The use of RAPD markers for the detection of gene introgression in potato

Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x - 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the HI parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual HI DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.

Random Amplified Polymorphic DNA (RAPD) and Derived Techniques

Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selection of core collections, determination of genetic distances, genome analysis, development of molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest, is cost-effective, and can be performed in a moderate laboratory for most of its applications. In addition, RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like arbitrarily primed polymerase chain reaction (AP-PCR), sequence characterized amplified region (SCAR), DNA amplification fingerprinting (DAF), sequence-related amplified polymorphism (SRAP), cleaved amplified polymorphic sequences (CAPS), random amplified microsatellite polymorphism (RAMPO), and random amplified hybridization microsatellites (RAHM) can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented along with the applications of RAPD in genetic diversity analysis, mapping, varietal identification, genetic fidelity testing, etc.

Genomic Outcomes of Haploid Induction Crosses in Potato (Solanum tuberosum L.)

The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.

Randomly amplified polymorphic DNA (RAPD) and derived techniques

Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, developing molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest and cost-effective and can be performed in a moderate laboratory for most of its applications. In addition RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like AP-PCR, SCAR, DAF, SRAP, CAPS, RAMPO, and RAHM can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented.

Genetic variability and phytogeography of Miscanthus sinensis var. condensatus, an apomictic grass, based on RAPD fingerprints

DNA fingerprinting using random amplified polymorphic DNA (RAPD) markers was employed to investigate the genetic variation within and among populations of Miscanthus Anderss. sinensis var. condensatus (Hack.) Makino, an apomictic grass distributed along the coasts of Taiwan and Ryukyu Islands. A total of 250 plants from three Taiwanese populations (Southeast Coast, Orchid Islet, and Green Islet) and two populations from Ryukyu (Ishigaki and Amami-O-Shima Islets) were sampled. The amplified products of 40 random primers showed monomorphic banding patterns within all populations as well as among the three populations from Taiwan. Low genetic variation (with only two polymorphic loci), but significant differentiation, was detected between populations from Taiwan and Ryukyu (ΦCT = 0.864) and between populations (ΦST = 1.0) from Ishigaki and Amami-O-Shima Islets. In contrast, a high level of variation was exhibited in the outcrossing Miscanthus sinensis var. glaber (Nakai) Li. In addition to apomictic reproduction, low genetic variation across populations of M. sinensis var. condensatus may be a result of high salinity acting as a selective agent. With the cost of reduced genetic heterogeneity, apomixis may have provided a mechanism for avoiding the transmission of endophytic fungi. The phytogeographic pattern of M. sinensis var. condensatus, as reflected by the RAPD data, likely represents isolation between Taiwan and Ryukyu since the mid-Pleistocene.Key words: apomixis, Miscanthus sinensis var. condensatus, phytogeography, population differentiation, RAPD, system of mating.

Evidence for somatic translocation during potato dihaploid induction

Potato dihaploid PDH55 (Solanum tuberosum) is exclusively euploid (2n = 24) but apparently contains and expresses DNA from dihaploid inducer IVP48 (S. phureja). Genomic in situ hybridization (GISH) suggested IVP48 DNA incorporated stably into PDH55 by somatic translocation. This finding has two important implications. Firstly, the long-held implicit assumption that euploid dihaploids produced by dihaploid inducers are pure S. tuberosum seems incorrect. This may complicate meiotic, genetical and molecular studies involving potato dihaploids. Secondly, if such translocations are not rare, the phenomenon may offer a novel way to introduce useful traits directly from wild dihaploid-inducing species into S. tuberosum.

Random-amplified-polymorphic DNA markers in sorghum

Conditions have been identified that allow reproducible amplification of RAPD markers in sorghum. High resolution of RAPD markers was accomplished by radiolabeling PCR-amplified DNAs followed by separation on denaturing 5% polyacrylamide gels. Reaction parameters including MgCl2 concentration and temperature significantly influenced yield and the type of amplification products synthesized. Unexplained amplified DNAs increased when more than 35 cycles of PCR amplification were used. Under standard conditions, approximately 80% of the primers tested amplified DNA, and most revealed 1-5 polymorphisms between BTx 623 and IS 3620C. Primers were used to amplify RAPDs in 32 genotypes of sorghum. In addition, 8 primers detected RAPDs in a population previously used to create an RFLP map for sorghum. These RAPDs were mapped successfully using a population of 50 F2 plants.

Detection of genetic diversity within snail intermediate hosts of the genus Bulinus by using random amplified polymorphic DNA markers (RAPDs)

A polymerase chain reaction-based polymorphic assay procedure (RAPD) was used to study the genetic diversity of intermediate host snails within the genus Bulinus. Genetic differentiation was detected between two closely related species: Bulinus globosus and Bulinus umbilicatus. Evidence is presented demonstrating the potential of RAPD markers for differentiating populations of B. forskalii from different countries (Cameroon, Equatorial Guinea and Ivory Coast) or from the same country (Cameroon). RAPDs may be also used to identify offspring from cross- and self-fertilized hermaphrodite bulinid snails. RAPDs provide a cost-effective and routine method for genetic studies of snails transmitting schistosomiasis and for the evaluation of diversity between snail populations.