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1. Unlikely heroes on the long and winding road to potato inbreeding

   https://doi.org/10.1007/s42994-023-00109-5  

   Comai, Luca ( July 2023 , aBIOTECH)

   Sanwen Huang, William Lucas (Ed.)

   Conversion of potato from a tetraploid, heterozygous, vegetatively propagated crop to a diploid F1 hybrid, propagated via botanical seed, would constitute a considerable advance for global agriculture, but faces multiple challenges. One such challenge is the difficulty in inbreeding potato, which involves purging deleterious alleles from its genome. This commentary discusses possible reasons for this difficulty and highlights a recent sequence-based effort to classify SNP variation, in potato germplasm, according to its deleterious potential. Tools and strategies connected to this database may facilitate development of F1 hybrids.

    

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2. Genome evolution and diversity of wild and cultivated potatoes

   https://doi.org/10.1038/s41586-022-04822-x  

   Tang, Dié ; Jia, Yuxin ; Zhang, Jinzhe ; Li, Hongbo ; Cheng, Lin ; Wang, Pei ; Bao, Zhigui ; Liu, Zhihong ; Feng, Shuangshuang ; Zhu, Xijian ; et al ( June 2022 , Nature)

   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 production 1–4 . 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. 

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3. Extensive genome heterogeneity leads to preferential allele expression and copy number‐dependent expression in cultivated potato

   https://doi.org/10.1111/tpj.13706  

   Pham, Gina M. ; Newton, Linsey ; Wiegert‐Rininger, Krystle ; Vaillancourt, Brieanne ; Douches, David S. ; Buell, C. Robin ( October 2017 , The Plant Journal)

   Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (Solanum tuberosumL.),a vegetatively propagated autotetraploid and their impact on the transcriptome. Sequence diversity was high with a mean single nucleotide polymorphisms (SNP) rate of approximately 1 per 50 bases suggestive of high levels of allelic diversity. Additive gene expression was observed in leaves (3605 genes) and tubers (6156 genes) that contrasted the preferential allele expression of between 2180 and 3502 and 3367 and 5270 genes in the leaf and tuber transcriptome, respectively. Preferential allele expression was significantly associated with evolutionarily conserved genes suggesting selection of specific alleles of genes responsible for biological processes common to angiosperms during the breeding selection process. Copy number variation was rampant with between 16 098 and 18 921 genes in each cultivar exhibiting duplication or deletion. Copy number variable genes tended to be evolutionarily recent, lowly expressed, and enriched in genes that show increased expression in response to biotic and abiotic stress treatments suggestive of a role in adaptation. Gene copy number impacts on gene expression were detected with 528 genes having correlations between copy number and gene expression. Collectively, these data suggest that in addition to allelic variation of coding sequence, the heterogenous nature of the tetraploid potato genome contributes to a highly dynamic transcriptome impacted by allele preferential and copy number‐dependent expression effects.

    

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4. Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy

   https://doi.org/10.1111/1755-0998.12935  

   Shan, Shengchen ; Mavrodiev, Evgeny V. ; Li, Riqing ; Zhang, Zhengzhi ; Hauser, Bernard A. ; Soltis, Pamela S. ; Soltis, Douglas E. ; Yang, Bing ( September 2018 , Molecular Ecology Resources)

   Tragopogon(Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9‐based genome editing platform inTragopogonwill facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 inTragopogon. We have established a feasible tissue culture and transformation protocol forTragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted forTragopogon) was capable of introducing site‐specific mutations inTragopogonprotoplasts.Agrobacterium‐mediated transformation with Cas9‐sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles ofTraPDSin albino shoots fromTragopogon porrifolius(2x) andTragopogon mirus(4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9‐based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed inTragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene‐balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other nongenetic model plant systems.

    

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5. A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance

   https://doi.org/10.1093/hr/uhac247  

   Wu, Bo ; Yu, Qibin ; Deng, Zhanao ; Duan, Yongping ; Luo, Feng ; Gmitter Jr, Frederick ( January 2023 , Horticulture Research)

   Abstract Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles from the two species cooperate in shaping sweet orange phenotypes under distinct circumstances is unknown. Here, we assembled a chromosome-level phased diploid Valencia sweet orange (DVS) genome with over 99.999% base accuracy and 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for sweet orange and other hybrids between pummelo and mandarin. We first configured an allele-aware transcriptomic profiling pipeline and applied it to 740 sweet orange transcriptomes. On average, 32.5% of genes have a significantly biased allelic expression in the transcriptomes. Different cultivars, transgenic lineages, tissues, development stages, and disease status all impacted allelic expressions and resulted in diversified allelic expression patterns in sweet orange, but particularly citrus Huanglongbing (HLB) shifted the allelic expression of hundreds of genes in leaves and calyx abscission zones. In addition, we detected allelic structural mutations in an HLB-tolerant mutant (T19) and a more sensitive mutant (T78) through long-read sequencing. The irradiation-induced structural mutations mostly involved double-strand breaks, while most spontaneous structural mutations were transposon insertions. In the mutants, most genes with significant allelic expression ratio alterations (≥1.5-fold) were directly affected by those structural mutations. In T19, alleles located at a translocated segment terminal were upregulated, including CsDnaJ, CsHSP17.4B, and CsCEBPZ. Their upregulation is inferred to keep phloem protein homeostasis under the stress from HLB and enable subsequent stress responses observed in T19. DVS will advance allelic level studies in citrus. 

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