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At least 163 records · Page 9Linked to original sources
PubMed1995

Isolation, characterization and RFLP linkage mapping of a DNA repeat family of Solanum spegazzinii by which chromosome ends can be localized on the genetic map of potato.

In a random sample of 2263 cloned genomic DNA fragments of the wild potato species Solanum spegazzinii six related, highly repetitive fragments (SPG repeat family) were identified that were present in much higher copy numbers in S. spegazzinii when compared with the closely related cultivated potato S. tuberosum. The SPG repeat family was organized in long arrays of multiple copies. Cross hybridization experiments with 29 wild and cultivated Solanum species and with the related tomato showed specificity of the SPG repeat family for tuber-bearing Solanum species. Among tuber bearing Solanum species a high degree of variation was observed for restriction fragment length and copy number. The variation in copy number was not correlated with established taxonomic relationships between tuber-bearing Solanum species. DNA sequence analysis revealed a subrepeat structure of 120-140 base pairs embedded in longer repeat units of variable length. Length polymorphisms between highly repeated restriction fragments detected by the SPG probes were used for segregation- and linkage analysis in four mapping populations of potato, for which RFLP maps had been constructed. Twelve loci were identified, eleven of which mapped to the distal ends of nine linkage groups. All the evidence suggested that the SPG repeat family represents a satellite repeat members of which are localized in the subtelomeric region of potato chromosomes. The SPG repeat family could be used, therefore, for completing the genetic map of potato.

Base Sequence↗
PubMed2004

A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates.

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH(5000) panel to 1913. Of these, 1463 have significant BLASTN hits (E < e(-5)) against the human genome sequence. A cattle-human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle-human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

Animals↗
PubMed2005

Aphid resistance in Medicago truncatula involves antixenosis and phloem-specific, inducible antibiosis, and maps to a single locus flanked by NBS-LRR resistance gene analogs.

Aphids and related insects feed from a single cell type in plants: the phloem sieve element. Genetic resistance to Acyrthosiphon kondoi Shinji (bluegreen aphid or blue alfalfa aphid) has been identified in Medicago truncatula Gaert. (barrel medic) and backcrossed into susceptible cultivars. The status of M. truncatula as a model legume allows an in-depth study of defense against this aphid at physiological, biochemical, and molecular levels. In this study, two closely related resistant and susceptible genotypes were used to characterize the aphid-resistance phenotype. Resistance conditions antixenosis since migratory aphids were deterred from settling on resistant plants within 6 h of release, preferring to settle on susceptible plants. Analysis of feeding behavior revealed the trait affects A. kondoi at the level of the phloem sieve element. Aphid reproduction on excised shoots demonstrated that resistance requires an intact plant. Antibiosis against A. kondoi is enhanced by prior infestation, indicating induction of this phloem-specific defense. Resistance segregates as a single dominant gene, AKR (Acyrthosiphon kondoi resistance), in two mapping populations, which have been used to map the locus to a region flanked by resistance gene analogs predicted to encode the CC-NBS-LRR subfamily of resistance proteins. This work provides the basis for future molecular analysis of defense against phloem parasitism in a plant model system.

Animals↗
PubMed2004

The R3 resistance to Phytophthora infestans in potato is conferred by two closely linked R genes with distinct specificities.

The R3 locus of potato (Solanum tuberosum L.) confers full resistance to avirulent isolates of Phytophthora infestans, the causal agent of late blight. R3 resides in the distal part of chromosome 11 and segregates in a potato mapping population, from which a well-saturated amplified fragment length polymorphism map is available. Using a population of 1,748 plants, we constructed a high-resolution genetic map at the R3 locus. Using the combination of fine mapping and accurate disease testing with specific P. infestans isolates, we detected that the R3 locus is composed of two genes with distinct specificities. The two genes R3a and R3b are 0.4 cM apart and have both been introgressed from S. demissum, the 'donor' species of most characterized race-specific R genes to P. infestans. A natural recombinant between R3a and R3b was discovered in one accession of S. demissum. The synteny between the R3 locus and the tomato I2 locus is discussed.

Base Sequence↗
PubMed1997

Use of allele specificity of comigrating AFLP markers to align genetic maps from different potato genotypes.

The allele specificity of AFLP markers was assessed in five relatively unrelated potato genotypes. To this end, two diploid mapping populations of potato, F1SH x RH and F1AM x RH, were analysed using four and six AFLP primer combinations, respectively, recently applied to the analysis of the genetically well characterized backcross population BC_C x E. The AFLP profiles of the five parents revealed 733 AFLP markers and, when identical primer combinations were used, 131 comigrating AFLP markers were identified. After construction of five parental maps, the genomic positions of these comigrating AFLP markers were compared and 117 markers (89%) which targeted the same genomic region were assumed to be homologous. Of these putative homologues, 20 markers, each cloned from at least two genotypes, were sequenced and 19 sets of amplification products were shown to be nearly identical. The number of AFLP markers previously mapped in population BC_C x E ranged from three to eleven per chromosome, which allowed a reliable assessment of chromosome numbers from individual linkage groups obtained in populations F1SH x RH and F1AM x RH. The high incidence of corresponding AFLP alleles was confirmed by using an additional set of five primer combinations. The 733 AFLP markers localized provide a valuable reference collection for future mapping studies in potato. As a consequence AFLP analysis may replace more laborious locus-specific marker techniques.

Alleles↗
PubMed2002

Effectiveness of selective genotyping for detection of quantitative trait loci: an analysis of grain and malt quality traits in three barley populations.

Marker genotype data and grain and malt quality phenotype data from three barley (Hordeum vulgare L.) mapping populations were used to investigate the feasibility of selective genotyping for detection of quantitative trait loci (QTLs). With selective genotyping, only individuals with high and low phenotypic values for the trait of interest are genotyped. Here, genotyping of 10 to 70% of each population (i.e., 5 to 35% in each tail of the phenotypic distribution) was considered. Genomic positions detected by selective genotyping were compared to QTL position estimates from interval mapping analysis using marker genotype data from the entire population. Selective genotyping reliably detected almost all of the mapped QTLs, often with only 10% of the population genotyped. Selective genotyping also detected spurious QTLs in regions of the genome where no significant QTL had been mapped. Even with additional genotyping to verify putative QTLs, the total genotyping effort for detection of QTLs for a single trait by selective genotyping was usually less than 30% of that required for conventional interval mapping. Simultaneous investigation of two or more traits by selective genotyping would require additional genotyping effort, but could still be worthwhile.

Genotype↗
PubMed2003

Tests of candidate genes in breed cross populations for QTL mapping in livestock.

In recent years, several F(2) crosses between outbred lines of livestock have been developed to identify quantitative trait loci (QTL). These populations are valuable for further genetic analysis, including positional candidate gene loci (CGL). Analysis of CGL in F(2) populations is, however, hindered by extensive between-breed linkage disequilibrium (LD). The objectives here were to develop and evaluate three tests for CGL in simulated F(2) breed-cross populations. 1) A standard association test, based on the fixed effect of CGL genotype. This test was significant for CGL at considerable distances from the QTL. 2) A marker-assisted association test, based on a test at the CGL of the fixed effect of CGL genotype in a breed-cross QTL interval mapping model. This removed the impact of between-breed LD, but was not powerful in detecting CGL closely linked to the QTL, unless the CGL was the QTL. 3) An F-drop test, comparing F ratios for a QTL at the CGL with and without the CGL included as fixed effect. It had low power to distinguish close from distant CGL. Power to distinguish two CGL within 10 cM from the QTL was limited and little improved by including QTL effects associated with markers to remove between-breed LD, although the power was greater when one of the CGL was the causative mutation. Therefore, while we conclude that candidate gene tests in QTL mapping populations must be interpreted with caution, we now have a clearer picture of the value of candidate gene tests in these populations.

Animals↗
PubMed1999

Linkage analysis by genotyping of sibling populations: a genetic map for the potato cyst nematode constructed using a "pseudo-F2" mapping strategy.

A mapping strategy is described for the construction of a linkage map of a non-inbred species in which individual offspring genotypes are not amenable to marker analysis. After one extra generation of random mating, the segregating progeny was propagated, and bulked populations of offspring were analyzed. Although the resulting population structure is different from that of commonly used mapping populations, we show that the maximum likelihood formula for a normal F2 is applicable for the estimation of recombination. This "pseudo-F2" mapping strategy, in combination with the development of an AFLP assay for single cysts, facilitated the construction of a linkage map for the potato cyst nematode Globodera rostochiensis. Using 12 pre-selected AFLP primer combinations, a total of 66 segregating markers were identified, 62 of which were mapped to nine linkage groups. These 62 AFLP markers are randomly distributed and cover about 65% of the genome. An estimate of the physical size of the Globodera genome was obtained from comparisons of the number of AFLP fragments obtained with the values for Caenorhabditis elegans. The methodology presented here resulted in the first genomic map for a cyst nematode. The low value of the kilobase/centimorgan (kb/cM) ratio for the Globodera genome will facilitate map-based cloning of genes that mediate the interaction between the nematode and its host plant.

Animals↗
PubMed2003

Constructing linkage maps in autotetraploid species using simulated annealing.

In this paper we demonstrate how molecular markers segregating in a full-sib autotetraploid mapping population can be ordered to form a linkage map using simulated annealing. This approach facilitates the examination of orders close to the optimum to see which marker placings are fixed and identify the markers whose position is less certain. A simulation study investigates the effects of population size, marker spacing, ratio of dominant to codominant markers, typing errors and missing values. The method is applied to map 30 amplified fragment length polymorphism and microsatellite markers on linkage group IV of potato.

Chromosome Mapping↗
PubMed2005

Power of in silico QTL mapping from phenotypic, pedigree, and marker data in a hybrid breeding program.

Most quantitative trait locus (QTL) mapping studies in plants have used designed mapping populations. As an alternative to traditional QTL mapping, in silico mapping via a mixed-model approach simultaneously exploits phenotypic, genotypic, and pedigree data already available in breeding programs. The statistical power of this in silico mapping method, however, remains unknown. Our objective was to evaluate the power of in silico mapping via a mixed-model approach in hybrid crops. We used maize (Zea mays L.) as a model species to study, by computer simulation, the influence of number of QTLs (20 or 80), heritability (0.40 or 0.70), number of markers (200 or 400), and sample size (600 or 2,400 hybrids). We found that the average power to detect QTLs ranged from 0.11 to 0.59 for a significance level of alpha=0.01, and from 0.01 to 0.47 for alpha=0.0001. The false discovery rate ranged from 0.22 to 0.74 for alpha=0.01, and from 0.05 to 0.46 for alpha=0.0001. As with designed mapping experiments, a large sample size, high marker density, high heritability, and small number of QTLs led to the highest power for in silico mapping via a mixed-model approach. The power to detect QTLs with large effects was greater than the power to detect QTL with small effects. We conclude that gene discovery in hybrid crops can be initiated by in silico mapping. Finding an acceptable compromise, however, between the power to detect QTL and the proportion of false QTL would be necessary.

Breeding↗
PubMed2006

A perennial ryegrass CBF gene cluster is located in a region predicted by conserved synteny between Poaceae species.

CBF/DREB1 proteins are the most important regulators of the cold temperature signaling pathway in many plants. CBF genes are candidates for low-temperature tolerance QTL in wheat and barley. Ten novel putative CBF cDNAs of perennial ryegrass (Lolium perenne L.) have been isolated from cold-treated leaf tissue. Their primary structures contain some conserved motifs, characteristic of the gene class. Phylogenetic analysis revealed that LpCBF genes were attributable to the HvCBF3-, and HvCBF4-subgroups following the previously proposed classification of barley CBF genes. RT-PCR analysis revealed that the expression of LpCBF genes was rapidly induced in response to low temperature and that the expression pattern under the low-temperature conditions for a long period was different between the various LpCBF genes. Five of the ten LpCBF genes were assigned to the genetic linkage map using the p150/112 reference mapping population. LpCBFIb, LpCBFII, LpCBFIIIb and LpCBFIIIc were mapped on LG5 forming a cluster within 2.2 cM, while LpCBFVb was located on LG1. Based on comparative genetic studies, conserved synteny for CBF gene family was observed between the Triticeae cereals and perennial ryegrass. Information on the perennial ryegrass CBF genes at both the molecular and genetic level obtained in this study would be useful for the further study on the role of CBF genes and low-temperature tolerance in grasses.

Amino Acid Sequence↗
PubMed2002

The identification of common haplotypes on bovine chromosome 5 within commercial lines of Bos taurus and their associations with growth traits.

The cosegregation between a genetic marker and the QTL in a well-designed mapping population is the basis for successful QTL mapping. Linkage disequilibria are, however, also expected among individuals that descended from the same breeding line, and some common haplotypes should carry on and segregate among individuals of the line. These identical by descent haplotypes make it possible to identify and locate the QTL segregating in the line. We report the identification of common haplotypes within commercial lines of Bos taurus and their associations with growth traits. One hundred and seventy six male calves and their 12 sires (9 to 30 male calves of each sire) of the Beefbooster, Inc., M1 line selected for maternal traits over 30 yr were genotyped using 16 microsatellite markers chosen from bovine chromosome 5 for the initial haplotype and growth association analysis. In order to verify the results from the M1 line, another 170 male calves and their 14 sires from the Beefbooster M3 line were genotyped using nine microsatellite markers chosen from bovine chromosome 5. The alleles of each male calf contributed by the sire and by the dam were identified, and haplotypes in the M1 line were established along 93% of bovine chromosome 5. The haplotypes in the M3 line were established along the chosen regions of bovine chromosome 5. Regression analysis detected 10 haplotypes in three chromosomal regions (0 to 30 cM, 55 to 70 cM, and 70 to 80 cM) that showed significant associations with birth weight, preweaning average daily gain, and average daily gain on feed in M1 line and 9 haplotypes associated with the growth traits in the same chromosomal regions in the M3 line at the comparisonwise threshold level. On average, the 19 haplotypes have an effect of 0.68 SD on the growth traits, ranging from 0.41 SD to 1.02 SD The results provide a useful reference for further positional candidate gene research and marker-assisted selection.

Alleles↗
PubMed2000

Linkage mapping and nucleotide polymorphisms of the 6-SFT gene of cool-season grasses.

Fructan plays an important role as an alternate carbohydrate and may contribute to drought and cold-stress tolerances in various plant species. The gene coding for sucrose:fructan 6-fructosyltransferase (6-SFT; EC 2.4.1.10), an enzyme that catalyzes the formation and extension of beta-2,6-linked fructans (levans), is important to fructan synthesis in many cool-season grasses, including cereal species. In this study, we compared a conserved sequence from the 6-SFT gene in barley with comparable sequences in 20 other cool-season grasses. We detected several DNA length polymorphisms, including variations in one simple-sequence repeat (SSR) in a 6-SFT intron of the barley cultivars Steptoe and Morex. Using the 'Steptoe' x 'Morex' doubled-haploid mapping population, the 6-SFT gene was genetically mapped to the distal region in the short arm of barley chromosome 1 (7H), where it is closely linked with trait locus Rpg1. Primers designed from other conserved regions of the barley 6-SFT gene successfully amplified 351- or 354-bp sequences of this gene from diverse cool season grass species. Sequence identities of the PCR products were greater than 80% among the 21 species. Phylogeny, as determined using these DNA sequences, is similar to that obtained from rDNA ITS sequences, and congruent with our current knowledge of genome relationships.

Base Sequence↗
PubMed2005

Characterization of rice mutants with enhanced susceptibility to rice blast.

As a first step towards identifying genes involving in the signal transduction pathways mediating rice blast resistance, we isolated 3 mutants lines that showed enhanced susceptibility to rice blast KJ105 (91-033) from a T-DNA insertion library of the japonica rice cultivar, Hwayeong. Since none of the susceptible phenotypes co-segregated with the T-DNA insertion we adapted a map-based cloning strategy to isolate the gene(s) responsible for the enhanced susceptibility of the Hwayeong mutants. A genetic mapping population was produced by crossing the resistant wild type Hwayeong with the susceptible cultivar, Nagdong. Chi-square analysis of the F2 segregating population indicated that resistance in Hwayeong was controlled by a single major gene that we tentatively named Pi-hy. Randomly selected susceptible plants in the F2 population were used to build an initial map of Pi-hy. The SSLP marker RM2265 on chromosome 2 was closely linked to resistance. High resolution mapping using 105 F2 plants revealed that the resistance gene was tightly linked, or identical, to Pib, a resistance gene with a nucleotide binding sequence and leucine-rich repeats (NB-LRR) previously isolated. Sequence analysis of the Pib locus amplified from three susceptible mutants revealed lesions within this gene, demonstrating that the Pi-hy gene is Pib. The Pib mutations in 1D-22-10-13, 1D-54-16-8, and 1C-143-16-1 were, respectively, a missense mutation in the conserved NB domain 3, a nonsense mutation in the 5th LRR, and a nonsense mutation in the C terminus following the LRRs that causes a small deletion of the C terminus. These findings provide evidence that NB domain 3 and the C terminus are required for full activity of the plant R gene. They also suggest that alterations of the resistance gene can cause major differences in pathogen specificity by affecting interactions with an avirulence factor.

Carrier Proteins↗
PubMed2006

[A simulated study on mapping QTL in a segregating sub-population].

For mapping QTLs, phenotypes of the traits in segregating population derived from the cross between two isogenic lines of the targeted QTL may reflect its genotype if the effect of the QTL is relatively large. In order to map the QTL, it is necessary to use a large sample under the high density of markers around the QTL. However, it increases experimental costs. In order to save the costs, it is possible to map the QTL using the sub-population that consists of plants with homogenous recessive. In this paper, the sub-population was used to estimate the recombination fraction between the marker and the QTL, and its standard error for F2, backcross (BC), double haploid (DH) and recombinant inbred lines (RIL) populations, respectively. The results from Monte Carlo simulation showed that the estimation of recombination fraction based on the sub-population is consistent with that obtained from the full population, and the precision of the former is same as that of the later under the same sample size.

Genetic Markers↗
PubMed2006

SNAP: Combine and Map modules for multilocus population genetic analysis.

We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) for working with DNA sequences sampled from populations. SNAP Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding insertions or deletions, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype-phenotype associations. SNAP Combine merges multiple DNA sequence alignments into a single multiple alignment file. The resulting file can be the union or intersection of the input files. SNAP Combine currently reads from and writes to several sequence alignment file formats including both sequential and interleaved formats. Combine also keeps track of the start and end positions of each separate alignment file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

Algorithms↗
PubMed2005

Molecular mapping of a fertility restorer gene for Owen cytoplasmic male sterility in sugar beet.

We report here the molecular mapping of a fertility restorer gene (named Rf1) for Owen cytoplasmic male sterility in sugar beet. Eight AFLP and two RAPD markers, tightly linked to the Rf1 locus, were identified using bulked segregant analysis. Three AFLP markers, mAFEM972, mAFEM976 and mAFEM985, were found to co-segregate with the Rf1 allele in our mapping populations. With the help of RFLP markers, previously mapped on the sugar beet genome, we showed that Rf1 is positioned in the terminal region of linkage group Kiel III/Koeln IV. This map location agrees well with that found for the restorer gene X, which suggests that the Rf1 locus corresponds to the X locus. The availability of the molecular markers will facilitate the selection of maintainer-pollinator lines in breeding program and provide the foundation for map-based cloning of the Rf1 gene.

Beta vulgaris↗
PubMed2004

Distribution of genomic regions differentiating oak species assessed by QTL detection.

Pedunculate oak and sessile oak are two sympatric interfertile species that exhibit leaf morphological differences. We aimed to detect quantitative trait loci (QTLs) of these traits in order to locate genomic regions involved in species differentiation. A total of 15 leaf morphological traits were assessed in a mixed forest stand composed of Quercus petraea and Q. robur and in a full-sib pedigree of Q. robur. The progeny of the full-sib family were vegetatively propagated in two successive experiments comprising 174 and 216 sibs, and assessments were made on two leaves collected on each of the 1080 and 1530 cuttings corresponding to the two experiments. Traits that exhibited strong species differences in the mixed stand tended also to have higher repeatability values in the mapping population, thus indicating higher genetic control. A genetic map was constructed for QTL detection. Composite interval mapping with the one QTL model was used for QTL detection. From one to three QTLs were detected for 13 traits. In-depth analysis of the QTLs, controlling the five morphological traits that exhibited the highest interspecific differences in the mixed stand, indicated that they were distributed on six linkage groups, with two clusters comprising QTLs of at least two discriminant traits. These results were reinforced when error 1 for QTL detection was set at 5% at the chromosome level, as up to nine clusters could be identified. In conclusion, traits involved in interspecific differentiation of oaks are under polygenic control and widespread in clusters across the genome.

Analysis of Variance↗