Addendum: Genome evolution and diversity of wild and cultivated potatoes

Abstract

By analyses of potato pan-genome and transcriptome, we discovered a TCP transcription factor, Soltu.DM.06G025210, determining tuber identity, on the basis of which we named this gene Identity of Tuber 1 (IT1).After our manuscript was accepted in principle, a study by Nicolas et al. 1 showed that BRANCHED1b acts as a tuberization repressor in aerial axillary buds in tetraploid potato. We note that IT1 and BRANCHED1b are the same gene. The name BRANCHED1b represents the A. thaliana nomenclature system 2 . We chose the name IT1 because the function of Soltu.DM.06G025210 in potato had not been reported before and our study suggests that it acts as a key regulator in potato tuberization, a new function that is different from its orthologue in tomato and Arabidopsis where it represses branching. Considering the difference in the function, we proposed the new name IT1 for Soltu.DM.06G025210.Both studies confirmed that IT1/BRANCHED1b interacts with the mobile tuberization inductive signal SP6A and plays an essential role in tuberization. Further investigation is awaited into how the same gene promotes tuberization in underground shoots (stolons) and represses tuberization in aerial axillary buds.

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

“…We searched in our co-expression network for co-expression clusters harboring genes, StSP6A and IT1, involved in tuberization (Tang et al 2022 ). We found two co-expression clusters, Cluster_23 and Cluster_97, containing IT1 and StSP6A, respectively.…”

“…We used the CDS sequences of 14 Rpi genes (Armstrong et al 2019 ) and the protein sequence of PhAN2 (UniProt ID: A4GRV2) (Laimbeer et al 2020 ) to identify their homologs in the reference genome. We used the protein sequences of the tuber identity gene (IT1; ID: Soltu.DM.06G025210) and the SELF-PRUNING 6A (SP6A; ID: Soltu.DM.05G026370) genes to identify respective homologs in the reference genome (Tang et al 2022 ). We used the CDS sequences of eight S-RNases involved in self-incompatibility, as mentioned in Dzidzienyo et al ( 2016 ), to identify their homologs in the reference genome.…”

“…To develop improved cultivars, researchers have employed diverse omics approaches, which have been instrumental in augmenting crop productivity (Yang et al 2021 ). A milestone in potato omics-based research was the availability of several reference-quality, chromosome-scale and haplotype-resolved genome assemblies, which helped in understanding the complexity and evolution of the potato genome (Potato Genome Sequencing Consortium 2011 ; Tang et al 2022 ; Sun et al 2022 ; Hoopes et al 2022 ; Bao et al 2022 ; Freire et al 2021 ; Leisner et al 2018 ; Zhou et al 2020 ). These potato whole-genome sequencing projects have also contributed to the significant rise in potato transcriptome studies and reported spatiotemporal changes occurring in various potato tissues using RNA-seq (e.g., Massa et al 2011 ; Chandrasekar et al 2022 ; Tiwari et al 2020 ; Pieczynski et al 2018 ; Chen et al 2019 ; Cao et al 2020 ; Tai et al 2020 ).…”

A global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

“…All these genes accomplish the defense responses by detecting the molecules secreted by pathogens and activating a suite of dense response processes against the pathogens (Feehan et al, 2020). In this study, we identi ed 578 NLR genes (Table S27), which is signi cantly lower than the number of predicted NLR genes for most potato accessions (Tang et al, 2022) but slightly higher than for the wild relatives of sweet potato species, Ipomoea tri da (547 NLR genes) and Ipomoea triloba (569 NLR genes) (Wu et al, 2018). We found 226 NLR genes present in 43 co-expression clusters, which enriched for various biological processes involved in defense responses, of which several co-expression clusters enriched for defense response processes against multiple pathogens (Fungi/Bacterium/Virus) (Table S28).…”

“…The FLOWERING LOCUS T (FT) protein (StSP6A) controls potato tuberization (Navarro et al, 2011). In addition, a TCP TF, called Identity of Tuber 1 (IT1), interacts with StSP6A and forms a protein complex which regulates the tuber initiation (Tang et al, 2022). Nevertheless, insights into the transcriptional complexity behind tuberization still need to be discovered that may identify unknown genes playing an essential role in tuber development.…”