Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)

Abstract

BackgroundRecent genomic studies have drastically altered our knowledge of polyploid evolution. Wild potatoes (Solanum section Petota) are a highly diverse and economically important group of about 100 species widely distributed throughout the Americas. Thirty-six percent of the species in section Petota are polyploid or with diploid and polyploid cytotypes. However, the group is poorly understood at the genomic level and the series is ideal to study polyploid evolution. Two separate studies using the nuclear orthologs GBSSI and nitrate reductase confirmed prior hypotheses of polyploid origins in potato and have shown new origins not proposed before. These studies have been limited, however, by the use of few accessions per polyploid species and by low taxonomic resolution, providing clade-specific, but not species-specific origins within clades. The purpose of the present study is to use six nuclear orthologs, within 54 accessions of 11 polyploid species, 34 accessions of 29 diploid species of section Petota representing their putative progenitors, and two outgroups, to see if phenomena typical of other polyploid groups occur within wild potatoes, to include multiple origins, loss of alleles, or gain of new alleles.ResultsOur results increase resolution within clades, giving better ideas of diploid progenitors, and show unexpected complexity of allele sharing within clades. While some species have little diversity among accessions and concur with the GBSSI and nitrate reductase results, such as S. agrimonifolium, S. colombianum, S. hjertingii, and S. moscopanum, the results give much better resolution of species-specific progenitors. Seven other species, however, show variant patterns of allele distributions suggesting multiple origins and allele loss. Complex three-genome origins are supported for S. hougasii, and S. schenckii, and one of the ten accessions of S. stoloniferum. A very unexpected shared presence of alleles occurs within one clade of S. verrucosum from Central America, and S. berthaultii from South America in six polyploid species S. demissum, S. hjertingii, S. hougasii, S. iopetalum, S. schenckii, and S. stoloniferum.ConclusionsOur results document considerable genomic complexity of some wild potato polyploids. These can be explained by multiple hybrid origins and allele losses that provide a clear biological explanation for the taxonomic complexity in wild potato polyploids. These results are of theoretical and practical benefit to potato breeders, and add to a growing body of evidence showing considerable complexity in polyploid plants in general.

Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)

“…(), Ames and Spooner (), Fajardo and Spooner (), and Cai et al. (). Markers C2At1g13380, C2At5g14320, C2At1g32130, C2At1g20050, C2At2g38020 were initially amplified and sequenced following Rodríguez et al.…”

“…Plastid DNA restriction site studies (Spooner et al., ; Spooner and Sytsma, ; Rodríguez and Spooner, ; Spooner and Castillo, ) recognized four main clades in section Petota , referred to as clades 1–4. Subsequent studies using nuclear orthologs (Spooner et al., ; Rodríguez and Spooner, ; Cai et al., ) recovered three main clades, with similar interspecific relationships except they combined clades 1 and 2 with the nuclear clades then referred to as 1+2, 3, and 4. In‐depth studies of these individual clades have been conducted with morphological and molecular data in clade 1+2 (Rodríguez and Spooner, ; Lara‐Cabrera and Spooner, , ) and clade 3 (Ames et al., ; Ames and Spooner, ).…”

Phylogeny of a Genomically Diverse Group of Elymus (Poaceae) Allopolyploids Reveals Multiple Levels of Reticulation

“…Polyploid origins can be even more difficult to unravel when allopolyploid species form recurrently (e.g., [10,18,43-45]). Subsequent hybridization among them [19,20,22,46-50] can yield individuals with alleles indirectly acquired from many different diploid individuals.…”

Species delimitations in plants: lessons learned from potato taxonomy by a practicing taxonomist

“…Nuclear DNA orthologs have the potential to show allopolyploid origins if it is relatively recent and if there is little genomic change subsequent to their formation. The GBSSI and NIA studies, and a later study of Cai et al (2012) documented allopolyploid origins for most of the polyploid species of section Petota. Like many such studies in other groups, Cai et al (2012) documented considerable genomic complexity of some of the wild potato polyploids that could be explained by multiple hybrid origins and allele losses that theoretically could provide a biological explanation for the taxonomic complexity in wild potato polyploids.…”

“…The GBSSI and NIA studies, and a later study of Cai et al (2012) documented allopolyploid origins for most of the polyploid species of section Petota. Like many such studies in other groups, Cai et al (2012) documented considerable genomic complexity of some of the wild potato polyploids that could be explained by multiple hybrid origins and allele losses that theoretically could provide a biological explanation for the taxonomic complexity in wild potato polyploids. Complimentary genomic in situ hybridization (GISH) studies and fluorescence in situ hybridization (FISH) techniques (Pendinen et al, 2008(Pendinen et al, , 2012 also supported allopolyploid origins of Mexican polyploids (tetraploid species of the Longipedicellata group [S. hjertingii and S. stoloniferum] and hexaploid species of the Iopetala group [S. hougasii, S. iopetalum and S. schenckii]), and supported the diploid Mexican species S. verrucosum (or its ancestral species) as an 'A' genome contributor in all Mexican allopolyploids, confirming the prior hypothesis of classical cytogenetic analysis (Marks, 1965) and DNA sequence data ).…”