Diploid Potato Research Articles

Evaluation of diploid potato germplasm for applications of genome editing and genetic engineering

Evaluation of diploid potato germplasm for applications of genome editing and genetic engineering

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder’s efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Allelic variation for alpha-Glucan Water Dikinase is associated with starch phosphate content in tetraploid potato

Key messageAssociation analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations.Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (StGWD) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (Ho = 0.765). The average number of different haplotypes per individual (Ai) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO4/mg starch to 38 nmol PO4/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.

Crop Cycle Length Determines Optimal Transplanting Date for Seedlings from Hybrid True Potato Seeds

AbstractThe technology of hybrid breeding in diploid potatoes creates opportunities to design novel and improved cultivation systems based on hybrid true potato seeds. A promising cultivation pathway to produce seed or ware tubers is by transplanting greenhouse-raised seedlings into the field. This study explored the effects of transplanting date and seedling age on tuber yield, using greenhouse-raised seedlings. Field trials with experimental hybrid genotypes were conducted in three consecutive years. In 2017 and 2018, 4- and 6-week-old seedlings were transplanted at four dates: March, April, May and June. In 2019, transplanting dates included April, May and June and seedling age was 5 weeks. In 2018, the March planting experienced severe frost during the initial field period resulting in crop failure. In 2017 and 2019, plants could withstand shorter and less severe frost events. Seedling age did not significantly affect tuber parameters. Transplanting in June resulted in lower marketable yield (> 28 mm) compared with earlier transplanting dates when crops were harvested in September. At full crop senescence, no differences in marketable yield were observed. The optimal transplanting window, taking into account weather-related risks, is approximately between early April and end May. For some genotypes, crop cycle length was observed to be a more important yield-determining factor than transplanting date.

Genome-Wide Identification and Analysis of NAC Transcription Factor Family in Two Diploid Wild Relatives of Cultivated Sweet Potato Uncovers Potential NAC Genes Related to Drought Tolerance.

NAC (NAM, ATAF1/2, and CUC2) proteins play a pivotal role in modulating plant development and offer protection against biotic and abiotic stresses. Until now, no systematic knowledge of NAC family genes is available for the food security crop, sweet potato. Here, a comprehensive genome-wide survey of NAC domain-containing proteins identified 130 ItbNAC and 144 ItfNAC genes with full length sequences in the genomes of two diploid wild relatives of cultivated sweet potato, Ipomoea triloba and Ipomoea trifida, respectively. These genes were physically mapped onto 15 I. triloba and 16 I. trifida chromosomes, respectively. Phylogenetic analysis divided all 274 NAC proteins into 20 subgroups together with NAC transcription factors (TFs) from Arabidopsis. There were 9 and 15 tandem duplication events in the I. triloba and I. trifida genomes, respectively, indicating an important role of tandem duplication in sweet potato gene expansion and evolution. Moreover, synteny analysis suggested that most NAC genes in the two diploid sweet potato species had a similar origin and evolutionary process. Gene expression patterns based on RNA-Seq data in different tissues and in response to various hormone, biotic or abiotic treatments revealed their possible involvement in organ development and response to various biotic/abiotic stresses. The expression of 36 NAC TFs, which were upregulated in the five tissues and in response to mannitol treatment, was also determined by real-time quantitative polymerase chain reaction (RT-qPCR) in hexaploid cultivated sweet potato exposed to drought stress. Those results largely corroborated the expression profile of mannitol treatment uncovered by the RNA-Seq data. Some significantly up-regulated genes related to drought stress, such as ItbNAC110, ItbNAC114, ItfNAC15, ItfNAC28, and especially ItfNAC62, which had a conservative spatial conformation with a closely related paralogous gene, ANAC019, may be potential candidate genes for a sweet potato drought tolerance breeding program. This analysis provides comprehensive and systematic information about NAC family genes in two diploid wild relatives of cultivated sweet potato, and will provide a blueprint for their functional characterization and exploitation to improve the tolerance of sweet potato to abiotic stresses.

Genome-Wide Identification and Analysis of NAC Transcription Factor Family in Two Diploid Wild Relatives of Cultivated Sweet Potato Uncovers Potential NAC Genes Related to Drought Tolerance

NAC (NAM, ATAF1/2, and CUC2) proteins play a pivotal role in modulating plant development and offer protection against biotic and abiotic stresses. Until now, no systematic knowledge of NAC family genes is available for the food security crop, sweet potato. Here, a comprehensive genome-wide survey of NAC domain-containing proteins identified 130 ItbNAC and 144 ItfNAC genes with full length sequences in the genomes of two diploid wild relatives of cultivated sweet potato, Ipomoea triloba and Ipomoea trifida, respectively. These genes were physically mapped onto 15 I. triloba and 16 I. trifida chromosomes, respectively. Phylogenetic analysis divided all 274 NAC proteins into 20 subgroups together with NAC transcription factors (TFs) from Arabidopsis. There were 9 and 15 tandem duplication events in the I. triloba and I. trifida genomes, respectively, indicating an important role of tandem duplication in sweet potato gene expansion and evolution. Moreover, synteny analysis suggested that most NAC genes in the two diploid sweet potato species had a similar origin and evolutionary process. Gene expression patterns based on RNA-Seq data in different tissues and in response to various hormone, biotic or abiotic treatments revealed their possible involvement in organ development and response to various biotic/abiotic stresses. The expression of 36 NAC TFs, which were upregulated in the five tissues and in response to mannitol treatment, was also determined by real-time quantitative polymerase chain reaction (RT-qPCR) in hexaploid cultivated sweet potato exposed to drought stress. Those results largely corroborated the expression profile of mannitol treatment uncovered by the RNA-Seq data. Some significantly up-regulated genes related to drought stress, such as ItbNAC110, ItbNAC114, ItfNAC15, ItfNAC28, and especially ItfNAC62, which had a conservative spatial conformation with a closely related paralogous gene, ANAC019, may be potential candidate genes for a sweet potato drought tolerance breeding program. This analysis provides comprehensive and systematic information about NAC family genes in two diploid wild relatives of cultivated sweet potato, and will provide a blueprint for their functional characterization and exploitation to improve the tolerance of sweet potato to abiotic stresses.

A breeding consortium to realize the potential of hybrid diploid potato for food security.

Hybrid diploid breeding is a radical innovation that promises to revolutionize breeding practices in potato, the world’s third-largest food crop. Yet concerted efforts are needed to ensure this innovation can be harnessed for food security.

Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS.

Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

Incomplete genome doubling enables to consistently enhance plant growth for maximum biomass production by altering multiple transcript co-expression networks in potato.

Cytochimera potato plants, which mixed with diploid and tetraploid cells, could cause the highest and significantly increased biomass yield than the polyploid and diploid potato plants. Polyploidization is an important approach in crop breeding for agronomic trait improvement, especially for biomass production. Cytochimera contains two or more mixed cells with different levels of ploidy, which is considered a failure in whole genome duplication. Using colchicine treatment with diploid (Dip) potato (Solanum chacoense) plantlets, this study generated tetraploid (Tet) and cytochimera (Cyt) lines, which, respectively, contained complete and partial cells with genome duplication. Compared to the Dip potato, we observed remarkably enhanced plant growth and biomass yields in Tet and Cyt lines. Notably, the Cyt potato straw, which was generated from incomplete genome doubling, was of significantly higher biomass yield than that of the Tet with a distinctively altered cell wall composition. Meanwhile, we observed that one layer of the tetraploid cells (about 30%) in Cyt plants was sufficient to trigger a gene expression pattern similar to that of Tet, suggesting that the biomass dominance of Cyt may be related to the proportion of different ploidy cells. Further genome-wide analyses of co-expression networks indicated that down-regulation (against Dip) of spliceosomal-related transcripts might lead to differential alternative splicing for specifically improved agronomic traits such as plant growth, biomass yield, and lignocellulose composition in Tet and Cyt plants. In addition, this work examined that the genome of Cyt line was relatively stable after years of asexual reproduction. Hence, this study has demonstrated that incomplete genome doubling is a promising strategy to maximize biomass production in potatoes and beyond.

Hybridization and polyploidization effects on LTR-retrotransposon activation in potato genome.

Hybridization and polyploidization are major forces in plant evolution and potatoes are not an exception. It is proposed that the proliferation of Long Terminal Repeat-retrotransposons (LTR-RT) is related to genome reorganization caused by hybridization and/or polyploidization. The main purpose of the present work was to evaluate the effect of interspecific hybridization and polyploidization on the activation of LTR-RT. We evaluated the proliferation of putative active LTR-RT in a diploid hybrid between the cultivated potato Solanum tuberosum and the wild diploid potato species S. kurtzianum, allotetraploid lines derived from this interspecific hybrid and S. kurtzianum autotetraploid lines (ktz-autotetraploid) using the S-SAP (sequence-specific amplified polymorphism) technique and normalized copy number determination by qPCR. Twenty-nine LTR-RT copies were activated in the hybrid and present in the allotetraploid lines. Major LTR-RT activity was detected in Copia-27, Copia-12, Copia-14 and, Gypsy-22. According to our results, LTR-RT copies were activated principally in the hybrid, there was no activation in allotetraploid lines and only one copy was activated in the autotetraploid.

The World’s First Diploid Recombinant Inbred Potato Population

CSA NewsVolume 66, Issue 11 p. 6-11 FEATURES The World’s First Diploid Recombinant Inbred Potato Population DJ McCauley, DJ McCauleySearch for more papers by this author DJ McCauley, DJ McCauleySearch for more papers by this author First published: 04 October 2021 https://doi.org/10.1002/csan.20602Citations: 1Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Video Short The World’s First Diploid Recombinant Inbred Potato Population by McCauley Volume66, Issue11November 2021Pages 6-11 RelatedInformation

Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety.

Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly’s usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

Comparison of statistical indices for the evaluation of crop models performance

This study presents a comparison of the usual statistical methods used for crop model assessment. A case study was conducted using a data set from observations of the total dry weight in diploid potato crop, and six simulated data sets derived from the observationsaimed to predict the measured data. Statistical indices such as the coefficient of determination, the root mean squared error, the relative root mean squared error, mean error, index of agreement, modified index of agreement, revised index of agreement, modeling efficiency, and revised modeling efficiency were compared. The results showed that the coefficient of determination is not a useful statistical index for model evaluation. The root mean squared error together with the relative root mean squared error offer an excellent notion of how deviated the simulations are in the same unit of the variable and percentage terms, and they leave no doubt when evaluating the quality of the simulations of a model.

Features and genetic basis of chlorogenic acid formation in diploid potatoes

The concentration of chlorogenic acids (CGAs), is tightly associated with the appearance, taste, and nutrient content of potato tubers. Manipulation of tuber CGA concentrations allows for the breeding of quality traits in potatoes. Currently, a hybrid potato breeding system that aims to convert tetraploid potato into a diploid seed crop represents a new development in potato breeding. Unfortunately, however, a systematic study of CGA formation is very limited in diploid potatoes. Here, using a diverse panel of diploid potatoes, including 40 ancestors and 374 landraces, we analyzed the influence of location, environment, genetic basis, as well as expression of enzymes, in affecting the CGA concentrations in diploid lines. We revealed a selection of the decreased CGA level of tuber flesh in the domestication of diploid potatoes. Moreover, we identified 18 SNPs associated with tuber CGA levels using re-sequenced genome data. This study provides a basis for the breeding of high-quality potato by taking into consideration customer preferences.

Self‐fertility and resistance to the Colorado potato beetle (Leptinotarsa decemlineata) in a diploid Solanum chacoense recombinant inbred line population

AbstractA diploid potato (Solanum tuberosum L.) recombinant inbred line population was derived from a cross between Solanum chacoense inbred line M6 and S. chacoense accession USDA8380‐1 (80‐1) to identify loci associated with self‐compatibility and Colorado potato beetle resistance. Individuals from the F4 and F5 generations were genotyped on the Illumina Infinium V3 22K Single Nucleotide Polymorphism (SNP) Array and a genetic map constructed. All F5 individuals contain at least one copy of the dominant S‐locus inhibitor (Sli) haplotype; however, not all F5 individuals set fruit. Pollen tubes reached the ovaries of both self‐fruitful and self‐unfruitful plants, indicating that the presence of the dominant Sli allele is not sufficient for selfed fruit and seed production. Loci on chromosomes 3, 5, 6, and 12 were identified as novel targets for self‐fertility improvement. Evaluation of fruit and seed set upon selfing in the F4 generation over two greenhouse seasons revealed environmental influence on self‐fertility. Loci exhibiting residual heterozygosity were found on all chromosomes except chromosomes 3 and 11 in F5 inbreds, but none of the measured self‐fertility traits were correlated with the level of heterozygosity based on SNP genotyping. Four SNPs on chromosome 2 between 22,151,711 and 22,381,719 bp were associated with foliar leptine glycoalkaloid synthesis and Colorado potato beetle resistance in the recombinant inbred line population. Robust inbred lines carrying Colorado potato beetle resistance were developed without field selection during the inbreeding process and beetle resistance was introgressed into diploid breeding lines.

The complete mitogenome assemblies of 10 diploid potato clones reveal recombination and overlapping variants.

The potato mitogenome is complex and to understand various biological functions and nuclear–cytoplasmic interactions, it is important to characterize its gene content and structure. In this study, the complete mitogenome sequences of nine diploid potato clones along with a diploid Solanum okadae clone were characterized. Each mitogenome was assembled and annotated from Pacific Biosciences (PacBio) long reads and 10X genomics short reads. The results show that each mitogenome consists of multiple circular molecules with similar structure and gene organization, though two groups (clones 07506-01, DW84-1457, 08675-21 and H412-1 in one group, and clones W5281-2, 12625-02, 12120-03 and 11379-03 in another group) could be distinguished, and two mitogenomes (clone 10908-06 and OKA15) were not consistent with those or with each other. Significant differences in the repeat structure of the 10 mitogenomes were found, as was recombination events leading to multiple sub-genomic circles. Comparison between individual molecules revealed a translocation of ∼774 bp region located between a short repeat of 40 bp in molecule 3 of each mitogenome, and an insertion of the same in molecule 2 of the 10908-06 mitogenome. Finally, phylogenetic analyses revealed a close relationship between the mitogenomes of these clones and previously published potato mitogenomes.

A nonS-locus F-box gene breaks self-incompatibility in diploid potatoes

Potato is the third most important staple food crop. To address challenges associated with global food security, a hybrid potato breeding system, aimed at converting potato from a tuber-propagated tetraploid crop into a seed-propagated diploid crop through crossing inbred lines, is under development. However, given that most diploid potatoes are self-incompatible, this represents a major obstacle which needs to be addressed in order to develop inbred lines. Here, we report on a self-compatible diploid potato, RH89-039-16 (RH), which can efficiently induce a mating transition from self-incompatibility to self-compatibility, when crossed to self-incompatible lines. We identify the S-locusinhibitor (Sli) gene in RH, capable of interacting with multiple allelic variants of the pistil-specific S-ribonucleases (S-RNases). Further, Sli gene functions like a general S-RNase inhibitor, to impart SC to RH and other self-incompatible potatoes. Discovery of Sli now offers a path forward for the diploid hybrid breeding program.

Neofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato

Genetic gain in potato is hampered by the heterozygous tetraploid genome of cultivated potato. Converting potato into a diploid inbred-line based F1-hybrid crop provides a promising route towards increased genetic gain. The introduction of a dominant S-locus inhibitor (Sli) gene into diploid potato germplasm allows efficient generation of self-fertilized seeds and thus the development of potato inbred lines. Little is known about the structure and function of the Sli locus. Here we describe the mapping of Sli to a 12.6 kb interval on chromosome 12 using a recombinant screen approach. One of two candidate genes present in this interval shows a unique sequence that is exclusively present in self-compatible lines. We describe an expression vector that converts self-incompatible genotypes into self-compatible and a CRISPR-Cas9 vector that converts SC genotypes into SI. The Sli gene encodes an F-box protein that is specifically expressed in pollen from self-compatible plants. A 533 bp insertion in the promotor of that gene leads to a gain of function mutation, which overcomes self-pollen rejection.

The magic of genomics in creating hybrid potato

The magic of genomics in creating hybrid potato

Variation of mineral contents with nutritional interest in a collection of Solanum tuberosum group Phureja tubers

SummaryColombia has a biodiversity centre of diploid potatoes located at south of the country. This study evaluated the amounts of potassium (K), calcium (Ca), iron (Fe) and zinc (Zn) in a biodiversity panel of potato tubers, constituting native cultivars, accessions of the Working Collection of Potato Breeding Program at the Universidad Nacional de Colombia (CCC) and commercial cultivars. The highest quantity of minerals found were as follows: 34 333 ± 4509 mg K kg−1 potato dry weight (DW; CCC112), 1965 ± 898 mg Ca kg−1 potato DW (CCC23), 87.5 ± 8.8 mg Fe kg−1 potato DW (CCC116) and 60.7 ± 5.1 mg Zn kg−1 potato DW (CCC31). As compared to those in commercial cultivars, the currently evaluated tubers had an increase of 1.4, 12.5, 3.5 and 3.6‐fold in K, Ca, Fe and Zn. These genotypes can be used in the future breeding programmes to enhance specific mineral contents in tubers.