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Cho KS, Lee HO, Lee SC, Park HJ, Seo JH, Cho JH, Park YE, Choi JG, Yang TJ. Mitochondrial genome recombination in somatic hybrids of Solanum commersonii and S. tuberosum. Sci Rep 2022; 12:8659. [PMID: 35606486 PMCID: PMC9127095 DOI: 10.1038/s41598-022-12661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.
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Affiliation(s)
- Kwang-Soo Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, 50424, Republic of Korea.
| | - Hyun-Oh Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,Phyzen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Sang-Choon Lee
- Phyzen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Hyun-Jin Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jin-Hee Seo
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Ji-Hong Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Young-Eun Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jang-Gyu Choi
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Paluchowska P, Śliwka J, Yin Z. Late blight resistance genes in potato breeding. PLANTA 2022; 255:127. [PMID: 35576021 PMCID: PMC9110483 DOI: 10.1007/s00425-022-03910-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
Using late blight resistance genes targeting conservative effectors of Phytophthora infestans and the constructing gene pyramids may lead to durable, broad-spectrum resistance, which could be accelerated through genetic engineering. Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. In 2020, potato production was estimated to be more than 359 million tons according to the Food and Agriculture Organization (FAO). Potato is affected by many pathogens, among which Phytophthora infestans, causing late blight, is of the most economic importance. Crop protection against late blight requires intensive use of fungicides, which has an impact on the environment and humans. Therefore, new potato cultivars have been bred using resistance genes against P. infestans (Rpi genes) that originate from wild relatives of potato. Such programmes were initiated 100 years ago, but the process is complex and long. The development of genetic engineering techniques has enabled the direct transfer of resistance genes from potato wild species to cultivars and easier pyramiding of multiple Rpi genes, which potentially increases the durability and spectrum of potato resistance to rapidly evolving P. infestans strains. In this review, we summarize the current knowledge concerning Rpi genes. We also discuss the use of Rpi genes in breeding as well as their detection in existing potato cultivars. Last, we review new sources of Rpi genes and new methods used to identify them and discuss interactions between P. infestans and host.
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Affiliation(s)
- Paulina Paluchowska
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Zhimin Yin
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
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Sharma S, Sundaresha S, Bhardwaj V. Biotechnological approaches in management of oomycetes diseases. 3 Biotech 2021; 11:274. [PMID: 34040923 DOI: 10.1007/s13205-021-02810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/24/2021] [Indexed: 11/26/2022] Open
Abstract
Plant pathogenic oomycetes cause significant impact on agriculture and, therefore, their management is utmost important. Though conventional methods to combat these pathogens (resistance breeding and use of fungicides) are available but these are limited by the availability of resistant cultivars due to evolution of new pathogenic races, development of resistance in the pathogens against agrochemicals and their potential hazardous effects on the environment and human health. This has fuelled a continual search for novel and alternate strategies for management of phytopathogens. The recent advances in oomycetes genome (Phytophthora infestans, P. ramorum, P. sojae, Pythium ultimum, Albugo candida etc.) would further help in understanding host-pathogen interactions essentially needed for designing effective management strategies. In the present communication the novel and alternate strategies for the management of oomycetes diseases are discussed.
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Affiliation(s)
- Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - S Sundaresha
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
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Handayani T, Gilani SA, Watanabe KN. Climatic changes and potatoes: How can we cope with the abiotic stresses? BREEDING SCIENCE 2019; 69:545-563. [PMID: 31988619 PMCID: PMC6977456 DOI: 10.1270/jsbbs.19070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/10/2019] [Indexed: 05/06/2023]
Abstract
Climate change triggers increases in temperature, drought, and/or salinity that threaten potato production, because they necessitate specific amounts and quality of water, meanwhile lower temperatures generally support stable crop yields. Various cultivation techniques have been developed to reduce the negative effects of drought, heat and/or salinity stresses on potato. Developing innovative varieties with relevant tolerance to abiotic stress is absolutely necessary to guarantee competitive production under sub-optimal environments. Commercial varieties are sensitive to abiotic stresses, and substantial changes to their higher tolerance levels are not easily achieved because their genetic base is narrow. Nonetheless, there are several other possibilities for genetic enhancement using landraces and wild relatives. The complexity of polysomic genetics and heterozygosity in potato hamper the phenotype evaluation over abiotic stresses and consequent conventional introgression of tolerance traits, which are more challenging than previous successes shown over diseases and insects resistances. Today, potatoes face more challenges with severe abiotic stresses. Potato wild relatives can be explored further using innovative genomic, transcriptomic, proteomic, and metabolomic approaches. At the field level, appropriate cultivation techniques must be applied along with precision farming technology and tolerant varieties developed from various breeding techniques, in order to realize high yield under multiple stresses.
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Affiliation(s)
- Tri Handayani
- Graduate School of Life & Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
- Indonesian Vegetable Research Institute,
Jl. Tangkuban Perahu 517, Lembang, West Bandung, West Java, 40391,
Indonesia
| | - Syed Abdullah Gilani
- Department of Biological Sciences and Chemistry, University of Nizwa,
P. O. Box 33, PC 616, Birkat Al Mouz, Nizwa,
Sultanate of Oman
| | - Kazuo N. Watanabe
- Tsukuba-Plant Innovation Research Center, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
- Corresponding author (e-mail: )
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Smyda-Dajmund P, Śliwka J, Wasilewicz-Flis I, Jakuczun H, Zimnoch-Guzowska E. Genetic composition of interspecific potato somatic hybrids and autofused 4x plants evaluated by DArT and cytoplasmic DNA markers. PLANT CELL REPORTS 2016; 35:1345-58. [PMID: 26993327 PMCID: PMC4869754 DOI: 10.1007/s00299-016-1966-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/01/2016] [Indexed: 05/24/2023]
Abstract
Using DArT analysis, we demonstrated that all Solanum × michoacanum (+) S. tuberosum somatic hybrids contained all parental chromosomes. However, from 13.9 to 29.6 % of the markers from both parents were lost in the hybrids. Somatic hybrids are an interesting material for research of nucleus-cytoplasm interaction and sources of new nuclear and cytoplasmic combinations. Analyses of genomes of somatic hybrids are essential for studies on genome compatibility between species, its evolution and are important for their efficient exploitation. Diversity array technology (DArT) permits analysis of the composition of nuclear DNA of somatic hybrids. The nuclear genome compositions of 97 Solanum × michoacanum (+) S. tuberosum [mch (+) tbr] somatic hybrids from five fusion combinations and 11 autofused 4x mch were analyzed for the first time based on DArT markers. Out of 5358 DArT markers generated in a single assay, greater than 2000 markers were polymorphic between parents, of which more than 1500 have a known chromosomal location on potato genetic or physical map. DArT markers were distributed along the entire length of 12 chromosomes. We noticed elimination of markers of wild and tbr fusion components. The nuclear genome of individual somatic hybrids was diversified. Mch is a source of resistance to Phytophthora infestans. From 97 mch (+) tbr somatic hybrids, two hybrids and all 11 autofused 4x mch were resistant to P. infestans. The analysis of the structure of particular hybrids' chromosomes indicated the presence of markers from both parental genomes as well as missing markers spread along the full length of the chromosome. Markers specific to chloroplast DNA and mitochondrial DNA were used for analysis of changes within the organellar genomes of somatic hybrids. Random and non-random segregations of organellar DNA were noted.
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Affiliation(s)
- Paulina Smyda-Dajmund
- Plant Breeding and Acclimatization Institute - National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland.
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute - National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute - National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute - National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Ewa Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute - National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
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Castañeda-Álvarez NP, de Haan S, Juárez H, Khoury CK, Achicanoy HA, Sosa CC, Bernau V, Salas A, Heider B, Simon R, Maxted N, Spooner DM. Ex situ conservation priorities for the wild relatives of potato (solanum L. Section petota). PLoS One 2015; 10:e0122599. [PMID: 25923711 PMCID: PMC4414521 DOI: 10.1371/journal.pone.0122599] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/11/2015] [Indexed: 12/28/2022] Open
Abstract
Crop wild relatives have a long history of use in potato breeding, particularly for pest and disease resistance, and are expected to be increasingly used in the search for tolerance to biotic and abiotic stresses. Their current and future use in crop improvement depends on their availability in ex situ germplasm collections. As these plants are impacted in the wild by habitat destruction and climate change, actions to ensure their conservation ex situ become ever more urgent. We analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota) with the aim of establishing priorities for further collecting to fill important gaps in germplasm collections. A total of 32 species (43.8%), were assigned high priority for further collecting due to severe gaps in their ex situ collections. Such gaps are most pronounced in the geographic center of diversity of the wild relatives in Peru. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, with only three species determined to be sufficiently represented currently. Priorities for further collecting include: (i) species completely lacking representation in germplasm collections; (ii) other high priority taxa, with geographic emphasis on the center of species diversity; (iii) medium priority species. Such collecting efforts combined with further emphasis on improving ex situ conservation technologies and methods, performing genotypic and phenotypic characterization of wild relative diversity, monitoring wild populations in situ, and making conserved wild relatives and their associated data accessible to the global research community, represent key steps in ensuring the long-term availability of the wild genetic resources of this important crop.
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Affiliation(s)
- Nora P. Castañeda-Álvarez
- Decision and Policy Analysis Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Stef de Haan
- Global Program Genetic Resources, International Potato Center (CIP), Lima, Peru
| | - Henry Juárez
- Global Program Genetic Resources, International Potato Center (CIP), Lima, Peru
| | - Colin K. Khoury
- Decision and Policy Analysis Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Centre for Crop Systems Analysis, Wageningen University, Wageningen, The Netherlands
| | - Harold A. Achicanoy
- Decision and Policy Analysis Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Chrystian C. Sosa
- Decision and Policy Analysis Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Vivian Bernau
- Decision and Policy Analysis Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Alberto Salas
- Global Program Genetic Resources, International Potato Center (CIP), Lima, Peru
| | - Bettina Heider
- Global Program Genetic Resources, International Potato Center (CIP), Lima, Peru
| | - Reinhard Simon
- Integrated IT and Computational Research Unit, International Potato Center (CIP), Lima, Peru
| | - Nigel Maxted
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - David M. Spooner
- USDA-ARS, Vegetable Crop Research Unit, Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
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Moustafa K. Toward breeding new land-sea plant hybrid species irrigable with seawater for dry regions. PLANT SIGNALING & BEHAVIOR 2015; 10:e992744. [PMID: 25806436 PMCID: PMC4622069 DOI: 10.4161/15592324.2014.992744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 06/04/2023]
Abstract
A plant species growing in sea or coastal saltmarsh is greatly tolerant to high concentrations of salts, and a plant species growing in desert or dry regions is highly tolerant to drought. Breeding a new plant hybrid species from both species by means of cellular grafting, genome fusion or nuclear transfer would generate, at least in theory, a hybrid plant species that should be strongly tolerant to harsh aridity and salinity and would be potentially irrigable with seawater. Such prospective species can be used for example as a fodder, biofuel crop or stabilizer species to protect soil from wind erosion and sandy storms in dry regions. Breeding such species would change the surface of the world and help to solve major challenges of starvation, malnutrition and poverty. Here, I propose potential approaches that would be worthy of investigation toward this purpose.
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Affiliation(s)
- Khaled Moustafa
- Conservatoire National des Arts et Métiers (CNAM); Paris, France
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