Molecular Marker Map Research Articles

An intervarietal molecular marker map in Triticum aestivum L. Em. Thell. and comparison with a map from a wide cross

An intervarietal molecular marker map covering most of the nuclear genome was developed in Triticum aestivum. One hundred and six androgenetic-derived doubled haploid lines obtained from the F1 between monosomics of ‘Chinese Spring’ and ‘Courtot’ were analysed for genetic mapping. The map covered 18 of the 21 chromosomes with an identical distribution of markers in the A and B genome, and only small segments of the D genome. Distorted markers were mapped using Bailey’s 2-point method and revealed skewed regions on 1A, 1DS, 2A, 2B, 4AS and 6B. Comparison with a wide cross [‘Opata’×Synthetic hexaploid (T. tauschii/‘Altar 84’)] showed colinearity for markers on homologous chromosomes, but revealed a large proportion (25%) of markers mapped on non-homoeologous chromosomes, i. e. heterologous markers. The origin of the material and distortion segregation are discussed with particular emphasis on investigations of D-genome markers.

Progress in Prunus Mapping and Application of Molecular Markers to Germplasm Improvement

Progress in Prunus Mapping and Application of Molecular Markers to Germplasm Improvement

Aroma in rice: genetic analysis of a quantitative trait

A new approach was developed which succeeded in tagging for the first time a major gene and two QTLs controlling grain aroma in rice. It involved a combination of two techniques, quantification of volatile compounds in the cooking water by gas chromatography, and molecular marker mapping. Four types of molecular marker were used (RFLPs, RAPDs, STSs, isozymes). Evaluation and mapping were performed on a doubled haploid line population which (1) conferred a precise character evaluation by enabling the analysis of large quantities of grains per genotype and (2) made possible the comparison of gas chromatography results and sensitive tests. The population size (135 lines) provided a good mapping precision. Several markers on chromosome 8 were found to be closely linked to a major gene controlling the presence of 2-acetyl-1-pyrroline (AcPy), the main compound of rice aroma. Moreover, our results showed that AcPy concentration in plants is regulated by at least two chromosomal regions. Estimations of recombination fractions on chromosome 8 were corrected for strong segregation distortion. This study confirms that AcPy is the major component of aroma. Use of the markers linked to AcPy major gene and QTLs for marker-assisted selection by successive backcrosses may be envisaged.

Quantitative Trait Loci Determining Resistance to Bacterial Wilt in Tomato Cultivar Hawaii7996

Several loci governing resistance to bacterial wilt, a disease caused by Ralstonia solanacearum, have been mapped in tomato (Lycopersicon esculentum). An F2 population derived from a cross between a highly resistant cultivar, Hawaii7996, and a very susceptible line of L. pimpinellifolium, WVa700, was used to develop a map of molecular markers. The parental lines were screened for polymorphism using 462 RFLP probes with 14 restriction enzymes. Genetic mapping revealed that the distribution of polymorphisms was very uneven. Nevertheless, the extensive screening permitted development of a map covering much of the genome. Nine independent resistance tests were done on cuttings from plants of this population in a controlled environment culture chamber. In addition to the most important QTL detected on chromosome 6, analyses of our data using either nonparametric or interval mapping tests suggest the presence of another QTL on chromosome 4 (2 QTL) and weaker putative QTL at other map positions. Together these loci, all derived from the resistant parent Hawaii7996, account for 30 to 56% of the phenotypic variation observed.

Progress in Prunus Mapping and Application of Molecular Markers to Germplasm Improvement

Prunus, which includes peach/nectarine, almond, apricot, cherry, and plum, is a large and economically important genus in the family Rosaceae. The size and long generation time of these tree crops have hampered improvement through classical breeding and long-term selection programs. With the advent of DNA-based molecular diagnostics, an exciting era in germplasm improvement has dawned. Efforts are underway, notably in the United States (e.g., California, Michigan, North Carolina, and South Carolina) and the European Community (e.g., England, France, Italy, and Spain), to apply the tools of molecular mapping and marker-assisted selection to this important genus. The objective of these projects is to develop molecular linkage maps of sufficient marker density to tag phenotypic trait loci of agronomic importance. These include traits controlled by single genes (e.g., flower color, compatibility, flesh color, pest resistance), as well as more-complex, quantitative traits (e.g., cold hardiness, tree architecture, sugar content). An immediate outcome of these mapping efforts has been the development of DNA “fingerprints,” allowing for the discrimination of cultivars—both scion and rootstock. The maps will be used by breeders and molecular biologists to monitor gene introgression from wild species into elite lines, for marker-assisted selection of desired trait combinations, and for map-based cloning of specific genes. The molecular markers used in these mapping projects include RFLPs, RAPDs, and microsatellites. Each has their appropriate applications and advantages depending upon the resources at hand and the project's specific goals.

Molecular mapping of wheat. Homoeologous group 3

A prerequisite for molecular level genetic studies and breeding in wheat is a molecular marker map detailing its similarities with those of other grass species in the Gramineae family. We have constructed restriction fragment length polymorphism maps of the A-, B-, and D-genome chromosomes of homoeologous group 3 of hexaploid wheat (Triticum aestivum L. em. Thell) using 114 F7-8 lines from a synthetic x bread wheat cross. The map consists of 58 markers spanning 230 cM on chromosome 3A, 62 markers spanning 260 cM on 3B, and 40 markers spanning 171 cM on 3D. Thirteen libraries of genomic or cDNA clones from wheat, barley, and T. tauschii, the wheat D genome donor, are represented, facilitating the alignment and comparison of these maps with maps of other grass species. Twenty-four clones reveal homoeoloci on two of the three genomes and the associated linkages are largely comparable across genomes. A consensus sequence of orthologous loci in grass species genomes is assembled from this map and from existing maps of the chromosome-3 homoeologs in barley (Hordeum spp.), T. tauschii, and rice (Oryza spp.). It illustrates the close homoeology among the four species and the partial homoeology of wheat chromosome 3 with oat (Avena spp.) chromosome C. Two orthologous red grain color genes, R3 and R1, are mapped on chromosome arms 3BL and 3DL.

Plant Genomes: A Current Molecular Description

A major advance in plant genome analysis has been the development of molecular marker maps. These, in combination with repeated sequence analysis, have given considerable insight into the organization and evolution of many plant genomes. Physical mapping and sequencing of the genomes of the model plant species Arabidopsis thaliana and rice are progressing rapidly. The physical maps facilitate the isolation of genes by map-based cloning and will enable the organization of whole chromosomes to be analyzed. Comparative mapping studies between related plant species, using common sets of molecular markers, have revealed extensive collinearity over short chromosomal segments or whole chromosomes. Thus, in the future, collinearity as well as homology may be used to clone genes from many plant species, maximally exploiting the A. thaliana or rice physical maps.

Plant Genomes: A Current Molecular Description

A major advance in plant genome analysis has been the development of molecular marker maps. These, in combination with repeated sequence analysis, have given considerable insight into the organization and evolution of many plant genomes. Physical mapping and sequencing of the genomes of the model plant species Arabidopsis thaliana and rice are progressing rapidly. The physical maps facilitate the isolation of genes by map-based cloning and will enable the organization of whole chromosomes to be analyzed. Comparative mapping studies between related plant species, using common sets of molecular markers, have revealed extensive collinearity over short chromosomal segments or whole chromosomes. Thus, in the future, collinearity as well as homology may be used to clone genes from many plant species, maximally exploiting the A. thaliana or rice physical maps.

RFLP mapping of Brassica napus using doubled haploid lines

The combined use of doubled haploid lines and molecular markers can provide new genetic information for use in breeding programs. An F1-derived doubled haploid (DH) population of Brassica napus obtained from a cross between an annual canola cultivar ('Stellar') and a biennial rapeseed ('Major') was used to construct a linkage map of 132 restriction fragment length polymorphism loci. The marker loci were arranged into 22 linkage groups and six pairs of linked loci covering 1016 cM. The DH map was compared to a partial map constructed with a common set of markers for an F2 population derived from the same F1 plant, and the overall maps were not significantly different. Comparisons of maps in Brassica species suggest that less recombination occurs in B. napus (n = 19) than expected from the combined map distances of the two hypothesized diploid progenitors, B. oleracea (n = 9) and B. rapa (n=10). A high percentage (32%) of segregating marker loci were duplicated in the DH map, and conserved linkage arrangements of some duplicated loci indicated possible intergenome homoeology in the amphidiploid or intragenome duplications from the diploid progenitors. Deviation from Mendelian segregation ratios (P < 0.05) was observed for 30% of the marker loci in the DH population and for 24% in the F2 population. Deviation towards each parent occurred at equal frequencies in both populations and marker loci that showed deviation clustered in specific linkage groups. The DH lines and molecular marker map generated for this study can be used to map loci for agronomic traits segregating in this population.

Mapping of Molecular Markers on Brassica B‐Genome Chromosomes Added to Brassica napus

AbstractUsing interspecific hybridization among various Brassica species, B‐genome chromosomes from different sources of Brassica, i.e. B. nigra (BB, 2n = 18), B. carinata (BBCC), 2n = 34) and B. juncea (AABB, 2n = 36) were transferred into the Canadian variety ‘Andor’ of B. napus. Monosomic addition lines were selected (AACC + 1B, 2n = 39) by cytological control. For characterization of the alien chromosomes, series of isozymes, RFLPs and RAPD markers were employed. This permitted the identification of a total of 39 lines representing seven of the eight B‐genome chromosomes.

Molecular variation and restriction fragment length polymorphisms (RFLPs) within and between six species of Verticillium

Molecular variation within and between six species belonging to the fungal genus Verticillium has been examined, either by direct visualization of strongly fluorescing bands in DNA digests or by probing Southern blots with rDNA, mtDNA or random genomic clones derived from an isolate of V. albo-atrum . The two main plant pathogenic species studied, V. albo-atrum and V. dahliae , could be differentiated from each other and from the other four species by the direct visualization approach, although the bands were not always easily seen against the background smear of single or low copy number fragments. Variation was also revealed by probing with rDNA or mtDNA but this variation was generally not correlated with identified interspecific or intraspecific taxonomic groupings. When Southern blots were probed with random genomic clones, all isolates of V. albo-atrum originating from lucerne were clearly differentiated from all other isolates of this species tested which originated from a range of other hosts. There was, however, little variation within these two groups of V. albo-atrum isolates. V. dahliae was clearly differentiated from V. albo-atrum by probing with random genomic clones and considerable variation within this species was evident. Only a few other taxon-specific polymorphisms were identified when using the limited set of probes tested but others may be located when more probes have been examined. The location of genes involved in important attributes such as pathogenicity will require the construction of linkage maps of molecular markers and genes of interest. The results suggest that for the analysis of V. albo-atrum the most useful parasexual cross would be between a lucerne and a non-lucerne isolate and that for the analysis of V. dahliae sufficiently disparate pairs of isolates exist.