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Nishio S, Shirasawa K, Nishimura R, Takeuchi Y, Imai A, Mase N, Takada N. A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17. FRONTIERS IN PLANT SCIENCE 2024; 15:1360185. [PMID: 38504898 PMCID: PMC10948449 DOI: 10.3389/fpls.2024.1360185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (Pyrus pyrifolia Nakai), '415-1', by using γ-irradiated pollen. '415-1' carries the S-genotype S4dS5S5, with "d" indicating a duplication of S 5 responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F1 seedlings resulting from a cross between '515-20' (S1S3) and '415-1'. Amplicon sequencing of S-RNase and SFBB18 clearly detected S-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes S1S4dS5, S3S4dS5, S1S5dS5, S3S5dS5, and S3S4dS4 were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an S3S4dS4 seedling provided evidence for recombination between the duplicated S5 segment and the original S4haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.
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Affiliation(s)
- Sogo Nishio
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Ryotaro Nishimura
- Fruit Tree Smart Production Group, Division of Fruit Tree Production Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Higashihiroshima, Japan
| | - Yukie Takeuchi
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Atsushi Imai
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Nobuko Mase
- Citrus Breeding and Production Group, Division of Citrus Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Shizuoka, Japan
| | - Norio Takada
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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Claessen H, Van de Poel B, Keulemans W, De Storme N. A semi in vivo pollination technique to assess the level of gametophytic self-incompatibility and pollen tube growth in pear (Pyrus communis L.). PLANT REPRODUCTION 2022; 35:127-140. [PMID: 35032190 DOI: 10.1007/s00497-021-00435-y] [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: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
We describe a semi in vivo pollination technique to determine the compatibility relation between different pear cultivars. This assay provides a valuable addition to existing tools in GSI research. The gametophytic self-incompatibility (GSI) system in Pyrus inhibits fertilization by pollen that shares one of the two S-alleles of the style. Depending on their S-locus genotype, two pear cultivars therefore either show a cross-compatible, semi-compatible or incompatible interaction. Because GSI greatly influences seed and fruit set, accurate knowledge of the compatibility type of a cultivar is key for both pear fruit production and breeding. Currently, compatibility relations between different pear cultivars are generally assessed via S-genotyping. However, this approach is restricted to the currently known S-alleles in pear, and does not provide functional assessment of the level of (self-)incompatibility. We here present an optimized semi in vivo pollination assay, that enables quantitative analysis of (self-)incompatibility in pear, and that can also serve useful for more fundamental studies on pollen tube development and pollen-style interactions. This assay involves in vitro incubation of cut pollinated styles followed by microscopic counting of emerging pollen tubes at a specific time interval. The validity and selectivity of this method to determine compatibility interactions in pear is demonstrated in the cultivars "Celina" and "Packham's Triumph." Overall, this technique constitutes a valuable tool for quantitatively determining in vivo pollen tube growth and (cross-)compatibility in pear.
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Affiliation(s)
- Hanne Claessen
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3000, Leuven, Belgium
| | - Bram Van de Poel
- Laboratory for Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3000, Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3000, Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3000, Leuven, Belgium.
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Kulik T, Bilska K, Żelechowski M. Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA. Int J Mol Sci 2020; 21:E2645. [PMID: 32290169 PMCID: PMC7177237 DOI: 10.3390/ijms21072645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
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Muñoz-Sanz JV, Zuriaga E, Cruz-García F, McClure B, Romero C. Self-(In)compatibility Systems: Target Traits for Crop-Production, Plant Breeding, and Biotechnology. FRONTIERS IN PLANT SCIENCE 2020; 11:195. [PMID: 32265945 PMCID: PMC7098457 DOI: 10.3389/fpls.2020.00195] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/10/2020] [Indexed: 05/13/2023]
Abstract
Self-incompatibility (SI) mechanisms prevent self-fertilization in flowering plants based on specific discrimination between self- and non-self pollen. Since this trait promotes outcrossing and avoids inbreeding it is a widespread mechanism of controlling sexual plant reproduction. Growers and breeders have effectively exploited SI as a tool for manipulating domesticated crops for thousands of years. However, only within the past thirty years have studies begun to elucidate the underlying molecular features of SI. The specific S-determinants and some modifier factors controlling SI have been identified in the sporophytic system exhibited by Brassica species and in the two very distinct gametophytic systems present in Papaveraceae on one side and in Solanaceae, Rosaceae, and Plantaginaceae on the other. Molecular level studies have enabled SI to SC transitions (and vice versa) to be intentionally manipulated using marker assisted breeding and targeted approaches based on transgene integration, silencing, and more recently CRISPR knock-out of SI-related factors. These scientific advances have, in turn, provided a solid basis to implement new crop production and plant breeding practices. Applications of self-(in)compatibility include widely differing objectives such as crop yield and quality improvement, marker-assisted breeding through SI genotyping, and development of hybrids for overcoming intra- and interspecific reproductive barriers. Here, we review scientific progress as well as patented applications of SI, and also highlight future prospects including further elucidation of SI systems, deepening our understanding of SI-environment relationships, and new perspectives on plant self/non-self recognition.
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Affiliation(s)
| | - Elena Zuriaga
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Felipe Cruz-García
- Departmento de Bioquímica, Facultad de Química, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Bruce McClure
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Carlos Romero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat Politécnica de València (UPV), Valencia, Spain
- *Correspondence: Carlos Romero,
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Saito T. Transitions in Leading Japanese Pear Cultivars and Current Status of Pear Breeding at NIFTS, NARO, Japan. J JPN SOC FOOD SCI 2018. [DOI: 10.3136/nskkk.65.419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Toshihiro Saito
- Division of breeding and genetics, Institute of Fruit Tee and Tea Science, National Agriculture and Food Research Organization (NARO)
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Kasajima I, Kikuchi T, Yoshikawa N. Rapid identification of apple ( Malus× domestica Borkh.) S alleles using sequencing-based DNA marker APPLid. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2017; 34:97-106. [PMID: 31275014 PMCID: PMC6543762 DOI: 10.5511/plantbiotechnology.17.0503a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/03/2017] [Indexed: 06/09/2023]
Abstract
All apple cultivars harbor the trait called self-incompatibility. Self-incompatibility represents that the pistils of the flowers are not successfully fertilized with own, the same cultivar's pollens. Compatibility or incompatibility of apple flowers are determined by S alleles. For example, the most popular apple cultivar 'Fuji' possesses the S1 and S9 alleles (S1S9 ). Thus, 'Fuji' is incompatible with S1S9 cultivars, but is compatible with the cultivars possessing different combinations of S alleles such as S2S7 and S1S7 . Apple S alleles have been identified by performing a series of allele-specific PCR amplifications, to detect more than ten different S alleles separately. Here, we developed a new type of sequencing-based DNA marker of the apple S-RNase gene, which identifies S alleles. This DNA marker was named APPLid (apple S-allele identifier). A 53-base region in the first coding sequence of S-RNase is the target of APPLid sequencing. Variation in nucleotide sequences in this APPLid sequence enables allele identifications. This region is amplified from apple genomic DNA by using a pair of degenerate primers. The forward primer is attached with 'DS5 adaptor.' After PCR amplification, electrophoresis and gel extraction of 177-bp DNA fragments, APPLid sequence is determined by direct sequencing with a sequencing primer. The APPLid sequences of 20 apple cultivars completely matched their S alleles, which include triploid cultivars. In conclusion, APPLid identifies apple S alleles (S1 , S2 , S3 , S4 , S5 , S7 , S9 , S10 , S20 , S24 , S25 , S26 , S27 and S28 , so far) just by a single sequencing analysis.
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Affiliation(s)
- Ichiro Kasajima
- Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan
| | - Teppei Kikuchi
- Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan
| | - Nobuyuki Yoshikawa
- Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan
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Saito T. Advances in Japanese pear breeding in Japan. BREEDING SCIENCE 2016; 66:46-59. [PMID: 27069390 PMCID: PMC4780802 DOI: 10.1270/jsbbs.66.46] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/04/2015] [Indexed: 05/09/2023]
Abstract
The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan's history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars 'Chojuro' and 'Nijisseiki' around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars 'Niitaka' and 'Shinko' were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including 'Kosui', 'Hosui', and 'Akizuki', which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, 'Gold Nijisseiki' has become a leading cultivar. Moreover, 'Nansui' from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress.
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Yamamoto T, Terakami S. Genomics of pear and other Rosaceae fruit trees. BREEDING SCIENCE 2016; 66:148-59. [PMID: 27069399 PMCID: PMC4780798 DOI: 10.1270/jsbbs.66.148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 05/04/2023]
Abstract
The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.
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Affiliation(s)
- Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
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