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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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Phenotypic, molecular and biochemical evaluation of somatic hybrids between Solanum tuberosum and S. bulbocastanum. Sci Rep 2022; 12:4484. [PMID: 35296723 PMCID: PMC8927101 DOI: 10.1038/s41598-022-08424-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/28/2022] [Indexed: 01/10/2023] Open
Abstract
Somatic hybridization has been frequently used to overcome sexual incompatibility between potato and its secondary germplasm. The primary objective of this study was to produce and evaluate somatic hybrids of Solanum tuberosum (Stub) and S. bulbocastanum (Sblb) for breeding purposes. In 2007, 23 somatic hybrids were produced using an electrofusion of mesophyll protoplasts of diploid (2n = 2x = 24) potato line StubDH165 and S. bulbocastanum PI24351 (Sblb66). Phenotype of somatic hybrids in field conditions were evaluated, together with constitution and stability of 30 nuclear (ncSSR) and 27 cytoplasmic (cpSSR) microsatellite markers and content of main glycoalkaloids. All somatic hybrids had very high field resistance against late blight, but the plants were infertile: the viability of pollen grains insignificantly varied between 0.58 and 8.97%. A significant somaclonal variation was observed in terms of the morphology of plants, the date of emergence, the quantity of harvested tubers, the content of glycoalkaloids in foliage, and nuclear microsatellite markers (ncSSR). The analysis of ncSSR identified five distinct genotypes of hybrids partly associated with phenotype variations. The process of somatic hybridization with regeneration of shoots was identified as the most likely source of somaclonal variation because the ncSSR genotypes of hybrids, which were maintained in vitro, remained stable for more than 10 years. The infertile somatic hybrids have no practical breeding potential, but they are considered very suitable for advanced studies of the differential expression of genes in the pathways linked to dormancy of tubers and synthesis of glycoalkaloids.
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Smyda-Dajmund P, Śliwka J, Janiszewska M, Zimnoch-Guzowska E. Cytoplasmic diversity of potato relatives preserved at Plant Breeding and Acclimatization Institute in Poland. Mol Biol Rep 2020; 47:3929-3935. [PMID: 32406017 PMCID: PMC7239805 DOI: 10.1007/s11033-020-05486-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/30/2020] [Indexed: 11/06/2022]
Abstract
Among different types of potato cytoplasmic genomes, some are associated with male sterility or affect agronomic traits. The goal of this study was to analyze types of chloroplast and mitochondrial genomes of selected potato relatives originating from collection of the Institute of Plant Industry, Saint Petersburg, Russia, and preserved in Poland. Using chloroplast and mitochondrial markers the cytoplasm types were determined for 401 genotypes belonging to 43 seed accessions of 28 Solanum species. Among characterized genotypes, 201 (50.1%), 156 (38.9%) and 44 (11%) had cytoplasm types W, D, M, respectively. No accessions with the T, P or A cytoplasm were found. Within cytoplasm W, genotypes with the subtypes: W/α and W/β were identified, but not with W/γ. In S. famatinae, we detected unusual product of the T marker with 65 bp insertion earlier seen exclusively in S. vernei. Among the genotypes of S. leptophyes, two profiles of the ALM_4/ALM_5 marker were observed. S. famatinae and S. vernei come from Argentina, provinces Catamarca and Tucumán. Possibly the insertion in marker T occurred independently in two species, or the accessions were misidentified. Segregation of the ALM_4/ALM_5 marker within S. leptophyes indicates that potato seed accessions are heterogeneous not only due to nuclear DNA polymorphisms but have diversified cytoplasm, too. Our findings are important for exploitation of the tested material in potato breeding. Male-fertile cytoplasm types give a chance of avoiding fertility problems and widening the range of crosses in future generations of breeding materials.
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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
| | - Marta Janiszewska
- 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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Norman PE, Paterne AA, Danquah A, Tongoona PB, Danquah EY, De Koeyer D, Ikeogu UN, Asiedu R, Asfaw A. Paternity Assignment in White Guinea Yam ( Dioscorea Rotundata) Half-Sib Progenies from Polycross Mating Design Using SNP Markers. PLANTS 2020; 9:plants9040527. [PMID: 32325826 PMCID: PMC7238154 DOI: 10.3390/plants9040527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022]
Abstract
White Guinea yam is mostly a dioecious outcrossing crop with male and female flowers produced on distinct plants. Fertile parents produce high fruit set in an open pollination polycross block, which is a cost-effective and convenient way of generating variability in yam breeding. However, the pollen parent of progeny from polycross mating is usually unknown. This study aimed to determine paternity in white Guinea yam half-sib progenies from polycross mating design. A total of 394 half-sib progenies from random open pollination involving nine female and three male parents was genotyped with 6602 SNP markers from DArTSeq platform to recover full pedigree. A higher proportion of expected heterozygosity, allelic richness, and evenness were observed in the half-sib progenies. A complete pedigree was established for all progenies from two families (TDr1685 and TDr1688) with 100% accuracy, while in the remaining families, paternity was assigned successfully only for 56 to 98% of the progenies. Our results indicated unequal paternal contribution under natural open pollination in yam, suggesting unequal pollen migrations or gene flow among the crossing parents. A total of 3.8% of progenies lacking paternal identity due to foreign pollen contamination outside the polycross block was observed. This study established the efficient determination of parental reconstruction and allelic contributions in the white Guinea yam half-sib progenies generated from open pollination polycross using SNP markers. Findings are useful for parental reconstruction, accurate dissection of the genetic effects, and selection in white Guinea yam breeding program utilizing polycross mating design.
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Affiliation(s)
- Prince E. Norman
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown PMB 1313, Sierra Leone
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria; (A.A.P.); (R.A.); (A.A.)
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon PMB LG 30, Ghana; (A.D.); (P.B.T.); (E.Y.D.)
- Correspondence: ; Tel.: +232-76-618-454
| | - Agre A. Paterne
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria; (A.A.P.); (R.A.); (A.A.)
| | - Agyemang Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon PMB LG 30, Ghana; (A.D.); (P.B.T.); (E.Y.D.)
| | - Pangirayi B. Tongoona
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon PMB LG 30, Ghana; (A.D.); (P.B.T.); (E.Y.D.)
| | - Eric Y. Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon PMB LG 30, Ghana; (A.D.); (P.B.T.); (E.Y.D.)
| | - David De Koeyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, P.O. Box 20280, Fredericton, NB E3B 4Z7, Canada;
| | - Ugochukwu N. Ikeogu
- Integrative Plant Breeding, Cornell University, Ithaca, New York, NY 14850, USA
| | - Robert Asiedu
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria; (A.A.P.); (R.A.); (A.A.)
| | - Asrat Asfaw
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria; (A.A.P.); (R.A.); (A.A.)
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Varré JS, D'Agostino N, Touzet P, Gallina S, Tamburino R, Cantarella C, Ubrig E, Cardi T, Drouard L, Gualberto JM, Scotti N. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. Int J Mol Sci 2019; 20:E4788. [PMID: 31561566 PMCID: PMC6801519 DOI: 10.3390/ijms20194788] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/01/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.
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Affiliation(s)
- Jean-Stéphane Varré
- Univ. Lille, CNRS, Centrale Lille, UMR 9189-CRIStAL-Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Elodie Ubrig
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - José Manuel Gualberto
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
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Ruiz M, Pensabene-Bellavia G, Quiñones A, García-Lor A, Morillon R, Ollitrault P, Primo-Millo E, Navarro L, Aleza P. Molecular Characterization and Stress Tolerance Evaluation of New Allotetraploid Somatic Hybrids Between Carrizo Citrange and Citrus macrophylla W. rootstocks. FRONTIERS IN PLANT SCIENCE 2018; 9:901. [PMID: 30123223 PMCID: PMC6085489 DOI: 10.3389/fpls.2018.00901] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/07/2018] [Indexed: 05/18/2023]
Abstract
Polyploidy is one of the main forces that drives the evolution of plants and provides great advantages for breeding. Somatic hybridization by protoplast fusion is used in citrus breeding programs. This method allows combining the whole parental genomes in a single genotype, adding complementary dominant characters, regardless of parental heterozygosity. It also contributes to surpass limitations imposed by reproductive biology and quickly generates progenies that combine the required traits. Two allotetraploid somatic hybrids recovered from the citrus rootstocks-Citrus macrophylla (CM) and Carrizo citrange (CC)-were characterized for morphology, genome composition using molecular markers (SNP, SSR, and InDel), and their tolerance to iron chlorosis, salinity, and Citrus tristeza virus (CTV). Both hybrids combine the whole parental genomes even though the loss of parental alleles was detected in most linkage groups. Mitochondrial genome was inherited from CM in both the hybrids, whereas recombination was observed for chloroplastic genome. Thus, somatic hybrids differ from each other in their genome composition, indicating that losses and rearrangements occurred during the fusion process. Both inherited the tolerance to stem pitting caused by CTV from CC, are tolerant to iron chlorosis such as CM, and have a higher tolerance to salinity than the sensitive CC. These hybrids have potential as improved rootstocks to grow citrus in areas with calcareous and saline soils where CTV is present, such as the Mediterranean region. The provided knowledge on the effects of somatic hybridization on the genome composition, anatomy, and physiology of citrus rootstocks will be key for breeding programs that aim to address current and future needs of the citrus industry.
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Affiliation(s)
- Marta Ruiz
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Giovanni Pensabene-Bellavia
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Ana Quiñones
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Andrés García-Lor
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Raphaël Morillon
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Montpellier, France
| | - Patrick Ollitrault
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Montpellier, France
| | - Eduardo Primo-Millo
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
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Cho KS, Cheon KS, Hong SY, Cho JH, Im JS, Mekapogu M, Yu YS, Park TH. Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum. PLANT CELL REPORTS 2016; 35:2113-23. [PMID: 27417695 DOI: 10.1007/s00299-016-2022-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/29/2016] [Indexed: 05/09/2023]
Abstract
Chloroplast genome of Solanum commersonii and S olanum tuberosum were completely sequenced, and Indel markers were successfully applied to distinguish chlorotypes demonstrating the chloroplast genome was randomly distributed during protoplast fusion. Somatic hybridization has been widely employed for the introgression of resistance to several diseases from wild Solanum species to overcome sexual barriers in potato breeding. Solanum commersonii is a major resource used as a parent line in somatic hybridization to improve bacterial wilt resistance in interspecies transfer to cultivated potato (S. tuberosum). Here, we sequenced the complete chloroplast genomes of Lz3.2 (S. commersonii) and S. tuberosum (PT56), which were used to develop fusion products, then compared them with those of five members of the Solanaceae family, S. tuberosum, Capsicum annum, S. lycopersicum, S. bulbocastanum and S. nigrum and Coffea arabica as an out-group. We then developed Indel markers for application in chloroplast genotyping. The complete chloroplast genome of Lz3.2 is composed of 155,525 bp, which is larger than the PT56 genome with 155,296 bp. Gene content, order and orientation of the S. commersonii chloroplast genome were highly conserved with those of other Solanaceae species, and the phylogenetic tree revealed that S. commersonii is located within the same node of S. tuberosum. However, sequence alignment revealed nine Indels between S. commersonii and S. tuberosum in their chloroplast genomes, allowing two Indel markers to be developed. The markers could distinguish the two species and were successfully applied to chloroplast genotyping (chlorotype) in somatic hybrids and their progenies. The results obtained in this study confirmed the random distribution of the chloroplast genome during protoplast fusion and its maternal inheritance and can be applied to select proper plastid genotypes in potato breeding program.
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Affiliation(s)
- Kwang-Soo Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Kyeong-Sik Cheon
- Department of Biological Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Su-Young Hong
- 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
| | - Ju-Seong Im
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Manjulatha Mekapogu
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Yei-Soo Yu
- Phygen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Tae-Ho Park
- Department of Horticulture and Institute of Life and Environment, Daegu University, Gyeongsan, 38453, Republic of Korea.
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