Assessment of Genetic Diversity and Relatedness in an Andean Potato Collection from Argentina by High-Density Genotyping

Native potatoes are the most diverse among cultivated potato species and thus constitute a valuable source for identifying genes for potato improvement. Nevertheless, high-density mapping, needed to reveal allelic diversity, has not been performed for native Argentinian potatoes. We present a study of the genetic variability and population structure of 96 Andigena potatoes from Northwestern Argentina performed using a subset of 5035 SNPs with no missing data and full reproducibility. These high-density markers are distributed across the genome and present a good coverage of genomic regions. A Bayesian approach revealed the presence of: (I) a major group comprised of most of the Andean accessions; (II) a smaller group containing the out-group cv. Spunta and the sequenced genotype DM; and (III) a third group containing colored flesh potatoes. This grouping was also consistent when maximum likelihood trees were constructed and further confirmed by a principal coordinate analysis. A group of 19 accessions stored as Andean varieties clustered consistently with group Tuberosum accessions. This was in agreement with previous studies and we hypothesized that they may be reintroductions of European-bred long day-adapted potatoes. The present study constitutes a valuable source for allele mining of genes of interest and thus provides a tool for association mapping studies.

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.

MULTIVARIATE ANALYSES OF POTATO HYBRIDS. I. DISCRIMINATION BETWEEN TETRAPLOID-DIPLOID HYBRID FAMILIES AND THEIR RELATIONSHIP TO CULTIVARS

Clones of ten 4x-2x hybrid families were obtained by crossing five Group Tuberosum parents with each of two (Group Phureja × haploid Group Tuberosum) parents. The performances of horticultural traits of the 4x-2x progenies were distinctly different from those of the 4x parents and cultivars. Multivariate analyses of eight traits were performed on data of each of the three field trials in 1976, 1977 and 1978 and on the means of clones over the three years. Multivariate analyses of variance indicated significant differences between mean vectors of the 4x-2x families. Canonical analysis based on means of clones revealed clearly the effects of 4x and 2x parents on the distributions of the 4x-2x families. However, analysis of canonical distances between the hybrid families also suggested the possible existence of interactions of 4x and 2x parents. Substantial distance was observed between the 4x-2x families and the 4x parents and cultivars. The results lead to a discussion on future strategies of using the 4x-2x hybrids in potato breeding.