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Leuenberger J, Sharma SK, McLean K, Pellé R, Bérard A, Lesage ML, Porhel D, Dantec MA, Chauvin JE, Bryan GJ, Pilet-Nayel ML, Kerlan MC, Esnault F. A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines. FRONTIERS IN PLANT SCIENCE 2024; 15:1384401. [PMID: 38828224 PMCID: PMC11141163 DOI: 10.3389/fpls.2024.1384401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Affiliation(s)
- Julien Leuenberger
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
- Association des Créateurs de Variétés Nouvelle de Pomme de Terre (ACVNPT), Hanvec, France
| | - Sanjeev Kumar Sharma
- Cell & Molecular Science Department, The James Hutton Institute, Dundee, United Kingdom
| | - Karen McLean
- Cell & Molecular Science Department, The James Hutton Institute, Dundee, United Kingdom
| | - Roland Pellé
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | | | - Marie-Laure Lesage
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Danièle Porhel
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Marie-Ange Dantec
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Jean-Eric Chauvin
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Glenn J. Bryan
- Cell & Molecular Science Department, The James Hutton Institute, Dundee, United Kingdom
| | - Marie-Laure Pilet-Nayel
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Marie-Claire Kerlan
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Florence Esnault
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
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Ivanova-Pozdejeva A, Jakobson L, Ilves K, Kivistik A, Kann L, Aida J, Kübarsepp L, Tähtjärv T, Laanemets K. Studies of potato resistance to Globodera rostochiensis revealed novel alleles for 57R marker. BREEDING SCIENCE 2023; 73:300-312. [PMID: 37840978 PMCID: PMC10570887 DOI: 10.1270/jsbbs.22094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/22/2023] [Indexed: 10/17/2023]
Abstract
Globodera rostochiensis resistance has been an important trait in potato (Solanum tuberosum) breeding for decades. Our aim was to complement phenotypic testing with genetic marker analysis. We analysed the results of G. rostochiensis resistance greenhouse testing in 4601 tubers of 2918 breeding clones from 11 years. Applicability of H1 gene markers TG689 and 57R was compared. We implemented the latter with the positive predictive value of 99.1% and negative predictive value of 60.0% into the breeding scheme. The 57R marker alleles of 22 Estonian cultivars and 470 breeding clones were determined. Two unique 57R alleles, 57R-887 and 57R-1155, were found in Estonian cultivar 'Anti'. The 887 bp allele has two deletions (14 bp and 490 bp) accompanied by several other indels and SNPs within the 57R marker region. The 1155 bp allele has three deletions (7 bp, 20 bp and 210 bp) accompanied by several other indels and SNPs within the same region. Partial resistance to G. rostochiensis in 'Anti' suggests that the newly described alleles could affect the H1-mediated resistance directly or indirectly.
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Affiliation(s)
- Anna Ivanova-Pozdejeva
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Liina Jakobson
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Kai Ilves
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Agnes Kivistik
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Liina Kann
- Department of Plant Protection, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Jekaterina Aida
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Liisa Kübarsepp
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
| | - Terje Tähtjärv
- Department of Plant Breeding, Centre of Estonian Rural Research and Knowledge (METK), J. Aamisepa 1, Jõgeva 48309, Estonia
| | - Kristiina Laanemets
- Department of Plant Biotechnology, Centre of Estonian Rural Research and Knowledge (METK), M. Pilli haru 1, Jõgeva 48309, Estonia
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Resistance Evaluation for Native Potato Accessions against Late Blight Disease and Potato Cyst Nematodes by Molecular Markers and Phenotypic Screening in India. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010033. [PMID: 36675982 PMCID: PMC9860717 DOI: 10.3390/life13010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
The potato originated in southern Peru and north-western Bolivia (South America). However, native accessions have also been cultivated in India for many years. Late blight, caused by the fungus Phytophthora infestans, is the most devastating potato disease, while potato cyst nematode (Globodera spp.) (PCN) is another economically significant quarantine-requiring pest in India. In this study, we have generated a new Indian native collection of 94 potato accessions collected from different parts India. These accessions were screened against late blight and potato cyst nematode resistance by using gene-based molecular markers and phenotypic screening methods. Marker assisted selection using R1 gene-specific marker CosA210 revealed a late blight resistance gene in 11 accessions. PCN resistance bands were found in 3 accessions with marker TG689141, 5 accessions with marker 57R452, and 1 accession having Gro1-4-1602 marker for G. rostochiensis (Ro1,4), while 64 accessions amplified marker HC276 indicating G. pallida (Pa2,3) resistance gene (GpaVvrn QTL). On the other hand, phenotypic screening against late blight resistance under natural epiphytic conditions (hot-spot) revealed three accessions with high resistance, while others were resistant (1 accession), moderately resistant (5 accessions), susceptible (29 accessions), and highly susceptible (56 accessions). For G. rostochiensis (golden cyst nematode) and G. pallida (white cyst nematode) resistance, accessions were grouped into highly resistant (3, 3), resistant (0, 2), moderately resistant (6, 29), susceptible (32, 30), and highly susceptible (53, 30), respectively, for the two PCN species. Collectively, we identified promising accessions with high resistance to late blight (JG-1, Kanpuria Safed, and Rangpuria), and also highly resistant to both Globodera species (Garlentic, Jeevan Jyoti, and JG-1). Our findings suggested that these accessions would be useful for late blight and PCN resistance breeding, as well as future molecular studies in potatoes.
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RANGE DYNAMICS OF POTATO NEMATODE <i>GLOBODERA ROSTOCHIENSIS</i> (WOLLENWEBER, 1923) SKARBILOVICH, 1959 UNDER CONDITIONS OF GLOBAL CLIMATE CHANGE IN RUSSIA. RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2022. [DOI: 10.35885/1996-1499-15-3-135-159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Globodera rostochiensis is one of the 100 most dangerous invasive species in Russia, causing significant damage to agriculture. In Russia, this nematode was first founded in Kaliningrad Region in 1949. In this study, we used ensemble modeling (ESDM) methods to predict the potential distribution of G. rostochiensis in Russia and found that with changes in global climate and land use in the future, there would be a tendency to expand the range in two directions - from the south to the north and from the west to the east. The history of the distribution of the species on the territory of Russia, the current and potential ranges of the species from 2020 to 2100 with a step of 20 years in the implementation of various models and scenarios of climate change and land use are presented. Information on native range, features of biology, signs of host plant damage and injuriousness of G. rostochiensis , methods of pathotypes identification, invasion vectors, and control measures are shown. The predicted ranges of the species are important for the development of measures to minimize future invasion of G. rostochiensis and their negative consequences
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Milczarek D, Podlewska-Przetakiewicz A, Plich J, Tatarowska B, Flis B. The relations of broad nematode resistance to quality characteristics as a consequence of marker-assisted selection in potato breeding programs. BREEDING SCIENCE 2021; 71:609-614. [PMID: 35087325 PMCID: PMC8784344 DOI: 10.1270/jsbbs.20121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 08/05/2021] [Indexed: 06/14/2023]
Abstract
Cultivating resistant varieties of potato is the most effective and environmentally sound method of protecting potato crops against pests and diseases. Potato cyst nematodes (PCN) are major nematode pests causing severe constraints in potato production worldwide. There are five pathotypes of Globodrea rostochiensis (Ro1-Ro5) and three of G. pallida Pa1-Pa3. Cultivation of potato varieties with broad nematode resistance may influence the growth of the wide spectrum of PCN pathotypes, but there is limited availability of such varieties on the market. The use of molecular markers allows for the effective selection of resistant genotypes at early stages of breeding. However, the impact of early selection for nematode resistance on the agronomic value of the final selected clones is a cause of concern for potato breeders. This study investigates the relationships between the presence of the combined resistance genes H1, Gro1-4 and GpaVvrn , which confer resistance to the nematodes, and certain agricultural traits. Clones with broad nematode resistance conferred by the genes H1, Gro1-4 and GpaVvrn presented yields and tuber morphology traits similar to those of the clones without identified resistance genes.
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Affiliation(s)
- Dorota Milczarek
- Plant Breeding and Acclimatization Institute–National Research Institute, Research Centre Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Anna Podlewska-Przetakiewicz
- Plant Breeding and Acclimatization Institute–National Research Institute, Department of Plant Pathology, Radzików, 05-870 Błonie, Poland
| | - Jarosław Plich
- Plant Breeding and Acclimatization Institute–National Research Institute, Research Centre Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Beata Tatarowska
- Plant Breeding and Acclimatization Institute–National Research Institute, Research Centre Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Bogdan Flis
- Plant Breeding and Acclimatization Institute–National Research Institute, Research Centre Młochów, Platanowa 19, 05-831 Młochów, Poland
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Totsky IV, Rozanova IV, Safonova AD, Batov AS, Gureeva YA, Khlestkina EK, Kochetov AV. Genotyping of potato samples from the GenAgro ICG SB RAS collection using DNA markers of genes conferring resistance to phytopathogens. Vavilovskii Zhurnal Genet Selektsii 2021; 25:677-686. [PMID: 34755022 PMCID: PMC8553976 DOI: 10.18699/vj21.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/19/2022] Open
Abstract
Wart (a disease caused by Synchytrium endobioticum) and golden cyst potato nematode (Globodera rostochiensis), which parasitize the roots of the host plant, cause signif icant damage to potato crop. Both of these disease factors are quarantined in the Russian Federation, and each registered variety is tested for resistance to their most common races and pathotypes. The main method of opposing such diseases is by the development of resistant varieties. An important step in this process is the selection of resistant genotypes from the population and the estimation of the resistance of hybrids obtained by crosses during the breeding process. Conducting a permanent phenotypic evaluation is associated with diff iculties, for example, it is not always possible to work with pathogens, and phenotypic evaluation is very costly and time consuming. However, the use of DNA markers linked to resistance genes can signif icantly speed up and reduce the cost of the breeding process. The aim of the study was to screen the GenAgro potato collection of ICG SB RAS using known diagnostic PCR markers linked to golden potato cyst nematode and wart resistance. Genotyping was carried out on 73 potato samples using three DNA markers 57R, CP113, Gro1-4 associated with nematode resistance and one marker, NL25, associated with wart resistance. The genotyping data were compared with the data on the resistance of the collection samples. Only the 57R marker had a high level of correlation (Spearman R = 0.722008, p = 0.000000, p < 0.05) between resistance and the presence of a diagnostic fragment. The diagnostic eff iciency of the 57R marker was 86.11 %. This marker can be successfully used for screening a collection, searching for resistant genotypes and marker-assisted selection. The other markers showed a low correlation between the presence of the DNA marker and resistance. The diagnostic eff iciency of the CP113 marker was only 44.44 %. Spearman's correlation coeff icient (Spearman R = -0.109218, p = 0.361104, p < 0.05) did not show signif icant correlation between resistance and the DNA marker. The diagnostic eff iciency of the NL25 marker was 61.11 %. No signif icant correlation was found between the NL25 marker and resistance (Spearman R = -0.017946, p = 0.881061, p < 0.05). The use of these markers for the search for resistant samples is not advisable.
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Affiliation(s)
- I V Totsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Rozanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A D Safonova
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Batov
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu A Gureeva
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E K Khlestkina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Yamakawa H, Haque E, Tanaka M, Takagi H, Asano K, Shimosaka E, Akai K, Okamoto S, Katayama K, Tamiya S. Polyploid QTL-seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole-genome resequencing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2040-2051. [PMID: 34008333 PMCID: PMC8486255 DOI: 10.1111/pbi.13633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 05/27/2023]
Abstract
Potato (Solanum tuberosum L.) and sweetpotato (Ipomoea batatas L.), which are nutritionally and commercially important tuberous crops, possess a perplexing heredity because of their autopolyploid genomes. To reduce cross-breeding efforts for selecting superior cultivars from progenies with innumerable combinations of traits, DNA markers tightly linked to agronomical traits are required. To develop DNA markers, we developed a method for quantitative trait loci (QTL) mapping using whole-genome next-generation sequencing (NGS) in autopolyploid crops. To apply the NGS-based bulked segregant method, QTL-seq was modified. (1) Single parent-specific simplex (unique for one homologous chromosome) single-nucleotide polymorphisms (SNPs), which present a simple segregation ratio in the progenies, were exploited by filtering SNPs by SNP index (allele frequency). (2) Clusters of SNPs, which were inherited unevenly between bulked progenies with opposite phenotypes, especially those with an SNP index of 0 for the bulk that did not display the phenotypes of interest, were explored. These modifications allowed for separate tracking of alleles located on each of the multiple homologous chromosomes. By applying this method, clusters of SNPs linked to the potato cyst nematode resistance H1 gene and storage root anthocyanin (AN) content were identified in tetraploid potato and hexaploid sweetpotato, respectively, and completely linked DNA markers were developed at the site of the presented SNPs. Thus, polyploid QTL-seq is a versatile method that is free from specialized manipulation for sequencing and construction of elaborate linkage maps and facilitates rapid development of tightly linked DNA markers in autopolyploid crops, such as potato and sweetpotato.
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Affiliation(s)
- Hiromoto Yamakawa
- Institute of Crop ScienceNational Agriculture and Food Research Organization (NARO)TsukubaIbarakiJapan
| | - Emdadul Haque
- Kyushu‐Okinawa Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MiyakonojoMiyazakiJapan
| | - Masaru Tanaka
- Kyushu‐Okinawa Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MiyakonojoMiyazakiJapan
| | - Hiroki Takagi
- Department of Bioproduction ScienceIshikawa Prefectural UniversityNonoichi, IshikawaJapan
| | - Kenji Asano
- Hokkaido Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MemuroHokkaidoJapan
| | - Etsuo Shimosaka
- Hokkaido Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MemuroHokkaidoJapan
| | - Kotaro Akai
- Hokkaido Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MemuroHokkaidoJapan
| | - Satoshi Okamoto
- Hokkaido Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MemuroHokkaidoJapan
- Present address:
Center for Seeds and SeedlingsNational Agriculture and Food Research Organization (NARO)TsukubaIbarakiJapan
| | - Kenji Katayama
- Hokkaido Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MemuroHokkaidoJapan
| | - Seiji Tamiya
- Hokkaido Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MemuroHokkaidoJapan
- Present address:
Tohoku Agricultural Research CenterNational Agriculture and Food Research Organization (NARO)MoriokaIwateJapan
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Asano K, Shimosaka E, Yamashita Y, Narabu T, Aiba S, Sakata I, Akai K, Okamoto S, Tamiya S. Improvement of diagnostic markers for resistance to Globodera pallida and application for selection of resistant germplasms in potato breeding. BREEDING SCIENCE 2021; 71:354-364. [PMID: 34776742 PMCID: PMC8573550 DOI: 10.1270/jsbbs.20134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/22/2021] [Indexed: 06/13/2023]
Abstract
Occurrence of pale potato cyst nematode, Globodera pallida (Stone) Behrens, was first recorded in Japan in 2015. Among several control measures, cultivation of resistant potato (Solanum tuberosum L.) varieties is the most effective in cost and environmental impact. As no G. pallida-resistant varieties have yet been developed in Japan, great emphasis is being placed on screening of germplasm possessing the resistance and development of the resistant varieties. In this study, we first improved previously reported DNA markers linked to the G. pallida resistance loci (GpaIVs adg and Gpa5) and then used these to screen more than 1,000 germplasms to select several candidate germplasms with resistance. We performed inoculation testing on the selected candidates and identified several resistant germplasms to the Japanese G. pallida population. Furthermore, we developed a simultaneous detection method combining three DNA markers linked to G. pallida and Globodera rostochiensis (Wollenweber) Behrens resistance loci. We validated the ability of C237-I marker to select resistant allele of GpaIVs adg and predict the presence of resistance in a Japanese breeding population. Resistant germplasms identified in this study could potentially be used to develop G. pallida-resistant varieties. The marker evaluation methods developed in this study will contribute to the efficient development of resistant varieties.
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Affiliation(s)
- Kenji Asano
- Division of Field Crop Research and Development, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 9-4 Shinsei-minami, Memuro, Hokkaido 082-0081, Japan
| | - Etsuo Shimosaka
- Division of Field Crop Research and Development, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 9-4 Shinsei-minami, Memuro, Hokkaido 082-0081, Japan
| | - Yoko Yamashita
- Hokkaido Research Organization, Central Agricultural Experiment Station, Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395, Japan
| | - Takashi Narabu
- Division of Agro-environmental Research, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Satoshi Aiba
- Division of Agro-environmental Research, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Itaru Sakata
- Division of Agro-environmental Research, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Kotaro Akai
- Division of Field Crop Research and Development, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 9-4 Shinsei-minami, Memuro, Hokkaido 082-0081, Japan
| | - Satoshi Okamoto
- Division of Field Crop Research and Development, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 9-4 Shinsei-minami, Memuro, Hokkaido 082-0081, Japan
| | - Seiji Tamiya
- Division of Field Crop Research and Development, Hokkaido Agricultural Research Center, National Agricultural Research Organization, 9-4 Shinsei-minami, Memuro, Hokkaido 082-0081, Japan
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Gartner U, Hein I, Brown LH, Chen X, Mantelin S, Sharma SK, Dandurand LM, Kuhl JC, Jones JT, Bryan GJ, Blok VC. Resisting Potato Cyst Nematodes With Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:661194. [PMID: 33841485 PMCID: PMC8027921 DOI: 10.3389/fpls.2021.661194] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/03/2021] [Indexed: 05/17/2023]
Abstract
Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle-commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
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Affiliation(s)
- Ulrike Gartner
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lynn H. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Xinwei Chen
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sophie Mantelin
- INRAE UMR Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Sanjeev K. Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Louise-Marie Dandurand
- Entomology, Plant Pathology and Nematology Department, University of Idaho, Moscow, ID, United States
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - John T. Jones
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Vivian C. Blok
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Vivian C. Blok,
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Mironenko NV, Gavrilenko TA, Khiutti AV, Afanasenko OS. [Quarantine nematode species and pathotypes potentially dangerous for domestic potato production: populations diversity and the genetics of potato resistance]. Vavilovskii Zhurnal Genet Selektsii 2020; 24:705-721. [PMID: 33738388 PMCID: PMC7960448 DOI: 10.18699/vj20.665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Обзор посвящен проблеме потенциально опасных для отечественного картофелеводства каран-
тинных видов и патотипов нематод. Картофель поражают более 30 видов паразитических нематод, однако в
статье основное внимание уделено самым вредоносным, приносящим большой ущерб картофелеводству пред-
ставителям родов Globodera, Ditylenchus, Nacobbus и Meloidogyne. Проанализированы фитопатологические и
молекулярные методы идентификации видов и патотипов и основные достижения в изучении изменчивости
популяций паразитических нематод картофеля. Показано, что, благодаря особенностям жизненного цикла не-
матод и лабильности их геномов, генетическая изменчивость этих организмов очень велика, что создает угрозу
образования новых патогенных генотипов паразита. Сведения о внутри- и межпопуляционной изменчивости
нематод важны для изучения путей интродукции и распространения отдельных видов, а также поиска корреля-
ций молекулярных маркеров с определенным патотипом. Филогенетические исследования, основанные на со-
временных данных по генетической изменчивости популяций, позволили выявить комплексы видов у Globodera
pallida (Stone) Behrens и Nacobbus aberrans (Thorne) Thorne & Allen (sensu lato), включающие криптические виды.
К основным составляющим успешной защиты, предотвращающей массовое распространение паразитических
нематод, относятся карантинные мероприятия, агротехнические приемы, биологические способы защиты и
возделывание устойчивых сортов. Особое внимание в обзоре уделено вопросам селекции сортов картофеля с
длительной устойчивостью к различным видам нематод, поскольку возделывание таких сортов – экологически
наиболее безопасный и экономически выгодный способ предотвращения эпифитотий. В настоящее время до-
стигнуты значительные успехи в генетической защите сортов картофеля, особенно в отношении цистообразую-
щих нематод. Приведены сведения об источниках устойчивости картофеля к паразитическим нематодам, выде-
ленных в коллекциях диких и культурных видов. Проанализированы данные об идентифицированных R-генах и
QTL устойчивости, которые были интрогрессированы в селекционный материал с помощью различных методов
и подходов. Представлены результаты изучения структурной и функциональной
организации генов устойчиво-
сти к цистообразующим нематодам картофеля. Рассмотрены результаты исследований по использованию моле-
кулярных маркеров определенных генов в маркер-опосредованной селекции для создания новых устойчивых
сортов, в том числе с групповой устойчивостью.
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Affiliation(s)
- N V Mironenko
- All-Russian Research Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T A Gavrilenko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - A V Khiutti
- All-Russian Research Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O S Afanasenko
- All-Russian Research Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Li X, Xu J, Duan S, Zhang J, Bian C, Hu J, Li G, Jin L. Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato ( Solanum tuberosum L.). Int J Mol Sci 2018; 19:ijms19103065. [PMID: 30297627 PMCID: PMC6213731 DOI: 10.3390/ijms19103065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/22/2022] Open
Abstract
Early maturity is one of the most important agronomical traits in potato breeding. To identify the DNA segment that codes for early maturity, a tetraploid potato segregation population of “Zhongshu 19” × “Zhongshu 3” was genetically analyzed, using a combination of high throughput simplified genome sequencing (2b-RAD) and bulked segregant analysis (BSA). The DNA segment related to the early-maturity trait was identified at the 3.7~4.2 Mb locus on the short arm of chromosome 5. Eight molecular markers were developed, of which five were closely linked to the early-maturity trait loci. Additionally, 42 simple sequence repeats (SSR) markers were constructed based on the reference sequence of Solanum tuberosum group Phureja DM1-3 516 R44 (DM). Using the TetraploidMap software, the linkage map of chromosome 5 was constructed with 50 markers. The total map length was 172 centiMorgan (cM), with an average genetic distance of 3.44 cM. Correlating molecular and phenotypic data of the segregating population, the mapped Quantitative Trait Loci (QTL) on the short arm of chromosome 5 contributed to 33.55% of the early-maturity phenotype. The early-maturity QTL was located at 84 cM, flanked by the SSR5-85-1 and SCAR5-8 markers. The QTL was fine-mapped to 471 kb. Using DNA sequence annotation, 34 genes were identified in this region, 12 of them with unknown function. Among the other 22 annotated genes, E3 ubiquitin ligase gene PUB14 could be related to maturity and regulation of tuber formation. The constructed QTL map is a useful basic tool for the cloning of early-maturity related genes in tetraploid potatoes.
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Affiliation(s)
- Xingcui Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Jianfei Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Shaoguang Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Jiaojiao Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Chunsong Bian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Jun Hu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
| | - Liping Jin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affair, Beijing 100081, China.
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12
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Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Alpatyeva NV, Khiutti A, Afanasenko OS. Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. BMC PLANT BIOLOGY 2017; 17:251. [PMID: 29297325 PMCID: PMC5751396 DOI: 10.1186/s12870-017-1193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming. RESULTS Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes. However, compiling a list of candidate R genes for further segregation analysis was hampered by their scarce annotation. Nevertheless, combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the quality of the results and provided a reasonable number of candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode. CONCLUSION Combination of comparative analyses of tissue-specific transcriptomes in resistant and susceptible genotypes may be used as an approach for the rapid identification of candidate potato R genes for co-segregation analysis and may be used in parallel with more sophisticated studies based on genome resequencing.
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Affiliation(s)
- Alex V Kochetov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
- Novosibirsk State Agrarian University, Novosibirsk, 630039, Russia.
| | - Anastasiya Y Glagoleva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | - Elena K Khlestkina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | | | | | | | | | - Nikolay A Shmakov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
| | - Olga Y Antonova
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Tatyana A Gavrilenko
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
- St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Natalia V Alpatyeva
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Alexander Khiutti
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
| | - Olga S Afanasenko
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
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13
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Gabriel J, Veramendi S, Pinto L, Pariente L, Angulo A. Asociaciones de marcadores moleculares con la resistencia a enfermedades, caracteres morfológicos y agronómicos en familias diploides de papa (Solanum tuberosum L.). REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2016. [DOI: 10.15446/rev.colomb.biote.v18n1.57712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>Quince familias de papa (840 genotipos) provenientes de cruzas inter-específicas entre especies de Solanum stenotomum, S. goniocalyx y S. phureja fueron genotipadas, con el objetivo de asociar seis marcadores moleculares (GP94, HC, Nl25, Gro 1-4, RYSC3 y CP60) con genes mayores de resistencia para tizón tardío (Phytophthora infestans), verruga (Synchytrium endobioticum), nematodo - quiste (Globodera pallida y G. rostochiensis) y virus PVY y PVX. Los resultados mostraron que cinco de los marcadores aplicados fueron polimórficos y amplificaron en más del 80% de las familias. El marcador RYSC3 que co-localiza con el gen Ry no amplificó en ninguna de las familias evaluadas. La familia 8 amplificó la banda para tres marcadores (CP60, GP94 y NL25) en la totalidad de sus clones. La prueba de χsup2 se utilizó para determinar el ajuste de las proporciones de segregación de cada familia para cada marcador y genotipar los progenitores. Nueve caracteres agronómicos y morfológicos fueron evaluados en la cosecha. Mediante agrupamiento cluster fueron seleccionados 107 clones con resistencia a PVX, P. infestans, G. rostochiensis y S. endobioticum, alto rendimiento y volumen de tubérculos, elevado número de tubérculos y ojos superficiales. Sobre la base de estos resultados, aspectos prácticos para la aplicación eficiente de la selección asistida por marcadores moleculares son discutidos en este artículo.</p>
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14
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Mori K, Asano K, Tamiya S, Nakao T, Mori M. Challenges of breeding potato cultivars to grow in various environments and to meet different demands. BREEDING SCIENCE 2015; 65:3-16. [PMID: 25931976 PMCID: PMC4374562 DOI: 10.1270/jsbbs.65.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/09/2014] [Indexed: 06/01/2023]
Abstract
The potato (Solanum tuberosum L.) is cultivated all year round in Japan by using four types of cropping: summer and winter croppings, and double cropping in spring and fall. In each cropping season, growth conditions such as temperature, day length, and growing period, differ drastically; thus, different cultivars adapted to each environment are required. Breeding stations are located in both summer cropping areas and double cropping areas, and cultivars suitable for each cropping system are developed. The required cultivars differ according to cropping type and according to use such as table use, food processing, and starch production. The qualities necessary for each purpose differ and are therefore evaluated accordingly. Improvements in pest and disease resistance and in yield abilities are important as common breeding targets for all purposes. To develop potato cultivars that meet different needs, breeders have continued efforts to improve these traits. In this review, we introduce our approaches to developing new potato cultivars. We also discuss problems predicted in the future and introduce our efforts on broadening genetic diversity.
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Affiliation(s)
- Kazuyuki Mori
- Nagasaki Agricultural and Forestry Technical Development Center,
2777 Otsu, Aino-cho, Unzen, Nagasaki 854-0302,
Japan
| | - Kenji Asano
- Upland Farming Resource Research Division, NARO Hokkaido Agricultural Research Center,
9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081,
Japan
| | - Seiji Tamiya
- Upland Farming Resource Research Division, NARO Hokkaido Agricultural Research Center,
9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081,
Japan
| | - Takashi Nakao
- Nagasaki Agricultural and Forestry Technical Development Center,
2777 Otsu, Aino-cho, Unzen, Nagasaki 854-0302,
Japan
| | - Motoyuki Mori
- Upland Farming Resource Research Division, NARO Hokkaido Agricultural Research Center,
9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081,
Japan
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