markers assigned to 15 linkage groups
and covering more than 902 cM of the genome. The map of 82–1134 consists of 167 markers assigned to 14 linkage groups and
covering more than 682 cM of the genome. In the AFLP analysis, EcoRI/MseI generated nearly twice as many markers per run than PstI/MseI. Markers developed with three restriction enzyme combinations showed a mixed distribution throughout the maps. A gene controlling
the prickles on the petiole was located at the end of linkage group 7 on the map of 86–7. A gene for malate dehydrogenase
locus 2 was located in the middle of linkage group 4 on the map of 86–7. These first-generation maps provide initial tools
for marker- assisted selection and gene introgression for the improvement of modern tetraploid roses.
Received: 20 June 2000 / Accepted: 13 January 2001 相似文献
13.
Schouten HJ van de Weg WE Carling J Khan SA McKay SJ van Kaauwen MP Wittenberg AH Koehorst-van Putten HJ Noordijk Y Gao Z Rees DJ Van Dyk MM Jaccoud D Considine MJ Kilian A 《Molecular breeding : new strategies in plant improvement》2012,29(3):645-660
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users. 相似文献
14.
15.
Mathias Lorieux 《Molecular breeding : new strategies in plant improvement》2012,30(2):1231-1235
Several options are available to the scientific community for genetic map construction but few are simple to install and use. Available programs either lack intuitive interface or are commercial, expensive for many laboratories. We present MapDisto, a free, user-friendly and powerful program for constructing genetic maps from experimental segregating populations. MapDisto is freely available at http://mapdisto.free.fr/DL/. Current version: 1.7.5. 相似文献
16.
Comparison between Poncirus and Citrus genetic linkage maps 总被引:2,自引:0,他引:2
Ruiz C Asins MJ 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,106(5):826-836
Five genetic linkage maps were constructed for the parents of three progenies: Citrus aurantium (A) x Poncirus trifoliata var. Flying Dragon (Pa), C. volkameriana (V) x P. trifoliata var. Rubidoux (Pv) and a self-pollination of P. trifoliata var. Flying Dragon (Pp). The number of polymorphic markers assayed ranged from 48 for Pa to 120 for A according to the heterozygosity of each parental. As our focus was on genome comparison, most of the markers were newly generated simple sequence repeats. Inter-retrotransposon amplified polymorphisms based on four retrotransposon sequences isolated from Citrus spp were also used to saturate the maps. These polymorphisms were much more frequent in A (53) than in Pa (15) and randomly distributed throughout both genomes. Since comparative genomics and quantitative trait locus analysis applicability depends on the reliability of marker ordering, the causes of variation in marker order were investigated. Around 25% of the markers showed gametal segregation distortions. Segregation distortions were also observed at the zygotic level towards a reduction in the observed frequency of homozygotes from that expected in linkage groups 5 and 7. The presence of balanced lethal factors or gametal incompatibility genes in those genomic regions would explain a zygotic advantage of heterozygotes at these specific regions. Four differences in genomic organization were observed; three are putative translocations and affect homeologous linkage groups 3, 7 and 11, where highly distorted markers are found. Other causes of variation in marker order are also discussed: the introduction of new markers in the map, lowering the LOD score and the mapping software. These results represent the first comparative mapping analysis among Citrus and Poncirus species. 相似文献
17.
RAPD-based genetic linkage maps of Tribolium castaneum. 总被引:6,自引:0,他引:6
A genetic map of the red flour beetle (Tribolium castaneum) integrating molecular with morphological markers was constructed using a backcross population of 147 siblings. The map defines 10 linkage groups (LGs), presumably corresponding to the 10 chromosomes, and consists of 122 randomly amplified polymorphic DNA (RAPD) markers, six molecular markers representing identified genes, and five morphological markers. The total map length is 570 cM, giving an average marker resolution of 4.3 cM. The average physical distance per genetic distance was estimated at 350 kb/cM. A cluster of loci showing distorted segregation was detected on LG9. The process of converting RAPD markers to sequence-tagged site markers was initiated: 18 RAPD markers were cloned and sequenced, and single-strand conformational polymorphisms were identified for 4 of the 18. The map positions of all 4 coincided with those of the parent RAPD markers. 相似文献
18.
Integration of turkey genetic maps and their associated markers is essential to increase marker density in support of map-based genetic studies. The objectives of this study were to integrate 2 microsatellite-based turkey genetic maps--the Roslin map and the University of Minnesota (UMN) map--by genotyping markers from the Roslin study on the mapping families of the UMN study. A total of 279 markers was tested, and 240 were subsequently screened for polymorphisms in the UMN/Nicholas Turkey Breeding Farms (NTBF) mapping families. Of the 240 markers, 89 were genetically informative and were used for genotyping the F2 offspring. Significant genetic linkages (log of odds > 3.0) were found for 84 markers from the Roslin study. BLASTn comparison of marker sequences with the draft assembly of the chicken genome found 263 significant matches. The combination of genetic and in silico mapping allowed for the alignment of all linkage groups of the Roslin map with those of the UMN map. With the addition of the markers from the Roslin map, 438 markers are now genetically linked in the UMN/NTBF families, and more than 1700 turkey sequences have now been assigned to likely positions in the chicken-genome sequence. 相似文献
19.
Constructing genetic linkage maps under a tetrasomic model 总被引:6,自引:1,他引:5
An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species. 相似文献
20.
Molecular linkage maps of the Populus genome. 总被引:7,自引:0,他引:7
Tongming Yin Xinye Zhang Minren Huang Minxiu Wang Qiang Zhuge Shengming Tu Li-Huang Zhu Rongling Wu 《Génome》2002,45(3):541-555
We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification. 相似文献