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Frontini A, Negro C, Accogli R, Minonne F, Luvisi A, De Bellis L. Valorization of a Local Italian Pear ( Pyrus communis L. cv. 'Petrucina'). Foods 2024; 13:1528. [PMID: 38790827 PMCID: PMC11120312 DOI: 10.3390/foods13101528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
In recent decades, the food production chain has undergone transformations that have profoundly affected the way food is supplied, causing changes in the quality of the final products. Moreover, biodiversity is seriously threatened worldwide, and the valorization of local germplasm is a priority goal for most sectorial policies in Europe and elsewhere. Southern Italy and the Mediterranean basin present a vast heritage of fruit tree cultivars that is gradually being lost. Through this work, we aim to valorize a well-adapted local pear cultivar named Petrucina from the Salento area (southeastern Italy, Apulia region), which has never been studied before in detail. With this aim, the nutritional and nutraceutical features of pear flesh were characterized and compared with a reference pear cultivar that is widespread and well-known in Europe (cv. 'Conference'). Petrucina fruits have shown a peculiar aromatic compound profile, and a content of up to 398.3, 30.9, and 4.7 mg/100 g FW of malic acid, citric acid, and ascorbic acid, respectively, much higher than that of Conference fruits. Additionally, Petrucina flesh presents a more than triple total phenolic content and an antioxidant activity more than double that of Conference, making Petrucina a true functional food that deserves wide appreciation.
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Affiliation(s)
- Alessandro Frontini
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Salento University, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (A.F.); (R.A.); (A.L.); (L.D.B.)
| | - Carmine Negro
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Salento University, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (A.F.); (R.A.); (A.L.); (L.D.B.)
| | - Rita Accogli
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Salento University, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (A.F.); (R.A.); (A.L.); (L.D.B.)
| | - Francesco Minonne
- Comitato Esecutivo Parco “Costa Otrranto-Leuca e Bosco di Tricase”, 73039 Tricase, Italy;
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Salento University, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (A.F.); (R.A.); (A.L.); (L.D.B.)
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Salento University, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (A.F.); (R.A.); (A.L.); (L.D.B.)
- National Biodiversity Future Center, 90133 Palermo, Italy
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Yang S, Yu X, Gao X, Fatima K, Tahir Ul Qamar M. Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns. Front Genet 2024; 15:1393487. [PMID: 38798703 PMCID: PMC11116618 DOI: 10.3389/fgene.2024.1393487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024] Open
Abstract
In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d'Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.
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Affiliation(s)
- Sheng Yang
- Pomology Institute, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, China
| | - Xiaomei Yu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Xinke Gao
- College of Horticulture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
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Ma Y, Sun J, Zhang X, Sadaqat M, Tahir Ul Qamar M, Liu T. Comparative genomics analysis of pheophorbide a oxygenase ( PAO) genes in eight pyrus genomes and their regulatory role in multiple stress responses in Chinese pear ( Pyrus bretschneideri). Front Genet 2024; 15:1396744. [PMID: 38689648 PMCID: PMC11058654 DOI: 10.3389/fgene.2024.1396744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d'Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs. Cis-elements, protein-protein interactions (PPI), and the Gene Ontology (GO) enrichment analyses show their potential biological functions. Furthermore, their expression in various tissues, fruit hardening conditions, and drought stress conditions is also studied. Based on phylogenetics, the identified PAOs were divided into four groups. The expansion of this gene family in Pyrus is caused by both tandem and segmental duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The Pyrus PAO genes were enriched in hormones-related, light, development, and stress-related elements. RNA-seq data analysis showed that PAOs have varied levels of expression under diseased and abiotic stress conditions. The 3D structures of PAOs are also predicted to get more insights into functional conservation. Our research can be used further to get a deeper knowledge of the PAO gene family in Pyrus and to guide future research on improving the genetic composition of Pyrus to enhance stress tolerance.
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Affiliation(s)
- Yuchen Ma
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Jiao Sun
- Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Shanxi Datong University, Datong, China
- Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Shanxi Datong University, Datong, China
| | - Xiao Zhang
- Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Shanxi Datong University, Datong, China
- Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Shanxi Datong University, Datong, China
| | - Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Tingting Liu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
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Chen S, Sun M, Xu S, Xue C, Wei S, Zheng P, Gu K, Qiao Z, Liu Z, Zhang M, Wu J. The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp. BMC PLANT BIOLOGY 2023; 23:430. [PMID: 37710163 PMCID: PMC10503127 DOI: 10.1186/s12870-023-04406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data. DESCRIPTION Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services. CONCLUSIONS The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.
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Affiliation(s)
- Shulin Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Manyi Sun
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaozhuo Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Cheng Xue
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Shuwei Wei
- Shandong Institute of Pomology, Tai'an, 271000, China
| | - Pengfei Zheng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwen Qiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Mingyue Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Jun Wu
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Regni L, Facchin SL, da Silva DF, Proietti P, Silvestri C, Micheli M. Optimization of the In Vitro Proliferation of an Ancient Pear Tree Cultivar ('Decana d'inverno') through the Use of Neem Oil. PLANTS (BASEL, SWITZERLAND) 2023; 12:1593. [PMID: 37111817 PMCID: PMC10146127 DOI: 10.3390/plants12081593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
In vitro culture, ensuring rapid multiplication and production of plant material under aseptic conditions, represents an excellent tool for ex-situ conservation of tree species biodiversity and can be used for the conservation, among others, of endangered and rare crops. Among the Pyrus communis L. cultivars that have been abandoned over the years due to changed cultivation requirements, but which are still used today in breeding programs, there is the 'Decana d'inverno'. Pear is generally considered a recalcitrant species for in vitro propagation due to weak multiplication rate, hyperhydricity, and susceptibility to phenolic oxidation. Therefore, the use of natural substances like neem oil (although little explored) represents one of the options to improve the in vitro plant's tissue culture. In this context, the aim of the present work was to evaluate the effect of adding neem oil (0.1 and 0.5 m L L-1) to the growth substrate in order to optimise the in vitro culture of the ancient pear tree cultivar 'Decana d'inverno'. The neem oil addition resulted in an increase in the number of shoots produced especially at both concentrations used. On the contrary, an increase in length of proliferated shoots was observed only with the addition of 0.1 mL L-1. The neem oil addition did not affect the explants viability, fresh and dry weights. Therefore, the present study demonstrated for the first time the possibility of using neem oil to optimise the in vitro culture of an ancient pear tree cultivar.
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Affiliation(s)
- Luca Regni
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 06121 Perugia, Italy; (S.L.F.); (P.P.); (M.M.)
| | - Simona Lucia Facchin
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 06121 Perugia, Italy; (S.L.F.); (P.P.); (M.M.)
| | - Daniel Fernandes da Silva
- Campus Marechal Cândido Rondon, Universidade Estadual do Oeste do Paraná, Rua Pernambuco 1777, Cascavel 85819-110, PR, Brazil;
| | - Primo Proietti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 06121 Perugia, Italy; (S.L.F.); (P.P.); (M.M.)
| | - Cristian Silvestri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy;
| | - Maurizio Micheli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 06121 Perugia, Italy; (S.L.F.); (P.P.); (M.M.)
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Draga S, Palumbo F, Miracolo Barbagiovanni I, Pati F, Barcaccia G. Management of genetic erosion: The (successful) case study of the pear ( Pyrus communis L.) germplasm of the Lazio region (Italy). FRONTIERS IN PLANT SCIENCE 2023; 13:1099420. [PMID: 36699862 PMCID: PMC9868429 DOI: 10.3389/fpls.2022.1099420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Pyrus communis L. is an important temperate fruit with high nutritional and economic value. Italy, as the largest pear producer in the EU and second in the world, has a particularly rich germplasm characterized by hundreds of local varieties. The Lazio Region was the first Italian region to start programs focused on safeguarding varieties at risk of extinction and has started a massive census of fruit varieties by combining molecular data and productive-territorial information. In this study, 311 pear accessions collected from the five provinces of the Lazio region were genetically characterized by the means of nine simple sequence repeat (SSR) markers, eight of which were recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR). The SSR analysis revealed 250 unique genotypes and 14 cases of synonymies, namely, accessions with different names but identical molecular profiles (100% genetic similarity). The microsatellite set showed a high polymorphism information content (PIC; mean PIC=0.77) and an exceptionally high discrimination power (DP = 0.99), making it particularly efficient both for the study of genetic diversity and for the prediction of the degree of ploidy. Notably, 20% of the accessions displayed triallelic profiles (i.e., accessions having ≥2 loci with a third allele), while the remaining accessions were diploids. These results were further confirmed by flow cytometry data analysis. Standardization of the molecular analyses at the national and international levels and harmonization of the SSR sets used for germplasm characterization are of paramount importance for producing molecular profiles useful for registration and variety maintenance.
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Affiliation(s)
- Samela Draga
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Padua, Italy
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Padua, Italy
| | | | - Francesco Pati
- ARSIAL, Agenzia Regionale per lo Sviluppo e l'Innovazione dell'Agricoltura del Lazio, Via Rodolfo Lanciani, Roma, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Padua, Italy
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Vinceti B, Elias M, Azimov R, Turdieva M, Aaliev S, Bobokalonov F, Butkov E, Kaparova E, Mukhsimov N, Shamuradova S, Turgunbaev K, Azizova N, Loo J. Home gardens of Central Asia: Reservoirs of diversity of fruit and nut tree species. PLoS One 2022; 17:e0271398. [PMID: 35901122 PMCID: PMC9333230 DOI: 10.1371/journal.pone.0271398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Central Asia is an important center of origin for many globally valued fruit and nut tree species. Forest degradation and deforestation are cause for concern for the conservation of these valuable species, now confined to small remnant populations. Home gardens have the important function of sustaining household food consumption and income generation, and can potentially play a critical role in conserving diversity of fruit and nut trees. These systems have been very poorly documented in the scientific literature. This study contributes to filling this gap by describing the diversity of fruit and nut trees in home gardens of Kyrgyzstan, Uzbekistan, and Tajikistan, examining their dynamic flow of planting material and its sources, understanding their future prospects, and looking at significant differences between the three countries. Home gardens show a similar portfolio of the most abundant tree species (apple, apricot, walnut, pear, and plum). Although the diversity of tree species and varieties recorded is significant, small population sizes can limit future possibilities for this diversity to thrive, given the pressure on natural stands and on habitats where the preferred species are found. Furthermore, the selection of species and varieties to be planted in home gardens is increasingly influenced by market opportunities and availability of exotic material. Some of the most abundant tree species recorded are represented largely by exotic varieties (apple, pear), while others (e.g., apricot, walnut, plum) are still mainly characterized by traditional local varieties that are not formally registered. Home gardens continue to play a critical role in rural livelihoods and in national economies, and many rural inhabitants still aspire to maintain them. Thus, home gardens should be integrated in national research and extension systems and closely linked to national conservation efforts. Changes and possible declines in the diversity they host, their health status, and resilience should be carefully monitored.
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Affiliation(s)
| | | | | | | | - Sagynbek Aaliev
- Kyrgyz National Agrarian University named after K. I. Skryabin, Bishkek, Kyrgyzstan
| | - Farhod Bobokalonov
- Institute of Horticulture and Vegetable Growing of Tajik Academy of Agricultural Sciences, Dushanbe, Tajikistan
| | - Evgeniy Butkov
- Republican Scientific and Production Center of Ornamental Gardening and Forestry, Tashkent, Uzbekistan
| | - Elmira Kaparova
- Kyrgyz National Agrarian University named after K. I. Skryabin, Bishkek, Kyrgyzstan
| | - Nurullo Mukhsimov
- Republican Scientific and Production Center of Ornamental Gardening and Forestry, Tashkent, Uzbekistan
| | - Svetlana Shamuradova
- Institute of Horticulture and Vegetable Growing of Tajik Academy of Agricultural Sciences, Dushanbe, Tajikistan
| | | | - Nodira Azizova
- National University of Uzbekistan named after Mirzo Ulugbek, Tashkent, Uzbekistan
| | - Judy Loo
- Bioversity International, Rome, Italy
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Aycan M, Baslam M, Asiloglu R, Mitsui T, Yildiz M. Development of new high-salt tolerant bread wheat (Triticum aestivum L.) genotypes and insight into the tolerance mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:314-327. [PMID: 34147724 DOI: 10.1016/j.plaphy.2021.05.041] [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: 03/14/2021] [Accepted: 05/24/2021] [Indexed: 05/24/2023]
Abstract
The loss of cropland soils, climate change, and population growth are directly affecting the food supply. Given the higher incidence of salinity and extreme events, the cereal performance and yield are substantially hampered. Wheat is forecast to decline over the coming years due to the salinization widespread as one of the oldest and most environmental severe constraints facing global cereal production. To increase salinity tolerance of wheat, in this study, we developed two new salt-tolerant bread wheats, named 'Maycan' and 'Yıldız'. The salinity tolerance of these lines, their parents, and a salt-sensitive cultivar has been tested from measurements of physiological, biochemical, and genes associated with osmotic adjustment/plant tolerance in cultures containing 0 and 150 mM NaCl at the seedling stage. Differential growth reductions to increased salinity were observed in the salt-sensitive cultivar, with those newly developed exhibiting significantly greater root length, growth of shoot and water content as salinity tolerances overall than their parents. 'Maycan' and 'Yıldız' had higher osmoregulator proline content and antioxidants enzyme activities under salinity than the other bread wheat tested. Notably, an important upregulation in the expression of genes related to cellular ion balance, osmolytes accumulation, and abscisic acid was observed in both new wheat germplasms, which may improve salt tolerance. These finding revealed that 'Maycan' and 'Yıldız' exhibit high-salt tolerance at the seedling stage and differing in their tolerance mechanisms to the other tested cultivars, thereby providing an opportunity for their exploitation as modern bread wheats.
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Affiliation(s)
- Murat Aycan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Rasit Asiloglu
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Mustafa Yildiz
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey.
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Trejo L, Reyes M, Cortés-Toto D, Romano-Grande E, Muñoz-Camacho LL. Morphological Diversity and Genetic Relationships in Pulque Production Agaves in Tlaxcala, Mexico, by Means of Unsupervised Learning and Gene Sequencing Analysis. FRONTIERS IN PLANT SCIENCE 2020; 11:524812. [PMID: 33013957 PMCID: PMC7505951 DOI: 10.3389/fpls.2020.524812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Pulque is one of the oldest fermented beverages, with its origins dating back to pre-Hispanic Mexico. Recently, public consumption has increased. However, the majority of Agave plantations for pulque production have disappeared or been abandoned in recent decades. To create strategies for the conservation and production of pulque agaves, it is necessary to first determine their taxonomic identities and to better understand their genetic and morphological diversity. Despite the historical importance of pulque in Mexico, little attention has been placed on the study of Agave plants used for its production. Therefore, we analyzed the morphological diversity of vegetative characters of nine landraces of two Agave species (A. salmiana and A. mapisaga) which are widely cultivated for pulque production in Tlaxcala, Mexico. The analysis of morphological characters showed that the landraces largely clustered based on classic taxonomic relationships. One cluster of landraces associated with Agave mapisaga var. mapisaga and another with A. salmiana subsp. salmiana, but with the exception of A. salmiana subsp. salmiana "Ayoteco", which is more closely related with A. mapisaga var. mapisaga. Additionally, we analyzed the genetic relationships between 14 landraces and wild individuals using molecular markers (trnL and ITS). The identified genetic variants or haplotypes and genetic pools mainly corresponded with the species. In the case of "Ayoteco", incongruence between markers was observed. Low selection intensity, genetic flow events, and the plasticity of morphological traits may explain the high number of landraces without clear differences in their morphological diversity (vegetative characters) or genetic pools. The use of reproductive traits and massive sequencing might be useful for identifying possible morphological and genetic changes in the Agave landraces used for pulque production.
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Affiliation(s)
- Laura Trejo
- Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, Universidad Nacional Autónoma de México, Tlaxcala, Mexico
| | - Miguel Reyes
- Departamento de Actuaría, Física y Matemáticas, Universidad de las Américas Puebla, Puebla, Mexico
| | - Daniela Cortés-Toto
- Departamento de Actuaría, Física y Matemáticas, Universidad de las Américas Puebla, Puebla, Mexico
| | - Elvira Romano-Grande
- Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, Universidad Nacional Autónoma de México, Tlaxcala, Mexico
| | - Lizbeth L. Muñoz-Camacho
- Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, Universidad Nacional Autónoma de México, Tlaxcala, Mexico
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10
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Lopes JML, de Carvalho HH, Zorzatto C, Azevedo ALS, Machado MA, Salimena FRG, Grazul RM, Gitzendanner MA, Soltis DE, Soltis PS, Viccini LF. Genetic relationships and polyploid origins in the Lippia alba complex. AMERICAN JOURNAL OF BOTANY 2020; 107:466-476. [PMID: 32115694 DOI: 10.1002/ajb2.1443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Plant genomes vary in size and complexity due in part to polyploidization. Latitudinal analyses of polyploidy are biased toward floras of temperate regions, with much less research done in the tropics. Lippia alba has been described as a tropical polyploid complex with diploid, triploid, tetraploid, and hexaploid accessions. However, no data regarding relationships among the ploidal levels and their origins have been reported. Our goals are to clarify the relationships among accessions of Lippia alba and the origins of each ploidal level. METHODS We investigated 98 samples representing all five geographical regions of Brazil and all ploidal levels using microsatellite (SSR) allelic variation and DNA sequences of ITS and trnL-F. Nine morphological structures were analyzed from 33 herbarium samples, and the chemical compounds of 78 accessions were analyzed by GC-MS. RESULTS Genetic distance analysis, the alignment block pattern, as well as RAxML and Bayesian trees showed that accessions grouped by ploidal level. The triploids form a well-defined group that originated from a single group of diploids. The tetraploids and hexaploid grouped together in SSR and trnL-F analyses. The recovered groups agree with chemical data and morphology. CONCLUSIONS The accessions grouped by ploidal level. Only one origin of triploids from a single group of diploids was observed. The tetraploid origin is uncertain; however, it appears to have contributed to the origin of the hexaploid. This framework reveals linkages among the ploidal levels, providing new insights into the evolution of a polyploid complex of tropical plants.
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Affiliation(s)
- Juliana M L Lopes
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - Cristiane Zorzatto
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
| | | | | | | | - Richard M Grazul
- Department of Chemistry, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
| | | | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Lyderson F Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
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11
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High diversity of Diaporthe species associated with pear shoot canker in China. Persoonia - Molecular Phylogeny and Evolution of Fungi 2020; 45:132-162. [PMID: 34456374 PMCID: PMC8375346 DOI: 10.3767/persoonia.2020.45.05] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/04/2019] [Indexed: 11/25/2022]
Abstract
Species of Diaporthe (syn. Phomopsis) are important endophytes, saprobes and pathogens, infecting a wide range of plants and resulting in important crop diseases. However, the species occurring on pear remain largely unresolved. In this study, a total of 453 Diaporthe isolates were obtained from branches of Pyrus plants (including P. bretschneideri, P. communis, P. pyrifolia and P. ussuriensis collected from 12 provinces in China) showing shoot canker symptoms. Phylogenetic analyses based on five loci (ITS, TEF, CAL, HIS, and TUB) coupled with morphology of 113 representative isolates revealed that 19 Diaporthe species were isolated, representing 13 known species (including D. caryae, D. cercidis, D. citrichinensis, D. eres, D. fusicola, D. ganjae, D. hongkongensis, D. padina, D.pescicola, D. sojae, D. taoicola, D. unshiuensis and D. velutina) and six new species described here as D. acuta, D. chongqingensis, D. fulvicolor, D. parvae, D. spinosa and D. zaobaisu. Although Koch’s postulates confirmed all species to be pathogenic, a high degree of variation in aggressiveness was observed. Moreover, these species have a high diversity, plasticity, and prevalence related to the geographical location and pear species involved.
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12
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Genetic Diversity and Structure of the Portuguese Pear (Pyrus communis L.) Germplasm. SUSTAINABILITY 2019. [DOI: 10.3390/su11195340] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A rich heritage of traditional pear varieties is kept in national Portuguese collections. Out of these varieties, “Rocha” dominates national pear production. Although a noticeable phenotypic variation among clones of this variety has been reported, little is known about its genetic variability, as to date molecular studies have been performed on a single “Rocha” clone. Eleven Simple Sequence Repeats (SSR) markers were used to assess the genetic diversity of 130 local cultivars, 80 of them being “Rocha” clones. The results allowed the differentiation of 75 genotypes of which 29 are “Rocha”. Three synonyms groups and four homonymous groups of other local varieties were confirmed. A Bayesian model-based clustering approach identified two distinct clusters. Using flow cytometry, six cultivars were found to be triploids. These results show high genetic variability among “Rocha” clones. In conclusion, there is a need for different “Rocha” clones to be preserved to enable the correct selection of the multiplication material.
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13
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Urrestarazu J, Kägi C, Bühlmann A, Gassmann J, Santesteban LG, Frey JE, Kellerhals M, Miranda C. Integration of expert knowledge in the definition of Swiss pear core collection. Sci Rep 2019; 9:8934. [PMID: 31221983 PMCID: PMC6586639 DOI: 10.1038/s41598-019-44871-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/15/2019] [Indexed: 12/20/2022] Open
Abstract
Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of approaches that combine formal analytical procedures and expert knowledge on the efficiency of CC definition through a case study to establish a pear CC from the Swiss National Pear Inventory. The CC had to represent a maximum of the genetic diversity, not to exceed 150 accessions, and required to include a priority set (SPPS) with 86 genotypes selected based on expert knowledge. In total, nine strategies were evaluated, resulting of combining compositions of the dataset sampled, sampling sizes and methods. The CCs sampled by mixed approaches provided similar scores, irrespective of the approach considered, and obtained similar efficiency in optimizing the genetic diversity retained. Therefore, mixed approaches can be an appropriate choice for applications involving genetic conservation in tree germplasm collections.
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Affiliation(s)
- J Urrestarazu
- Department of Agronomy, Biotechnology and Food Science, Public University of Navarre, 31006, Pamplona, Spain.
| | - C Kägi
- Federal Office for Agriculture, 3003, Bern, Switzerland
| | | | | | - L G Santesteban
- Department of Agronomy, Biotechnology and Food Science, Public University of Navarre, 31006, Pamplona, Spain
| | - J E Frey
- Agroscope, 8820, Wädenswil, Switzerland
| | | | - C Miranda
- Department of Agronomy, Biotechnology and Food Science, Public University of Navarre, 31006, Pamplona, Spain
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14
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Bennici S, Las Casas G, Distefano G, Di Guardo M, Continella A, Ferlito F, Gentile A, La Malfa S. Elucidating the contribution of wild related species on autochthonous pear germplasm: A case study from Mount Etna. PLoS One 2018; 13:e0198512. [PMID: 29856850 PMCID: PMC5983503 DOI: 10.1371/journal.pone.0198512] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022] Open
Abstract
The pear (genus Pyrus) is one of the most ancient and widely cultivated tree fruit crops in temperate climates. The Mount Etna area claims a large number of pear varieties differentiated due to a long history of cultivation and environmental variability, making this area particularly suitable for genetic studies. Ninety-five pear individuals were genotyped using the simple sequence repeat (SSR) methodology interrogating both the nuclear (nDNA) and chloroplast DNA (cpDNA) to combine an investigation of maternal inheritance of chloroplast SSRs (cpSSRs) with the high informativity of nuclear SSRs (nSSRs). The germplasm was selected ad hoc to include wild genotypes, local varieties, and national and international cultivated varieties. The objectives of this study were as follows: (i) estimate the level of differentiation within local varieties; (ii) elucidate the phylogenetic relationships between the cultivated genotypes and wild accessions; and (iii) estimate the potential genetic flow and the relationship among the germplasms in our analysis. Eight nSSRs detected a total of 136 alleles with an average minor allelic frequency and observed heterozygosity of 0.29 and 0.65, respectively, whereas cpSSRs allowed identification of eight haplotypes (S4 Table). These results shed light on the genetic relatedness between Italian varieties and wild genotypes. Among the wild species, compared with P. amygdaliformis, few P. pyraster genotypes exhibited higher genetic similarity to local pear varieties. Our analysis revealed the presence of genetic stratification with a 'wild' subpopulation characterizing the genetic makeup of wild species and the international cultivated varieties exhibiting the predominance of the 'cultivated' subpopulation.
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Affiliation(s)
- Stefania Bennici
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Giuseppina Las Casas
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Acireale, Italy
| | - Gaetano Distefano
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Mario Di Guardo
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Alberto Continella
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Filippo Ferlito
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Acireale, Italy
| | - Alessandra Gentile
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Stefano La Malfa
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
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15
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Yue X, Zheng X, Zong Y, Jiang S, Hu C, Yu P, Liu G, Cao Y, Hu H, Teng Y. Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia. FRONTIERS IN PLANT SCIENCE 2018; 9:591. [PMID: 29868056 PMCID: PMC5949605 DOI: 10.3389/fpls.2018.00591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/16/2018] [Indexed: 05/03/2023]
Abstract
Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP), Chinese white pear (CWP), Chinese sand pear (CSP), and Ussurian pear (UP), but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR) markers and two non-coding chloroplast DNA (cpDNA) regions (trnL-trnF and accD-psaI). High levels of genetic diversity were detected for both nSSRs (HE = 0.744) and cpDNAs (Hd = 0.792). The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a) JPs; (b) cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c) cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be originated from the interspecific hybridization of wild Pyrus ussuriensis with cultivated Pyrus pyrifolia. The combination of uniparental DNA sequences and nuclear markers give us a better understanding of origins and genetic relationships for Asian pear groups and will be beneficial for the future improvement of Asian pear cultivars.
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Affiliation(s)
- Xiaoyan Yue
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Xiaoyan Zheng
- College of Ecology, Lishui University, Lishui, China
| | - Yu Zong
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Shuang Jiang
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Chunyun Hu
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Peiyuan Yu
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
| | - Guoqin Liu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yufen Cao
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
| | - Hongju Hu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, Hangzhou, China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou, China
- *Correspondence: Yuanwen Teng,
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