Molecular maps and DNA libraries are now possible to construct in nearly every horticultural crop. Comparison of linkage relationships both within and among families of flowering plants is giving us the capability to predict where genes will be even in crops lacking linkage maps. The dissection of quantitative traits into Mendelian components has been successfully performed in many crops, and candidate genes have occasionally been matched with QTLs or morphological mutations on the basis of map position. Breeders are now able to predict what combination of traits will be difficult to achieve as a result of repulsion phase linkage and what traits might be associated with problems due to linkage drag. Maps and libraries also help in identification of homologous genes in different species and gene-rich regions within a chromosome. More generally, DNA libraries are giving us access to every gene in a genome, leading to much more powerful studies concerning the anatomy, ontogeny and physiology of horticultural crops.
Apple scab, Venturia inaequalis (Cke.) Wint., is one of the most damaging diseases of apples. Although fungicide sprays have been used to control the disease, genetic resistance in existing commercially important varieties would be desirable. Identification of molecular marker(s) would be helpful in devising biotechnological approaches to control the disease. We used bulk segregant analysis to identify RAPD markers that cosegregate or display a tight linkage with Vf gene in Prima × Spartan cross. Using this approach, we are saturating the region around the scab resistance gene for the purpose of bracketing the locus. We have identified several markers associated with the Vf locus. The closest markers have been isolated and sequenced to be used as SCARs. The relationship and distances of the markers with the Vf locus and other previously reported markers will be discussed.
Two half-sib populations (cross 1 = `Wijcik McIntosh' (WM) × NY 75441-67, and cross 2 = WM × NY 75441-58) were used to create maps for the parents and to find RAPD or isozyme markers for qualitative and quantitative traits. WM is a sport of `McIntosh' and is heterozygous for the dominant columnar (Co) gene for reduced branching. WM is of great interest in breeding because of the tremendous effect of the Co gene on many aspects of plant form. NY 75441-67 and NY 75441-58 are advanced selections with commercial fruit quality and resistance to scab (Vf resistance from M. floribunda). Traits examined included both tree (plant height, stem diameter, suckering, branching habit, leaf break, burr knot production) and fruit (size, shape, color, stem length, seed number) characters and fruit quality traits (pH, acid content, Brix). The conservation of RAPD markers in these closely related crosses will be examined and the usefulness of molecular markers to preselect for components of plant form and fruit quality will be discussed. Molecular markers will increase the efficiency of the apple breeding program by aiding the understanding and manipulation of complex genetic traits.
The S alleles of 15 Japanese apple cultivars were determined by using the allele-specific polymerase chain reaction amplification and restriction enzyme digestion system developed by Janssens et al. (1995). Both S alleles were identified in eight diploid cultivars, two S alleles in three triploid cultivars, and one S allele in the remaining four diploid cultivars. Two cultivars had S alleles different than those predicted by their parentage, and in one comparison of a cultivar with its sport, an identity problem was discovered. The technique helped to indicate the parent contributing the unreduced gamete in triploids.
Molecular markers (isozyme and DNA) have been used to map apple and have helped to elucidate the inheritance of some morphological traits. In this project random amplified polymorphic DNA (RAPD) and isozyme markers were used to create maps for `Wijcik McIntosh, a columnar (reduced branching) sport of `McIntosh' and NY 75441-67, an advanced selection from the multiple disease resistance breeding program. NY 75441-67 is resistant to scab source of resistance from M. floribunda) and resistant to cedar apple rust. `Wijcik McIntosh' is being used in the breeding program as a source of the dominant gene, Co, for reduced branching, but there is also interest in this genotype because of the tremendous variation in plant form observed in progenies segregating for columnar habit. Some of these form variants may be of greater commercial interest than the parental material. Morphological traits examined in this progeny included plant height, stem diameter, suckering, branching habit, spur production, and internode length. The usefulness of molecular markers to pre-select for components of plant form is being examined. Molecular markers promise to aid our understanding and manipulation of quantitative morphological traits.
Five morphological and developmental traits (branching habit, vegetative budbreak, reproductive budbreak, bloom time, and root suckering) were analyzed in a family obtained from the apple (Malus domestica Borkh) cross `Rome Beauty' × `White Angel'. The phenotypic variation in these traits was compared with a selected set of marker loci covering the known genome of each of the parents to locate genes with major effects on the traits. The contrasting branching habits of the two parents appeared to be controlled by at least two loci. One of these, Tb, governed the presence or absence of lateral branches, particularly on the lower half of shoots. The locus was heterozygous in `White Angel' and was mapped to a 5 CM interval on linkage group 6. At least one other locus conditioning spur-type branching appeared to be segregating, but the locus or loci could not be linked to segregating markers. The timing of initial vegetative growth was tightly associated with the chromosomal region in which the Tb gene is located and maybe a pleiotropic effect of this gene. Time of reproductive budbreak correlated with segregation at the isozyme marker, Prx-c, on linkage group 5. Variation in time of bloom and later stages in flower development appeared to be controlled by different genes not linked to Prx-c. The tendency to produce root suckers cosegregated with a marker on `White Angel' linkage group 1, suggesting control by a single locus, Rs. Data from a `Rome Beauty' x `Robusta 5' family provided additional information on the inheritance of these traits.
Genetic linkage maps were created for three apple (Malus ×domestica Borkh.) cultivars using data from two progenies (`Wijcik McIntosh' xNY 75441-67 and `Wijcik McIntosh' xNY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated `Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the `Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The `Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ≈5.0 cM.
We mapped DNA polymorphisms generated by 41 sets of Simple Sequence Repeat (SSR) primers, developed independently in four laboratories. All primer sets gave polymorphisms that could be located on our `White Angel' x `Rome Beauty' map for apple [Malus sylvestris (L.) Mill. Var. domestica (Borkh.) Mansf.]. The SSR primers were used to identify homologous linkage groups in `Wijcik McIntosh', NY 75441-58, `Golden Delicious', and `Liberty' cultivars for which relatively complete linkage maps have been constructed from isozyme and Random Amplified Polymorphic DNA (RAPD) markers. In several instances, two or more SSRs were syntenic, and except for an apparent translocation involving linkage group (LG) 6, these linkages were conserved throughout the six maps. Twenty-four SSR primers were consistently polymorphic, and these are recommended as standard anchor markers for apple maps. Experiments on a pear (Pyrus communis L.) population indicated that many of the apple SSRs would be useful for mapping in pear. However some of the primers produced fragments in pear significantly different in size than those in apple.
Genetic analysis of 11 allozyme polymorphisms was performed on the progeny of ‘Cayuga White’ × ‘Aurora’, two complex interspecific grape (Vitis) hybrids. Segregation for most of the polymorphisms closely approximated monogenic Mendelian ratios, and eight new isozyme loci were defined for grape. Joint segregation analysis among the isozyme loci revealed three multilocus linkage groups. These results demonstrate that sufficient allozyme polymorphism exists in grape to establish many multilocus linkage groups and that this genetic analysis can be accomplished using extant progeny or progeny readily produced from highly heterozygous clones.