Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species.

Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the Solanum section Petota, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of Solanum section Petota composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The Petota core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for Solanum section Petota.

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.

Screening South American Potato Landraces and Potato Wild Relatives for Novel Sources of Late Blight Resistance.

Late blight (LB) caused by the oomycete Phytophthora infestans is one of the most important biotic constraints for potato production worldwide. This study assessed 508 accessions (79 wild potato species and 429 landraces from a cultivated core collection) held at the International Potato Center genebank for resistance to LB. One P. infestans isolate belonging to the EC-1 lineage, which is currently the predominant type of P. infestans in Peru, Ecuador, and Colombia, was used in whole plant assays under greenhouse conditions. Novel sources of resistance to LB were found in accessions of Solanum albornozii, S. andreanum, S. lesteri, S. longiconicum, S. morelliforme, S. stenophyllidium, S. mochiquense, S. cajamarquense, and S. huancabambense. All of these species are endemic to South America and thus could provide novel sources of resistance for potato breeding programs. We found that the level of resistance to LB in wild species and potato landraces cannot be predicted from altitude and bioclimatic variables of the locations where the accessions were collected. The high percentage (73%) of potato landraces susceptible to LB in our study suggests the importance of implementing disease control measures, including planting susceptible genotypes in less humid areas and seasons or switching to genotypes identified as resistant. In addition, this study points out a high risk of genetic erosion in potato biodiversity at high altitudes of the Andes due to susceptibility to LB in the native landraces, which has been exacerbated by climatic change that favors the development of LB in those regions.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Complete plastome assemblies from a panel of 13 diverse potato taxa.

The chloroplasts are a crucial part of photosynthesizing plant cells and are extensively utilized in phylogenetic studies mainly due to their maternal inheritance. Characterization and analysis of complete plastome sequences is necessary to understand their diversity and evolutionary relationships. Here, a panel of thirteen plastomes from various potato taxa are presented. Though they are highly similar with respect to gene order and content, there is also a great extent of SNPs and InDels between them, with one of the Solanum bukasovii plastomes (BUK2) having the highest number of SNPs and InDels. Five different potato plastome types (C, S, A, W, W2) are present in the panel. Interestingly, the S. tuberosum subsp. tuberosum (TBR) accession has a W-type plastome, which is not commonly found in this species. The S-type plastome has a conserved 48 bp deletion not found in other types, which is responsible for the divergence of the S-type from the C-type plastome. Finally, a phylogenetic analysis shows that these plastomes cluster according to their types. Congruence between the nuclear genome and the plastome phylogeny of these accessions was seen, however with considerable differences, supporting the hypothesis of introgression and hybridization between potato species.

Genome assembly of six polyploid potato genomes.

Genome assembly of polyploid plant genomes is a laborious task as they contain more than two copies of the genome, are often highly heterozygous with a high level of repetitive DNA. Next Generation genome sequencing data representing one Chilean and five Peruvian polyploid potato (Solanum spp.) landrace genomes was used to construct genome assemblies comprising five taxa. Third Generation sequencing data (Linked and Long-read data) was used to improve the assembly for one of the genomes. Native landraces are valuable genetic resources for traits such as disease and pest resistance, environmental tolerance and other qualities of interest such as nutrition and fiber for breeding programs. The need for conservation and enhanced understanding of genetic diversity of cultivated potato from South America is also crucial to North American and European cultivars. Here, we report draft genomes from six polyploid potato landraces representing five taxa, illustrating how Third Generation Sequencing can aid in assembling polyploid genomes.

Structural genome analysis in cultivated potato taxa.

KEY MESSAGE: Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X-5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

The origins and adaptation of European potatoes reconstructed from historical genomes.

Potato, one of the most important staple crops, originates from the highlands of the equatorial Andes. There, potatoes propagate vegetatively via tubers under short days, constant throughout the year. After their introduction to Europe in the sixteenth century, potatoes adapted to a shorter growing season and to tuber formation under long days. Here, we traced the demographic and adaptive history of potato introduction to Europe. To this end, we sequenced 88 individuals that comprise landraces, modern cultivars and historical herbarium samples, including specimens collected by Darwin during the voyage of the Beagle. Our findings show that European potatoes collected during the period 1650-1750 were closely related to Andean landraces. After their introduction to Europe, potatoes admixed with Chilean genotypes. We identified candidate genes putatively involved in long-day pre-adaptation, and showed that the 1650-1750 European individuals were not long-day adapted through previously described allelic variants of the CYCLING DOF FACTOR1 gene. Such allelic variants were detected in Europe during the nineteenth century. Our study highlights the power of combining contemporary and historical genomes to understand the complex evolutionary history of crop adaptation to new environments.

Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection.

Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.