A test of the maximum heterozygosity hypothesis using molecular markers in tetraploid potatoes

It has been theorized that in cross-pollinated polyploid species hybrid vigor is maximized by the frequent occurrence of more than two alleles per chromosomal locus. In polyploid crops this condition of maximum heterozygosity has been reported to be associated with increased yield and optimum field performance. We report herein the first direct test of the maximum heterozygosity hypothesis. Molecular markers were used to examine the association between maximum heterozygosity and several components of yield in three different populations of tetraploid potatoes. The results indicate that the value of maximum heterozygosity is not universal but dependent on the genetic background of the material under evaluation. In a cross between adapted breeding lines, homozygosity was negatively correlated with tuber yield, and maximum heterozygosity was positively correlated with the proportion of tuber yield in the large-size fraction. In contrast, in crosses between adapted and unadapted parents, maximum heterozygosity had no detectable effect on any character. Quantitative trait locus (QTL) analysis of the three populations reveals that, regardless of the genetic background, additive genetic effects are more strongly correlated with the components of yield than are any measures of heterozygosity and that some common QTLs may be influencing yield in all three populations.     

An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning

The isolation of high quality megabase DNA from plant cells that is susceptible to a variety of molecular reagents is a critical first step in the physical analysis of complex genomes. A method for the isolation of such DNA by encapsulating plant protoplasts in agarose microbeads is presented. In comparison with the conventional agarose plug method, microbeads provide a dramatic increase in the surface area yielding megabase DNA that can be treated essentially as an aqueous DNA solution. Examples of the utility of DNA prepared by this technique for physical mapping, partial restriction enzyme digestion and cloning of large inserts as YACs are presented.     

Optimizing parental selection for genetic linkage maps.

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.     

fw 2.2:a major QTL controlling fruit weight is common to both red- and green-fruited tomato species

We have shown that a major QTL for fruit weight (fw2.2) maps to the same position on chromosome 2 in the green-fruited wild tomato species, Lycopersicon pennellii and in the red-fruited wild tomato species, L. pimpinellifolium. An introgression line F₂ derived from L. esculentum (tomato) x L. pennellii and a backcross 1 (BC₁) population derived from L. esculentum x L. pimpinellifolium both place fw2.2 near TG91 and TG167 on chromosome 2 of the tomato highdensity linkage map. fw2.2 accounts for 30% and 47% of the total phenotypic variance in the L. pimpinellifolium and L. pennellii populations, respectively, indicating that this is a major QTL controlling fruit weight in both species. Partial dominance (d/a of 0.44) was observed for the L. pennellii allele of fw 2.2 as compared with the L. esculentum allele. A QTL with very similar phenotypic affects and gene action has also been identified and mapped to the same chromosomal region in other wild tomato accessions: L. cheesmanii and L. pimpinellifolium. Together, these data suggest that fw2.2 represents an orthologous QTL (i.e., derived by speciation as opposed to duplication) common to most, if not all, wild tomato species. High-resolution mapping may ultimately lead to the cloning of this key locus controlling fruit development in tomato.     

An Interspecific Backcross of Lycopersicon Esculentum X L. Hirsutum: Linkage Analysis and a Qtl Study of Sexual Compatibility Factors and Floral Traits

A BC(1) population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was primarily the result of mutations at the S locus. Moreover, the major QTL controlling unilateral incongruity also mapped to the S locus, supporting the hypothesis that self-incompatibility and unilateral incongruity are not independent mechanisms. The mating behavior of near-isogenic lines carrying the L. hirsutum allele for the S locus on chromosome 1 in an otherwise L. esculentum background support these conclusions. The S locus region of chromosome 1 also harbors most major QTL for several floral traits important to pollination biology (e.g., number and size of flowers), suggesting a gene complex controlling both genetic and morphological mechanisms of reproduction control. Similar associations in other flowering plants suggest that such complex may have been conserved since early periods of plant evolution or else reflect a convergent evolutionary process.     

Overcoming crossing barriers between nontuber-bearing and tuber-bearing Solanum species: towards potato germplasm enhancement with a broad spectrum of solanaceous genetic resources.

The first direct sexual hybrids between diploid nontuber-bearing species and diploid potato breeding lines are reported here. Three nontuberous species of Solanum, S. brevidens, S. etuberosum, and S. fernandezianum, were used for sexual crosses, achieved by a combination of rescue pollinations and embryo rescue. Initial hybrid selection was made using an embryo spot marker, followed by the evaluation of morphological and reproductive traits. Putative hybrids were first tested for resistance to potato leaf roll virus derived from the wild species, and then were tested with molecular markers using species-specific DNA probes. Finally, the tuberization of several 2x hybrids was tested for actual potato germplasm enhancement. These hybrids are unique in terms of their potential to enhance recombination between chromosomes of wild species and those of cultivated potatoes in germplasm utilization, and to exploit the genetic nature of tuber formation. The finding that nontuber-bearing Solanum spp. can be directly crossed with tuber-bearing species also has important implications for the regulatory aspects of the use of genetically modified organisms.     

Molecular markers for four leaf rust resistance genes introgressed into wheat from wild relatives.

Near-isolines carrying four different genes for resistance to leaf rust were used to find linked molecular markers for these genes. Clones used to detect polymorphism were selected on the basis of the reported chromosomal location of the resistance genes. Both Lophopyron-derived resistance genes, Lr19 and Lr24, cosegregated with eight molecular markers assigned to chromosomes 7DL and 3DL, respectively. One clone cosegregated with Lr9 and two closely linked RFLP markers were found for Lr32, mapping at 3.3 +/- 2.6 and 6.9 +/- 3.6 cM from the resistance gene. The Lophopyron-chromatin segment in isolines carrying chromosomes 7E (Lr19) and 3E (Lr24) replaced a large portion of chromosome 7D and the distal portion of chromosome 3D, respectively. Clones assigned to these chromosomes on the basis of aneuploid analysis hybridized to 7E and 3E segments, thus confirming cytological results that these introgressed segments represent homoeologous chromosomes. The linked RFLP markers could be used to identify the resistance genes and generate new combinations in breeding populations, especially in the absence of disease in the environment or when virulence is lacking.     

Linkage relationships and chromosomal locations of enzyme-coding genes in pepper,Capsicum annuum

The linkage relationships and chromosomal locations of 14 enzyme-coding genes were investigated in Capsicum annuum L. (garden pepper) by monitoring segregations in backcross and F₂ progeny of an interspecific cross between C. annuum cv. NM6-4 and C. chinense CA4 and by studying allele dosage effects in five hybrid primary trisomics. These conclusions can be reached: 6Pgdh-i is on the metacentric chromosome corresponding to the noir trisomie; Idh-1 and Est-3 are on chromosome 12; an aerocentric chromosome which corresponds to the pourple trisomie; Idh-1 is near the centromere and Est-3 is distal on the long arm of that chromosome. The other loci can be arranged in the following linkage groups and are apparently not located on the trisome corresponding to any of the trisomics tested: Est-4-18cM-(Pgi-1-3cM-Pgm-1); Prx-7-2cM-Tk-1; Pgm-2-2cM-Skdh-1; Est-1-OcM-Est-7. Linkage and dosage data combined with karyotype and meiotic analyses of the two species and F₁ hybrids suggest that Idh-1 and Skdh-1/Pgm-2 are near the breakpoints on the two chromosomes involved in a reciprocal translocation for which the two species differ. One locus, Pgm-3, was detected only in C. annuum cultivars and is apparently the result of a duplication of Pgm-2 which codes for cytosolic phosphoglucomutase activity. Pgm-2 and Pgm-3 are not tightly linked (approximately 20% recombination) which supports the proposal that Pgm-3 originated from a mechanism other than unequal crossing over. A comparison of the linkage relationships of enzyme-coding genes in pepper with those of putative orthologous loci in tomato reveals that two linkage blocks, Est-1-Est-7 and Pgi-1-Est-4, may have remained intact since the divergence of Capsicum and Lycopersicon.     

Genetics of esterases in species of Lycopersicon

Summary Improvements in plant culture and electrophoretic technique permit detection and genetic analysis of seven esterase loci in Lycopersicon esculentum and related species with homosequential chromosomes. At all of these loci except one, each allele codes for a single anodal band, and the electrophoretic variants are inherited in monogenic fashion. For the exceptional Est-4, allozymes are 1–3 banded in various combinations at four positions, and rare recombinants in one cross appeared at a frequency of 0.0005, suggesting the existence of several very tightly linked genes. Est-2 segregated solely for intensity differences in dominant/recessive fashion; Est-3 and Est-4 behave as monomers; the remaining Est-l, 5, 6, and 7 — coding for contiguous bands in the region closest to the origin — are dimeric. The latter group are tightly linked inter se in the proximal portion of 2L (long arm of chromosome 2), the total map distance of the complex being approximately 1.5 cM; Est-2 is situated on 9L between ah and marm; Est-3 on 1L between inv and dgt; Est-4 has not yet been located. Even in the interspecific hybrids, map distances are similar to the standard values for L. esculentum. Tandem duplication is hypothesized for the origin of the Est-l, 5–7 complex, which adds another example to the growing list of linked mimic genes in the tomato genome. In respect to the position of their bands and tight inter se linkage, this series exactly parallels the EA, EB, EC esterase series in Hordeum vulgare — a fact which suggests great antiquity for this block of genes.     

High Density Molecular Linkage Maps of the Tomato and Potato Genomes

High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.