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Hojsgaard D, Nagel M, Feingold SE, Massa GA, Bradshaw JE. New Frontiers in Potato Breeding: Tinkering with Reproductive Genes and Apomixis. Biomolecules 2024; 14:614. [PMID: 38927018 PMCID: PMC11202281 DOI: 10.3390/biom14060614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Potato is the most important non-cereal crop worldwide, and, yet, genetic gains in potato have been traditionally delayed by the crop's biology, mostly the genetic heterozygosity of autotetraploid cultivars and the intricacies of the reproductive system. Novel site-directed genetic modification techniques provide opportunities for designing climate-smart cultivars, but they also pose new possibilities (and challenges) for breeding potato. As potato species show a remarkable reproductive diversity, and their ovules have a propensity to develop apomixis-like phenotypes, tinkering with reproductive genes in potato is opening new frontiers in potato breeding. Developing diploid varieties instead of tetraploid ones has been proposed as an alternative way to fill the gap in genetic gain, that is being achieved by using gene-edited self-compatible genotypes and inbred lines to exploit hybrid seed technology. In a similar way, modulating the formation of unreduced gametes and synthesizing apomixis in diploid or tetraploid potatoes may help to reinforce the transition to a diploid hybrid crop or enhance introgression schemes and fix highly heterozygous genotypes in tetraploid varieties. In any case, the induction of apomixis-like phenotypes will shorten the time and costs of developing new varieties by allowing the multi-generational propagation through true seeds. In this review, we summarize the current knowledge on potato reproductive phenotypes and underlying genes, discuss the advantages and disadvantages of using potato's natural variability to modulate reproductive steps during seed formation, and consider strategies to synthesize apomixis. However, before we can fully modulate the reproductive phenotypes, we need to understand the genetic basis of such diversity. Finally, we visualize an active, central role for genebanks in this endeavor by phenotyping properly genotyped genebank accessions and new introductions to provide scientists and breeders with reliable data and resources for developing innovations to exploit market opportunities.
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Affiliation(s)
- Diego Hojsgaard
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany;
| | - Manuela Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany;
| | - Sergio E. Feingold
- Laboratorio de Agrobiotecnología, EEA Balcarce-IPADS (UEDD INTA–CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce B7620, Argentina; (S.E.F.); (G.A.M.)
| | - Gabriela A. Massa
- Laboratorio de Agrobiotecnología, EEA Balcarce-IPADS (UEDD INTA–CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce B7620, Argentina; (S.E.F.); (G.A.M.)
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce B7620, Argentina
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Azariadis A, Andrzejczak OA, Carlsen FM, Westberg I, Brinch-Pedersen H, Petersen BL, Hebelstrup KH. A Walk on the Wild Side: Genome Editing of Tuber-Bearing Solanum bulbocastanum. PLANTS (BASEL, SWITZERLAND) 2024; 13:1044. [PMID: 38611572 PMCID: PMC11013279 DOI: 10.3390/plants13071044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
Solanum bulbocastanum is a wild diploid tuber-bearing plant. We here demonstrate transgene-free genome editing of S. bulbocastanum protoplasts and regeneration of gene-edited plants. We use ribonucleoproteins, consisting of Cas9 and sgRNA, assembled in vitro, to target a gene belonging to the nitrate and peptide transporter family. Four different sgRNAs were designed and we observed efficiency in gene-editing in the protoplast pool between 8.5% and 12.4%. Twenty-one plants were re-generated from microcalli developed from individual protoplasts. In three of the plants we found that the target gene had been edited. Two of the edited plants had deletion mutations introduced into both alleles, whereas one only had a mutation in one of the alleles. Our work demonstrates that protocols for the transformation of Solanum tuberosum can be optimized to be applied to a wild Solanum species.
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Affiliation(s)
- Aristotelis Azariadis
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| | - Olga A. Andrzejczak
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| | - Frida M. Carlsen
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark; (F.M.C.); (I.W.); (B.L.P.)
| | - Ida Westberg
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark; (F.M.C.); (I.W.); (B.L.P.)
| | - Henrik Brinch-Pedersen
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
| | - Bent L. Petersen
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark; (F.M.C.); (I.W.); (B.L.P.)
| | - Kim H. Hebelstrup
- Section for Crop Genetics & Biotechnology, Department of Agroecology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark; (A.A.); (H.B.-P.)
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Ye M, Yao M, Li C, Gong M. Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato. PeerJ 2023; 11:e15771. [PMID: 37547711 PMCID: PMC10399558 DOI: 10.7717/peerj.15771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
CRISPR/Cas9-mediated genome editing technology has been widely used for the study of gene function in crops, but the differences between species have led to widely varying genome editing efficiencies. The present study utilized a potato hairy root genetic transformation system and incorporated a rapid assay with GFP as a screening marker. The results clearly demonstrated that salt and osmotic stress induced by NaCl (10 to 50 mM) and mannitol (50 to 200 mM) treatments significantly increased the positive rates of genetic transformation mediated by A. rhizogenes and the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato. However, it was observed that the regeneration of potato roots was partially inhibited as a result. The analysis of CRISPR/Cas9-mediated mutation types revealed that chimeras accounted for the largest proportion, ranging from 62.50% to 100%. Moreover, the application of salt and osmotic stress resulted in an increased probability of null mutations in potato. Notably, the highest rate of null mutations, reaching 37.5%, was observed at a NaCl concentration of 10 mM. Three potential off-target sites were sequenced and no off-targeting was found. In conclusion, the application of appropriate salt and osmotic stress significantly improved the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato, with no observed off-target effects. However, there was a trade-off as the regeneration of potato roots was partially inhibited. Overall, these findings present a new and convenient approach to enhance the genome editing efficiency of the CRISPR/Cas9-mediated gene editing system in potato.
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Affiliation(s)
- Mingwang Ye
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
| | - Mengfan Yao
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
| | - Canhui Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
- Joint Academy of Potato Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Ming Gong
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, Yunnan, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology of Yunnan Province, Yunnan Normal University, Kunming, Yunnan, China
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Siddappa S, Sharma N, Salaria N, Thakur K, Pathania S, Singh B, Sharma H, Sood S, Bhardwaj V, Thakur AK, Mangal V, Kumar V, Muruthachallam R, Singh K, Tuli R. CRISPR/Cas9-mediated editing of phytoene desaturase ( PDS) gene in an important staple crop, potato. 3 Biotech 2023; 13:129. [PMID: 37064007 PMCID: PMC10097850 DOI: 10.1007/s13205-023-03543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
The gene editing using the CRISPR/Cas9 system has become an important biotechnological tool for studying gene function and improving crops. In this study, we have used CRISPR/Cas9 system for editing the phytoene desaturase gene (PDS) in popular Indian potato cultivar Kufri Chipsona-I. A construct (pHSE401) carrying two target gRNAs with glycine tRNA processing system under the control of Arabidopsis U6 promoter and the Cas9 protein was constructed and transformed in potato plants using Agrobacterium-mediated genetic transformations. The regeneration efficiency of 45% was observed in regenerated plants, out of which 81% of the putative transformants shoot lines exhibited mutant or bleached phenotype (albinism). The deletion mutations were detected within the StPDS gene in the genotyped plants and a mutation efficiency of 72% for gRNA1 and gRNA2 has been detected using Sanger sequencing. Hence, we set up a CRISPR/Cas9-mediated genome editing protocol which is efficient and generates mutations (deletions) within StPDS gene in potato. The bleached phenotype is easily detectable after only few weeks after Agrobacterium-mediated transformation. This is the first report as a proof of concept for CRISPR/Cas9-based editing of PDS gene in Indian potato cv. Kufri Chipsona-I. This study demonstrates that CRISPR/Cas9 can be used to edit genes at high frequency within the genome of the potato for various traits. Therefore, this study will aid in creating important mutants for modifying molecular mechanisms controlling traits of agronomic importance.
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Affiliation(s)
| | - Neha Sharma
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Neha Salaria
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Kajal Thakur
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Shruti Pathania
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Himani Sharma
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Ajay K. Thakur
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, H.P. 171001 India
| | - Ravi Muruthachallam
- Indian Institute of Science Education and Research, Thiruvananthapuram, 695016 India
| | - Kashmir Singh
- UIET, Panjab University, Chandigarh, Punjab 160015 India
| | - Rakesh Tuli
- UIET, Panjab University, Chandigarh, Punjab 160015 India
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Chincinska IA, Miklaszewska M, Sołtys-Kalina D. Recent advances and challenges in potato improvement using CRISPR/Cas genome editing. PLANTA 2022; 257:25. [PMID: 36562862 PMCID: PMC9789015 DOI: 10.1007/s00425-022-04054-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Genome editing using CRISPR/Cas technology improves the quality of potato as a food crop and enables its use as both a model plant in fundamental research and as a potential biofactory for producing valuable compounds for industrial applications. Potato (Solanum tuberosum L.) plays a significant role in ensuring global food and nutritional security. Tuber yield is negatively affected by biotic and abiotic stresses, and enzymatic browning and cold-induced sweetening significantly contribute to post-harvest quality losses. With the dual challenges of a growing population and a changing climate, potato enhancement is essential for its sustainable production. However, due to several characteristics of potato, including high levels of heterozygosity, tetrasomic inheritance, inbreeding depression, and self-incompatibility of diploid potato, conventional breeding practices are insufficient to achieve substantial trait improvement in tetraploid potato cultivars within a relatively short time. CRISPR/Cas-mediated genome editing has opened new possibilities to develop novel potato varieties with high commercialization potential. In this review, we summarize recent developments in optimizing CRISPR/Cas-based methods for potato genome editing, focusing on approaches addressing the challenging biology of this species. We also discuss the feasibility of obtaining transgene-free genome-edited potato varieties and explore different strategies to improve potato stress resistance, nutritional value, starch composition, and storage and processing characteristics. Altogether, this review provides insight into recent advances, possible bottlenecks, and future research directions in potato genome editing using CRISPR/Cas technology.
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Affiliation(s)
- Izabela Anna Chincinska
- Department of Plant Physiology and Biotechnology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Magdalena Miklaszewska
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
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Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
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D'Amelia V, Staiti A, D'Orso F, Maisto M, Piccolo V, Aversano R, Carputo D. Targeted mutagenesis of StISAC stabilizes the production of anthocyanins in potato cell culture. PLANT DIRECT 2022; 6:e433. [PMID: 35949953 PMCID: PMC9352536 DOI: 10.1002/pld3.433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
To increase the production of decorated anthocyanins in potato cell cultures, we knocked out a novel potato gene, named Inducer Silencing of Anthocyanins in Cell culture (StISAC), using CRISPR-Cas9 editing. Our results provided evidence that mutant cell lines doubled the accumulation level of anthocyanins biosynthesized. Moreover, the production of these important pigments was stabilized over time. Our study overcame important challenges in the efficient biotechnological production of these valuable pigments and reported the function of a novel anthocyanin biosynthesis repressor gene.
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Affiliation(s)
- Vincenzo D'Amelia
- Institute of Biosciences and Bioresources (IBBR)National Research Council of ItalyPorticiItaly
| | - Annalisa Staiti
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Fabio D'Orso
- Research Centre for Genomics and Bioinformatics (CREA‐GB)Council for Agricultural Research and EconomicsRomeItaly
| | - Maria Maisto
- Department of PharmacyUniversity of Naples Federico IINaplesItaly
| | - Vincenzo Piccolo
- Department of PharmacyUniversity of Naples Federico IINaplesItaly
| | - Riccardo Aversano
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Domenico Carputo
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
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