Diploid Potato Research Articles

CRISPR/Cas9-mediated genome editing in diploid and tetraploid potatoes

CRISPR/Cas9-mediated genome editing in diploid and tetraploid potatoes

Generation of Asynaptic Mutants in Potato by Disrupting StDMC1 Gene Using RNA Interference Approach.

Fixing the genomic composition and multiplication through true potato seed (TPS) is an important challenge in autotetraploid potato. Disrupted meiotic cDNA (DMC1) is a meiotic gene that plays a central role in DNA recombination through crossing over in meiosis. Using the Arabidopsis DMC1 (AtDMC1) gene sequence, we retrieved Solanum tuberosum DMC1(StDMC1) from the diploid potato genome, and subsequently, sense and antisense regions of the StDMC1 gene were amplified in potato cv. Kufri Jyoti. The sense and antisense fragments were confirmed by Sanger-sequencing and cloned in the pRI101 vector. Agrobacterium-mediated transformation of the RNAi construct resulted in 44% transformation efficiency, and a total of 137 mutant lines were obtained. These mutant lines were further validated through pollen viability testing, and selected lines were used for gene expression analysis. The acetocarmine-based pollen staining showed reduced pollen viability ranging from 14 to 21% in four DMC1 mutant lines (DMC4-37, DMC4-41, DMC6-20, and DMC6-21), as compared to the Kufri Jyoti control plants, which on average exhibited 78% pollen viability. The phenotypic data was supported by the reduced expression of the StDMC1 gene in these four mutant lines compared to the control Kufri Jyoti. The results confirmed the generation of StDMC1 knockdown lines. This is the first report of StDMC1 mutant line generation in tetraploid potatoes and will be a step forward in generating non-recombinant mutants through sexual reproduction in potatoes.

Converting Hybrid Potato Breeding Science into Practice

Research on diploid hybrid potato has made fast advances in recent years. In this review we give an overview of the most recent and relevant research outcomes. We define different components needed for a complete hybrid program: inbred line development, hybrid evaluation, cropping systems and variety registration. For each of these components the important research results are discussed and the outcomes and issues that merit further study are identified. We connect fundamental and applied research to application in a breeding program, based on the experiences at the breeding company Solynta. In the concluding remarks, we set hybrid breeding in a societal perspective, and we identify bottlenecks that need to be overcome to allow successful adoption of hybrid potato.

Efficiency in biomass accumulation of diploid potato cultivars (Solanum tuberosum, Phureja Group) in contrasting environments at elevation

Efficiency in biomass accumulation of diploid potato cultivars (Solanum tuberosum, Phureja Group) in contrasting environments at elevation

Insights and advances in integrating multi-omic approaches for potato crop improvement

In the forthcoming era of climate change and degradation of culturable land, there is an urgent need to secure global food supply in a sustainable manner. unraveling the genetic mysteries underlying interactions between functional genetic and metabolic networks through fostering the use of high-throughput -omic technologies can serve as a valuable tool towards characterizing plant phenotypic diversity and plasticity, to mitigate current threats of the climate change scenario on agriculture. Recently, a colossal number of -omic studies, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metagenomics, have enabled the identification of genes, proteins, and metabolites, that are related to desirable phenotypes, explaining the “holo-genetic” basis of agriculturally important traits, especially under resource-limiting environments. Undoubtedly, the integration of such big datasets with machine learning is highly demanding, mainly due to the lack of universal protocols to predict gene models or networks that govern various key traits. Among other important plant species contributing to food production, potato (Solanum tuberosum L.) represents one of top crop species worldwide, in terms of nutrition contribution, yielding capacity, and as a component of diverse cropping systems, especially for the developing counties. The potato genome is highly heterozygous as a result of self-incompatibility of the diploid potato species, suffering acute inbreeding depression. In this review, we discuss recent developments of high-throughput genomic technologies, as a useful tool for the selection of potato germplasm with improved nutritional value and quality traits.

Evaluación del tamaño y número de tubérculos de papa amarilla bajo diferentes densidades de siembra usando modelos cero inflados

A field study was carried out on the cultivation of the yellow diploid potato (Solanum tuberosum Phureja Group) to evaluate the influence of the planting density associated with distances between plants of 30, 40, and 50 cm and distances between the rows and paths of 100 cm on the tuber count with sizes less than 2 cm, 2-4 cm, 4-6 cm, and more than 6 cm. At the time of the harvest of the tubers, they were classified by size and respective count was made. The modelling of the counts was done by means of the usual negative binomial regression and by the inflated zeros option. The zero-inflated negative binomial regression models showed a significant effect of the sowing density on the tuber count in the sizes that were superior to 4 cm while the negative binomial model showed a significant effect it in the case of the sizes lower than 4 cm. The results on size and density are attributes of interest in both the agronomic management of this crop and in the industrial management of the tubers, so the relationship that we found can be adopted in both areas to generate the desired attributes of the crop for improving the production and guiding the process of industrialization.

Diploid Potatoes as a Catalyst for Change in the Potato Industry

AbstractIn response to increasing interest in diploid potato (Solanum tuberosum) breeding and the production of diploid inbred hybrid potato varieties, the Breeding and Genetics section of the Potato Association of America (PAA) organized a symposium on diploid breeding that took place during the 2021 PAA annual meeting. Proceedings from that symposium are documented in this manuscript. Speakers from academia, government and industry presented their unique perspectives. Presentations covered a wide range of topics. Potential advantages of diploid breeding were introduced, and reasons to be skeptical about diploid breeding were highlighted. The impact that diploid breeding might have on the potato seed industry was discussed. Advantages for genetics research were emphasized. Aspects of tomato breeding and production were reviewed and considered as potential models for diploid potato breeding and production activities. Lastly, an industry-centered view of diploid potato breeding was provided. Taken together, these presentations are a snapshot of how diploid potato breeding was viewed in the moment, a vision for how diploid breeding might be implemented, and a thoughtful reflection on how diploid breeding and inbred hybrid varieties might change the potato variety development process and impact the potato industry.

Morphological and anatomical characterization of yellow diploid potato flower for effective breeding program

The diploid yellow potato (Solanum tuberosum L. Phureja Group) is an important plant genetic resource. In this study, we report for the first time the characterization of anther development and pollen formation in the cultivar Criolla Colombia. The description of morphological and histological characters of buds and flowers at different developmental stages permitted to identify ten main stages, from the differentiation of the male cells of the sporangium, meiosis, microspores formation and maturation, to the release of mature pollen. In addition, the results provide a graphic guide of the development of the anther, through the sequential and orderly formation of the epidermis, the endothecium, the middle layer and the nutritive layer or tapetum. This microanatomical information will be useful for work focused on androgenesis and identification of gene regulation in floral biology and gamete formation. Therefore, this study determined that to efficiently obtain haploids, flower buds between 5 and 8.9 mm long (stage 6 to 8) should be used, in which tetrads and microspores are in the early uninucleate and binucleate stage.

Rychc Confers Extreme Resistance to Potato virus Y in Potato.

The Potato virus Y (PVY) is responsible for huge economic losses for the potato industry worldwide and is the fifth most consequential plant virus globally. The main strategies for virus control are to limit aphid vectors, produce virus-free seed potatoes, and breed virus-resistant varieties. The breeding of PVY-resistant varieties is the safest and most effective method in terms of cost and environmental protection. Rychc, a gene that confers extreme resistance to PVY, is from S. chacoense, which is a wild diploid potato species that is widely used in many PVY-resistant breeding projects. In this study, Rychc was fine mapped and successfully cloned from S. chacoense accession 40-3. We demonstrated that Rychc encodes a TIR-NLR protein by stably transforming a diploid susceptible cultivar named AC142 and a tetraploid potato variety named E3. The Rychc conferred extreme resistance to PVYO, PVYN:O and PVYNTN in both of the genotypes. To investigate the genetic events occurring during the evolution of the Rychc locus, we sequenced 160 Rychc homologs from 13 S. chacoense genotypes. Based on the pattern of sequence identities, 160 Rychc homologs were divided into 11 families. In Family 11 including Rychc, we found evidence for Type I evolutionary patterns with frequent sequence exchanges, obscured orthologous relationships and high non-synonymous to synonymous substitutions (Ka/Ks), which is consistent with rapid diversification and positive selection in response to rapid changes in the PVY genomes. Furthermore, a functional marker named MG64-17 was developed in this study that indicates the phenotype with 100% accuracy and, therefore, can be used for marker-assisted selection in breeding programs that use S. chacoense as a breeding resource.

Genome sequencing of adapted diploid potato clones.

Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.

The autotetraploid potato genome provides insights into highly heterozygous species.

SummaryPotato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day‐dependent tuber development. Herein, we present a high‐quality, chromosome‐scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein‐coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome‐wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.

Germplasm Release: True Potato Seed (TPS) from a Late Blight Resistant, Long-day Adapted Diploid Potato Population that is Segregating for Early Blight Resistance

Germplasm Release: True Potato Seed (TPS) from a Late Blight Resistant, Long-day Adapted Diploid Potato Population that is Segregating for Early Blight Resistance

Genome evolution and diversity of wild and cultivated potatoes

Potato (Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1–4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.

Molecular Approaches to Overcome Self-Incompatibility in Diploid Potatoes.

There has been an increased interest in true potato seeds (TPS) as planting material because of their advantages over seed tubers. TPS produced from a tetraploid heterozygous bi-parental population produces non-uniform segregating progenies, which have had limited uniformity in yield and quality in commercial cultivation, and, thus, limited success. Inbreeding depression and self-incompatibility hamper the development of inbred lines in both tetraploid and diploid potatoes, impeding hybrid development efforts. Diploid potatoes have gametophytic self-incompatibility (SI) controlled by S-locus, harboring the male-dependent S-locus F-box (SLF/SFB) and female-dependent Stylar-RNase (S-RNase). Manipulation of these genes using biotechnological tools may lead to loss of self-incompatibility. Self-compatibility can also be achieved by the introgression of S-locus inhibitor (Sli) found in the self-compatible (SC) natural mutants of Solanum chacoense. The introgression of Sli through conventional breeding methods has gained much success. Recently, the Sli gene has been cloned from diverse SC diploid potato lines. It is expressed gametophytically and can overcome the SI in different diploid potato genotypes through conventional breeding or transgenic approaches. Interestingly, it has a 533 bp insertion in its promoter elements, a MITE transposon, making it a SC allele. Sli gene encodes an F-box protein PP2-B10, which consists of an F-box domain linked to a lectin domain. Interaction studies have revealed that the C-terminal region of Sli interacts with most of the StS-RNases, except StS-RNase 3, 9, 10, and 13, while full-length Sli cannot interact with StS-RNase 3, 9, 11, 13, and 14. Thus, Sli may play an essential role in mediating the interactions between pollen and stigma and function like SLFs to interact with and detoxify the S-RNases during pollen tube elongation to confer SC to SI lines. These advancements have opened new avenues in the diploid potato hybrid.

Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes.

Potato (Solanum tuberosum L.) is the most important non-grain food crop. Tandem duplication significantly contributes to genome evolution. The objectives of this study were to (i) identify tandemly duplicated genes and compare their genomic distributions across potato genotypes, (ii) investigate the bias in functional specificities, (iii) explore the relationships among coding sequence, promoter and expression divergences associated with tandemly duplicated genes, (iv) examine the role of tandem duplication in generating and expanding lineage-specific gene families, (v) investigate the evolutionary forces affecting tandemly duplicated genes, and (vi) assess the similarities and differences with respect to above mentioned aspects between cultivated genotypes and their wild-relative. In this study, we used well-annotated and chromosome-scale de novo genome assemblies of multiple potato genotypes. Our results showed that tandemly duplicated genes are abundant and dispersed through the genome. We found that several functional specificities, such as disease resistance, stress-tolerance, and biosynthetic pathways of tandemly duplicated genes were differentially enriched across multiple potato genomes. Our results indicated the existence of a significant correlation among expression, promoter, and protein divergences in tandemly duplicated genes. We found about one fourth of tandemly duplicated gene clusters as lineage-specific among multiple potato genomes, and these tended to localize toward centromeres and revealed distinct selection signatures and expression patterns. Furthermore, our results showed that a majority of duplicated genes were retained through sub-functionalization followed by genetic redundancy, while only a small fraction of duplicated genes was retained though neo-functionalization. The lineage-specific expansion of gene families by tandem duplication coupled with functional bias might have significantly contributed to potato’s genotypic diversity, and, thus, to adaption to environmental stimuli.

Control of N-NH4+ and K+ leaching in potato using a carrageenan hydrogel

Potato cultivation requires fertilizers to sustain crop yields, but a significant percentage of added nutrients is lost by leaching. The use of coating materials for fertilizers is currently being considered to reduce these losses. The objective of this study was to determine if a carrageenin based hydrogel (CBH), used to coat fertilizer, decreases NH4+ and K+ leaching from a potato crop without affecting growth, specific gravity, and tuber yield. The CBH was tested in a diploid potato crop, cultivar Criolla Colombia (Solanum tuberosum L., Phureja Group) using a randomized full block design including the treatments noncoated fertilizer (T1), CBH coated fertilizer (T2), and no fertilizer (T3). Mineral nutrients in soil leachates together with dry biomass, foliar area, chlorophyll, tuber specific gravity, and yield were quantified. The nutrient content in leachates from T2 were below those from T1. No significant differences between treatments were observed for growth factors, yield, and tuber specific gravity. This study confirms the controlling effect of the CBH, ensuring the retention of the nutrients added in the fertilizer and preventing them from easily leaching. Future field studies are worthwhile to establish the amount of fertilizer this coating could save.

Little heterosis found in diploid hybrid potato: The genetic underpinnings of a new hybrid crop.

Hybrid potato breeding has become a novel alternative to conventional potato breeding allowing breeders to overcome intractable barriers (e.g. tetrasomic inheritance, masked deleterious alleles, obligate clonal propagation) with the benefit of seed-based propagule, flexible population design, and the potential of hybrid vigor. Until now, however, no formal inquiry has adequately examined the relevant genetic components for complex traits in hybrid potato populations. In this present study, we use a 2-step multivariate modeling approach to estimate the variance components to assess the magnitude of the general and specific combining abilities in diploid hybrid potato. Specific combining ability effects were identified for all yield components studied here warranting evidence of nonadditive genetic effects in hybrid potato yield. However, the estimated general combining ability effects were on average 2 times larger than their respective specific combining ability quantile across all yield phenotypes. Tuber number general combining abilities and specific combining abilities were found to be highly correlated with total yield’s genetic components. Tuber volume was shown to have the largest proportion of additive and nonadditive genetic variation suggesting under-selection of this phenotype in this population. The prominence of additive effects found for all traits presents evidence that the mid-parent value alone is useful for hybrid potato evaluation. Heterotic vigor stands to be useful in bolstering simpler traits but this will be dependent on target phenotypes and market requirements. This study represents the first diallel analysis of its kind in diploid potato using material derived from a commercial hybrid breeding program.

Breeding Diploid F1 Hybrid Potatoes for Propagation from Botanical Seed (TPS): Comparisons with Theory and Other Crops.

This paper reviews the progress and the way ahead in diploid F1 hybrid potato breeding by comparisons with expectations from the theory of inbreeding and crossbreeding, and experiences from other diploid outbreeding crops. Diploid potatoes can be converted from an outbreeding species, in which self-pollination is prevented by a gametophytic self-incompatibility system, into one where self-pollination is possible, either through a dominant self-incompatibility inhibitor gene (Sli) or knockout mutations in the incompatibility locus. As a result, diploid F1 hybrid breeding can be used to produce genetically uniform potato cultivars for propagation from true potato seeds by crossing two near-homozygous inbred lines, derived from a number of generations of self-pollination despite inbreeding depression. Molecular markers can be used to detect and remove deleterious recessive mutations of large effect, including those in tight repulsion linkage. Improvements to the inbred lines can be made by introducing and stacking genes and chromosome segments of large desirable effect from wild relatives by backcrossing. Improvements in quantitative traits require a number of cycles of inbreeding and crossbreeding. Seed production can be achieved by hand pollinations. F1 hybrid planting material can be delivered to farmers as true seeds or young plants, and mini-tubers derived from true seeds.

Phenotypic, molecular and biochemical evaluation of somatic hybrids between Solanum tuberosum and S. bulbocastanum

Somatic hybridization has been frequently used to overcome sexual incompatibility between potato and its secondary germplasm. The primary objective of this study was to produce and evaluate somatic hybrids of Solanum tuberosum (Stub) and S. bulbocastanum (Sblb) for breeding purposes. In 2007, 23 somatic hybrids were produced using an electrofusion of mesophyll protoplasts of diploid (2n = 2x = 24) potato line StubDH165 and S. bulbocastanum PI24351 (Sblb66). Phenotype of somatic hybrids in field conditions were evaluated, together with constitution and stability of 30 nuclear (ncSSR) and 27 cytoplasmic (cpSSR) microsatellite markers and content of main glycoalkaloids. All somatic hybrids had very high field resistance against late blight, but the plants were infertile: the viability of pollen grains insignificantly varied between 0.58 and 8.97%. A significant somaclonal variation was observed in terms of the morphology of plants, the date of emergence, the quantity of harvested tubers, the content of glycoalkaloids in foliage, and nuclear microsatellite markers (ncSSR). The analysis of ncSSR identified five distinct genotypes of hybrids partly associated with phenotype variations. The process of somatic hybridization with regeneration of shoots was identified as the most likely source of somaclonal variation because the ncSSR genotypes of hybrids, which were maintained in vitro, remained stable for more than 10 years. The infertile somatic hybrids have no practical breeding potential, but they are considered very suitable for advanced studies of the differential expression of genes in the pathways linked to dormancy of tubers and synthesis of glycoalkaloids.

The multi-omics basis of potato heterosis.

Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele-specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level. Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.