Cytological and molecular observations on Solanum phureja-induced dihaploid potatoes

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.

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.

Genome-wide Inference of Somatic Translocation Events During Potato Dihaploid Production

Potato ( L.) breeders often use dihaploids, which are 2× progeny derived from 4× autotetraploid parents. Dihaploids can be used in diploid crosses to introduce new genetic material into breeding germplasm that can be integrated into tetraploid breeding through the use of unreduced gametes in 4× by 2× crosses. Dihaploid potatoes are usually produced via pollination by haploid inducer lines known as in vitro pollinators (IVP). In vitro pollinator chromosomes are selectively degraded from initially full hybrid embryos, resulting in 2× seed. During this process, somatic translocation of IVP DNA may occur. In this study, a genome-wide approach was used to identify such events and other chromosome-scale abnormalities in a population of 95 dihaploids derived from a cross between potato cultivar Superior and the haploid inducing line IVP101. Most Superior dihaploids showed translocation rates of <1% at 16,947,718 assayable sites, yet two dihaploids showed translocation rates of 1.86 and 1.60%. Allelic ratios at translocation sites suggested that most translocations occurred in individual cell lineages and were thus not present in all cells of the adult plants. Translocations were enriched in sites associated with high gene expression and H3K4 dimethylation and H4K5 acetylation, suggesting that they tend to occur in regions of open chromatin. The translocations likely result as a consequence of double-stranded break repair in the dihaploid genomes via homologous recombination during which IVP chromosomes are used as templates. Additionally, primary trisomy was observed in eight individuals. As the trisomic chromosomes were derived from Superior, meiotic nondisjunction may be common in potato.

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits.

Epigenetics and its implications for plant biology 2. The 'epigenetic epiphany': epigenetics, evolution and beyond

SCOPE

In the second part of a two-part review, the ubiquity and universality of epigenetic systems is emphasized, and attention is drawn to the key roles they play, ranging from transducing environmental signals to altering gene expression, genomic architecture and defence.

KEY ISSUES

The importance of transience versus heritability in epigenetic marks is examined, as are the potential for stable epigenetic marks to contribute to plant evolution, and the mechanisms generating novel epigenetic variation, such as stress and interspecific hybridization.

FUTURE PROSPECTS

It is suggested that the ramifications of epigenetics in plant biology are immense, yet unappreciated. In contrast to the ease with which the DNA sequence can be studied, studying the complex patterns inherent in epigenetics poses many problems. Greater knowledge of patterns of epigenetic variation may be informative in taxonomy and systematics, as well as population biology and conservation.

Assessment of genetic variability of haploids extracted from tetraploid (2n = 4x = 48) Solanum tuberosum

The objectives of this study were to assess the genetic variability of haploids (2n = 2x = 24) extracted from tetraploid Solanum tuberosum through 4x x 2x crosses with Solanum phureja. Molecular and phenotypic analyses were performed to fingerprint the genotypes used and to evaluate their potential use in breeding programs. AFLP analysis revealed the presence of specific bands derived from the tetraploid seed parent S. phureja, as well as ex novo originated bands. On average, 210 bands were visualized per genotype, 149 (70%) of which were common to both parental genotypes. The percentage of S. tuberosum specific bands ranged from 25.1% to 18.6%, with an average of 22%. The fraction of genome coming from S. phureja ranged from 1.9% to 6.5%, with an average value of 4%. The percentage of ex novo bands varied from 1.9% to 9.0%. The presence of S. phureja DNA is very interesting because it indicated that S. phureja pollinator is involved in the mechanism of haploid formation. The characterization for resistance to Erwinia carotovora subsp. carotovora and potato virus X (PVX) provided evidence that haploids may express traits that are lacking in the tetraploids they come from, which can be useful for both genetic studies and breeding purposes. It is noteworthy that genotypes combining resistance to both diseases and good pollen stainability were identified. Other possible breeding implications owing to the presence of S. phureja genome in the haploids analyzed are discussed.

Molecular marker analysis of 24- and 25-chromosome plants obtained from Solanum tuberosum L. subsp. andigena (2n = 4x = 48) pollinated with a Solanum phureja haploid inducer

Clones with 24 or 25 chromosomes were obtained by pollinating an Andean cultivated tetraploid potato (Solanum tuberosum subsp. andigena clone 94H94, 2n = 4x = 48) with the Solanum phureja haploid-inducer clone 1.22. Their genetic composition was analyzed in an RAPD assay using 135 decamer primers and in an RFLP assay using 45 single-copy DNA probes. In total, 22 RAPD and 20 RFLP markers were found to be specific to S. phureja. None of these markers were found in the 24- and 25-chromosome clones. RFLP genotypes for the 45 RFLP loci were further determined for each clone. Genotypes of the 24-chromosome clones were characterized using two alleles randomly selected from four alleles of the parental tetraploid clone for almost all RFLP loci. Five 25-chromosome clones had extra alleles for all of the RFLP loci of chromosomes 4, 8, 10, 11, and 12, respectively, suggesting primary trisomy for one of these chromosomes. Clones with genotypes showing double reduction were also identified. Therefore, the obtained clones likely originated from random samples of female gametes, and hence are euhaploids or aneuhaploids of S. tuberosum subsp. andigena, strongly supporting parthenogenesis to be a primary mechanism for haploid induction in potato.

Examination of the leaf-drop symptom of virus-infected potato using anther culture-derived haploids

ABSTRACT Necrotic lesions and vein necrosis characteristic of the hypersensitive response (HR) controlled by the dominant resistance gene Ny develop in potato cv. Pito after infection with potato virus Y ordinary strain (PVY masculine) at a low temperature (16/18 degrees C night/day). In contrast, at high temperatures (19/24 degrees C night/day), large coalesced lesions develop in the lower infected leaves, which wither and remain hanging from stems forming the leaf-drop symptom; mosaic symptoms with no necrosis also develop in the top leaves. The genetic basis of the leaf-drop symptom and its dependence on temperature were examined using a novel approach involving 58 haploids (2n = 24) derived from 'Pito' (2n = 48) through anther culture. These haploids and 'Pito' were graft-inoculated with PVY(O) at 19/24 to 25 degrees C (night/day). Necrotic symptoms were expressed in 28 haploids, of which 18 haploids (phenotype class N) developed top necrosis, vein necrosis, or both and necrotic lesions that are characteristic of HR. Ten haploids showed leaf drop similar to 'Pito' (phenotype class LD). Thirty haploids were susceptible and showed only mosaic symptoms (phenotype class S). These data indicated that necrosis was induced by a single dominant gene, Ny, in the simplex condition. However, the three distinct phenotypic classes (N, LD, and S) among the haploids grown under the same environmental conditions showed that another locus (gene) was involved in modifying the HR triggered by Ny. Data suggested that this locus contains a dominant temperature-dependent modifier (Tdm) gene that alters the expression of PVY-induced HR at higher temperatures, resulting in leaf drop.

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.

Molecular characterisation of inter- and intra-specific somatic hybrids of potato using randomly amplified polymorphic DNA (RAPD) markers

Protoplast fusion allows the transfer of both mono- and polygenic traits between species that are sexually incompatible. This approach has particular relevance for potato, and somatic hybridisation has been used to introduce a range of disease resistance genes from sexually incompatible wild species into the cultivated potato gene pool. In addition, protoplast fusion allows the resynthesis of tetraploid genotypes from preselected diploid or dihaploid donor parents. A limiting factor for the efficient exploitation of this technology in potato breeding is the difficulty of unequivocally identifying nuclear hybrids (heterokaryons). In order to facilitate the identification of hybrids at an early stage following fusion, Randomly Amplified Polymorphic DNA markers (RAPDs) have been used to characterise molecularly both inter- and intra-specific somatic hybrids of potato. RAPD markers detect naturally occurring polymorphism in the donor genotypes and utilise short oligonucleotide primers of arbitrary nucleotide sequence in combination with the polymerase chain reaction (PCR). The exploitation of RAPDs in the characterisation of both somatic and sexual hybrids is discussed.