Genome evolution and diversity of wild and cultivated potatoes

Abstract

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.

Profiling of the Candidate Interacting Proteins of SELF-PRUNING 6A (SP6A) in Solanum tuberosum

“…However, the molecular mechanism of flowering and branching remains elusive. Some proteins interacting with StSP6A have been reported, including StFDL1, StABL1, StSWEET11, and BRC1b [ 6 , 7 , 8 , 9 , 11 ]. It is important to explore whether there are some other unknown StSP6A interactors involved in other functions.…”

“…It has been also reported that StSP6A is involved in branching and flowering [ 9 , 10 ]. A TCP transcription factor, BRANCHED1b (BRC1b), interacts with StSP6A to promote dormancy and repress tuberization [ 9 , 11 ]. Under SD conditions, the development of flower buds is repressed by the tuberization signal StSP6A [ 10 ].…”

Alternative Modes of Introgression-Mediated Selection Shaped Crop Adaptation to Novel Climates

“…1 c ; Hardigan et al 2017 ). A recent study on the potato pan-genome shows that both ILS and hybridization/introgression have contributed to blurring evolutionary relationships between wild potato species and landraces ( Tang et al 2022 ).…”

“…Confounding signals: The adaptive hybridization/introgression signal can be easily confounded with incomplete lineage sorting (ILS; Pamilo and Nei 1988 ; Doyle 1992 ; Maddison 1997 ; Rosenberg and Nordborg 2002 ; Blanco-Pastor et al 2011 ; Tang et al 2022 ). Analyses that distinguish both patterns (such as the four taxon f 4 [ Patterson et al 2012 ] or f d [ Martin et al 2015 ] statistics or the five-taxon D FOIL [ Pease and Hahn 2015 ] statistic, which are all related to the genome-wide summary ABBA-BABA test [ Green et al 2010 ]) are essential tools for detecting introgression.…”

TheSolanum americanumpangenome and effectoromics reveal new resistance genes against potato late blight

“…Phased, chromosome-level genome assemblies of heterozygous diploid and tetraploid potatoes are also available [17][18][19] . Pan-genome studies of crop plants including potato have also emerged, that shed light on the extensive genetic variation in these species [20][21][22][23] . To reduce the genomic complexity and sequencing costs, resistance gene enrichment sequencing (RenSeq) and RLP/K enrichment sequencing (RLP/KSeq) technologies were developed to sequence plant NLR and PRR gene repertoires [24][25][26] .…”