Phenotypic variation and ploidy level of plants regenerated from protoplasts of tetraploid potato (Solanum tuberosum L. cv. 'Bintje')

Haplotype-resolved genome analyses of a heterozygous diploid potato

Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.

Generation of self-compatible diploid potato by knockout of S-RNase

Re-domestication of potato into an inbred line-based diploid crop propagated by seed represents a promising alternative to traditional clonal propagation of tetraploid potato, but self-incompatibility has hindered the development of inbred lines. To address this problem, we created self-compatible diploid potatoes by knocking out the self-incompatibility gene S-RNase using the CRISPR-Cas9 system. This strategy opens new avenues for diploid potato breeding and will also be useful for studying other self-incompatible crops.

Genome composition of asymmetric hybrids in relation to the phylogenetic distance between the parents. Nucleus-chloroplast interaction

A series of fusion experiments were performed between protoplasts of a cytoplasmic albino mutant of tomato, Lycopersicon esculentum (ALRC), and gamma-irradiated protoplasts of L. hirsutum and the Solanum species S. commersonii, S. etuberosum and S. nigrum. These species were chosen for their different phylogenetic relationships to tomato. In all fusion combinations except from those between ALRC and S. nigrum, green calli were selected as putative fusion products and shoots regenerated from them. They were subsequently analyzed for their morphology, nuclear DNA composition and chloroplast DNA origin. The hybrids obtained between ALRC and L. hirsutum contained the chloroplasts of L. hirsutum and had the flower and leaf morphology of L. esculentum. After Southern blot analysis, using 13 restriction fragment length polymorphisms (RFLPs) randomly distributed over all chromosomes, all hybrids showed L. esculentum hybridization patterns. No chromosomes of L. hirsutum were found. These results indicate that these hybrids were true cybrids.The putative asymmetric hybrids, obtained with S. commersonii and S. etuberosum, showed phenotypic traits of both parents. After hybridization with species-specific repetitive nuclear DNA probes it was found that nuclear material of both parents was present in all plants. In the case of S. nigrum, which combination has the greatest phylogenetic distance between the fusion parents, no hybrid plants could be obtained. The chloroplast DNA of all hybrid plants was of the donor type suggesting that chloroplast transfer by asymmetric protoplast fusion can overcome problems associated with large phylogenetic distances between parental plants.

Somaclonal variation in tuber disc-derived populations of potato : I. Evidence of genetic stability across tuber generations and diverse locations

Approximately 1,600 potato (Solanum tuberosum L.) plants of the cultivar 'Superior' were regeneratedin vitro from meristems adventitiously initiated on tuber disc expiants. Direct regeneration from tuber disc cells, by passing a callus intermediary, is efficient and results in low frequencies of plants with gross phenotypic aberrations. The somaclonal plant population was statistically characterized in field plots over five asexual generations and in three diverse locations. When compared in advanced generations to a large population of control plants propagated from stem cuttings, the means of the somaclonal population were significantly different, often shifted in the desirable direction, for 16 of 22 horticulturally important traits. Somaclonal population variances statistically exceeded those of the controls for 13 of the 22 traits. Regressions between consecutive tuber generations and between locations or replications (blocks) within a generation were significant in the somaclonal population for all traits analyzed. In a few instances, significant control population regressions occurred that are interpreted to be the result of non-random, non-genetic factors primarily affecting control plants of low vigor. Selected somaclones exhibiting desirable alterations for yield, tuber number and shape, and vigor were stable over more than two consecutive asexual generations.

Insect-resistant plants with improved horticultural traits from interspecific potato hybrids grown in vitro

Plants were regenerated from petiole calli of interspecific hybrids of Solanum tuberosum x S. berthaultii, an insect-resistant wild species. Callus culture was used to generate genetic changes to overcome the restricted recombination between the two genomes. Two plants out of 58 (3.5%) from calli of hybrid J114-1 showed stable and heritable differences from the hybrid over two cycles of evaluations in the field. Replicated trials were conducted in 1987 and 1988, using two populations of plants propagated by nodal cuttings from the original regenerates maintained in vitro. One regenerate showed insect resistance and increased marketable yield (approximately two fold) in the field. The other had higher levels of phenolic exudate in one of the two types of foliar trichomes associated with the insect resistance mechanism. Some desirable changes were discernible only in sexual progeny of regenerates, not in the regenerates themselves. In a backcross to S. tuberosum, 7 of 14 (50%) regenerates from hybrid F743-4 showed more progeny (up to 15-fold) with improved trichome traits and horticultural characteristics than the original hybrid. The variations were not associated with changes in ploidy. Fifteen plants obtained from these crosses are currently being incorporated into breeding lines. These results suggest that a period of callus culture followed by plant regeneration may aid in the introgression of desirable traits from wild species into crop plants.

Transfer of cytoplasm from newBeta CMS sources to sugar beet by asymmetric fusion : 1. Shoot regeneration from mesophyll protoplasts and characterization of regenerated plants

For our program on the transfer of cytoplasmic male sterility (CMS) by cybridization inBeta vulgaris L. (sugar beet), we have developed a procedure for the isolation and culture of mesophyll protoplasts of sugar beet followed by shoot regeneration. A prerequisite proved to be the presence in the media of n-propylgallate (nPG), a lipoxygenase inhibitor. Sustained divisions were found in all accessions that were tested. Plating efficiencies and regeneration ability varied greatly from one experiment to the other and appeared to be accession-dependent. Shoots could be easily transferred to soil. A majority of the regenerants (72%) retained the diploid chromosome number. Somaclonar variation in phenotype was low (4.9%). Mitochondrial DNA probes, capable of discriminating different cytoplasms ofBeta spp. showed no rearrangements due to the protoplast and in vitro culture phase, indicating that these probes can be used to identify cybrids after asymmetric fusions. The data presented here open up possibilities for genetic engineering using protoplasts in one of the world's most important arable crops.

Selection of somatic hybrids between diploid clones of potato (Solanum tuberosum L.) transformed by direct gene transfer

Five diploid potato clones have been transformed by electroporation of protoplasts with different selectable markers. The resulting diploid regenerated plants have been used in somatic hybridization. It has been shown that hybrid cell selection on the basis of antibiotic or herbicide resistances brought by the two parents of fusion is an efficient method for the recovery of tetraploid somatic hybrids.

Genotype-independent leaf disc transformation of potato (Solanum tuberosum) using Agrobacterium tumefaciens

Leaves of the in vitro grown potato cultivars 'Bintje', 'Berolina', 'Desiree', and 'Russet Burbank' were wounded and co-cultivated with Agrobacterium strains having chimeric bar and nptII genes on a disarmed T-DNA. Each leaf from these cultivars formed numerous calli on kanamycin-containing medium, and almost all calli regenerated shoots. For 'Russet Burbank', it was necessary to include AgNO3 in the medium to obtain efficient shoot regeneration. The transformed plants have one to a few copies of the T-DNA, show NPT-II and PAT activities, and are resistant to high doses of the commercial preparation of phospinotricin (glufosinate). Almost no somaclonal variation was detected in trans-genic plants.

Genetic transformation in two potato cultivars with T-DNA from disarmed Agrobacterium

Derivatives of potato (Solanum tuberosum cv.'s 'Maris Bard' and 'Desiree') transformed with disarmed T-DNA from genetically engineered Agrobacterium tumefaciens strains were isolated. The transformed plants were recovered from shoot-forming tumours induced by infection of wounds with mixedcultures of shoot-inducing A. tumefaciens strains T37 and either Agrobacterium strain LBA1834(pRAL1834), (Hille et al. 1983) or LBA4404(pBIN6; pRAL4404), (Bevan 1984). Two small-scale feasibility experiments gave at least four 'Maris Bard' plants transformed with pRAL1834 T-DNA and two 'Desiree' plants with pBIN6 T-DNA. The transformed 'Maris Bard' plants were morphologically abnormal and highly aneuploid. This was probably an unfortunate side-effect of a tissue culture-step introduced to promote the efficiency of shoot regeneration. The transformed 'Desiree' plants, in contrast, were isolated without promoting additional shoot-growth. They were morphologically normal, contained 47 and the euploid 48 chromosomes per cell respectively and had improved growth on media containing kanamycin.

Field performance and cytology of protoplast-derived rice (Oryza sativa): high yield and low degree of variation of four japonica cultivars

Protoplast-derived rice plants of four Japanese cultivars, Nipponbare, Fujisaka 5, Norin 14 and Iwaimochi were individually cultivated in a submerged paddy field. They exhibited more stems, which resulted in more panicles than respective control plants. Other characteristics of protoplast-derived plants were (compared with controls): a slightly shorter or similar culm length, fewer spikelets per panicle, slightly lower seed fertility and similar or lighter 1,000 kernel weight. Grain yield of protoplast-derived plants was more than that of respective control plants in four cultivars. The cause of the higher yield of protoplast-derived plants seems to be mainly due to increased panicle number. Among 126 protoplast-derived plants, 1 triploid, 10 tetraploids and 1 aneuploid were found. Furthermore, 11 variants with low seed fertility showing no gross chromosomal anomalies and one plant with abnormal panicles were found. In total, about 80% of protoplastderived plants showed normal characters. The present results are encouraging for the possibility of rice breeding using protoplasts.

Flow cytometric analysis of polysomaty and in vitro genetic instability in potato

The analysis of nuclear DNA contents in various tissues of potato genotypes showed that flow cytometry is a rapid method to characterize large populations of cells for polysomaty, that is, the occurrence of cells with normal DNA levels together with cells containing endoreduplicated nuclei. The proportion of endoreduplicated nuclei varied in different tissues and genotypes of potato. The analysis of callus and cell cultures showed that the temporal changes in nuclear DNA contents during in vitro growth can be followed and the degree of polyploidization quantified. It is concluded that flow cytometry is a highly suitable method to detect ploidy changes in differentiated plant tissues and calli which are often not amenable for chromosome number determination.

Improvements in regeneration from protoplasts of potato and studies on chromosome stability : 1. The effect of initial culture media

Regeneration of plants from protoplasts of potato (Solanum tuberosum) cv. 'Maris Bard' has been achieved from four different initial culture media (ET2, ET3, CLG, VkCLG). These media differed in their hormone, salt and sugar content. Plating efficiencies were highest in the VkCLG medium, but no correlation was found between plating efficiency and regeneration frequency (i.e. the percentage of calli producing shoots). Regeneration frequencies were high on all four media; up to 95% on ET3. Chromosome counts of up to 50 regenerants selected at random from the four treatments showed no significant differences between any of the treatments, in the proportions of plants which were euploid (48), aneuploid at the tetraploid level (48±), and aneuploid with high chromosome numbers (48+ +). Highly significant differences were present, however, between shoots which rooted quickly (predominantly euploid) and those which rooted only after transfer to a rooting medium (predominantly 48+ +). Overall more than 60% of the regenerants were normal (2n=4x=48) and this is a considerable improvement on our earlier work in this cultivar (4% normal). These findings are discussed in relation to factors affecting chromosome stability. Chromosome structural rearrangements are also described.

Aberrant microtubule organization can result in genetic abnormalities in protoplast cultures of Vicia hajastana Grossh

Protoplast cultures of Vicia hajastana have a high division frequency. However, 20-40% of the microcolonies fail to develop beyond the 20-30-cell stage. Aneuploids and polyploids were found in early divisions and persisted in older cultures. The resulting protoplast-derived suspension culture differed karyologically from the original culture. Karyokinesis and cytokinesis were studied using simultaneous staining of microtubules (MT) by immunofluorescence, DNA by Hoechst 33258 (2-[2-(4-hydroxyphenyl)-6-benzimidazoyl]-6-[1-methyl-4-piperazyl]benzimidazole) and cell walls by Calcofluor. Freshly prepared protoplasts showed mitoses and high frequencies of binucleate cells, which probably resulted mainly from failure of cytokinesis. In early divisions, many mitoses showed metaphase chromosomes with kinetochore MT but lacking polar MT. These aberrant mitoses probably accounted for an increase in hyperploid cells observed in protoplast cultures. Multipolar spindles, which gave rise to hypoploid cells, were also seen in the early divisions. Telophase abnormalities included dislocated phragmoplasts and incomplete formation of cross walls. Many divisions resulted in daughter nuclei of unequal size. Unequal segregation of chromosomes was detected by cytofluorimetric measurements of telophase nuclei stained with Hoechst. After 5 d of culture, 91% of the divisions with incomplete cross walls also contained different-size nuclei; conversely, 78% of the divisions with fully formed cross walls contained nuclei of equal size. The malfunctioning of spindles and phragmoplasts in the same cells indicates a functional interdependence of the different MT configurations in mitosis. During the first 24 h of culture, a high frequency of abnormalities was found in spindles, cross-wall formation and chromosome segregation; this was reduced substantially in the cells undergoing first division by 48 h. The data indicate that it may be possible to manipulate the frequency of abnormalities by controlling the onset of the first division in protoplast cultures.

Somatic hybrids produced by protoplast fusion between S. tuberosum and S. brevidens: phenotypic variation under field conditions

Phenotypic and flowering characteristics of hybrid plants generated by protoplast fusion between a tetraploid S. tuberosum line and diploid S. brevidens were assessed under field conditions. Hybrids were compared to both clonal parental material and protoplast-derived plants of each parent. Almost all of the hybrids were hexaploid. A wide range of variation in morphological characters was observed for hybrids and protoclones. Flowering was markedly reduced in protoclones. The majority of hybrids flowered, had viable pollen and set tubers. Tuber and pollen characteristics of hybrids produced from individual fusion calli also varied. The potential usefulness of fusion hybrids in potato improvement is discussed.

Intra-specific fusions in Solanum tuberosum

Plants were regenerated from callus arising from protoplast fusion of two S. tuberosum diploids. Tetraploid progeny from the fusion of the two diploid partners had increased vigor. Isozyme analysis confirmed the presence of proteins from both partners in the fusion progeny. Pigmentation of tubers and anthers was heightened substantially in the fusion products. This fusion, the first intra-specific fusion within S. tuberosum, indicates that somatic fusion may be useful for transferring traits within this group.

Expression of shoot-inducing Ti TL-DNA in differentiated tissues of potato (Solanum tuberosum cv Maris Bard)

In potato line Mb1501B one or possibly two normal size Ti TL-DNA copies per tetraploid genome were detected by Southern blot analysis, but no TR-DNA. The TL-DNA probably contained the entire transposon Tn1831 inserted at the T-DNA auxin gene for transcript 2. Northern blot analyses of the steady-state RNA in different Mb1501B tissues isolated from (i) shoots cultured in vitro (ii) grafted plants and (iii) tubers, showed that that TL-DNA transcripts 3, 4, 6a and 7 were expressed most abundantly in the cultured shoots. They formed approximately 0.0023 to 0.0007% of the total poly(A) RNA. Transcripts 1, 5 and 6b were not detected in any of the tissues analysed. This indicated even lower levels of expression (below approximately 0.0001% of the total poly(A) RNA or, making certain assumptions, an abundance of less than one T-DNA derived RNA molecule per cell). As expected, transcript 2 was not detected in any of the Mb1501B tissues. The abundance of the transcripts was reduced in grafted plants and tubers compared with cultured shoots with the greatest decrease (5×) for transcripts 4, 6a and 7. Transcript 4, the one most responsible for the changed growth and development of Mb 1501 B, formed approximately 0.0003% of the poly(A) RNA from both grafted plants and tubers.

Genetic modification of potato development using Ri T-DNA

Forty-two potato plants were regenerated from a hairy-root line obtained after infection of a shoot of Solanum tuberosum cv 'Desiree' with Agrobacterium rhizogenes strain LBA 9402 (pRil855). Transformed plants were uniform and had a distinct phenotype and development compared with untransformed controls. Their growth was vigorous, especially early in their development, their roots were abundant and showed reduced geotropism, their leaves were slightly crinkled and glossy and they produced longer tubers with more frequent, prominent eyes. Cytological examination showed that ten of the forty-two transformed plants had either 47 or 49 chromosomes instead of the normal 48. In two of these aneuploids structural changes were observed.

Genetic instability in protoclones of potato (Solanum tuberosum L. cv. 'Bintje'): new types of variation after vegetative propagation

The transmission of variation from protoplast-derived plants of tetraploid potato cultivar 'Bintje' to tuber progeny was examined. The morphological alterations of a majority of the variant protoclones were transmitted to corresponding tuber progeny. Some of the normal and variant protoclones gave new phenotypes, or segregated into parental and new phenotypes after vegetative propagation. The ploidy levels of almost all these clones remained unchanged after propagation. It was concluded that the occurrence of variation after vegetative propagation was due to somatic segregation of chimeras resulting from gene mutations or chromosome structural rearrangements in only part of the regenerated plant. The origin of variation is discussed in the light of these results.