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Walas Ł, Alipour S, Haq SM, Alamri S. The potential range of west Asian apple species Malus orientalis Uglitzk. under climate change. BMC PLANT BIOLOGY 2024; 24:381. [PMID: 38724902 PMCID: PMC11080264 DOI: 10.1186/s12870-024-05081-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
The wild relatives of cultivated apples would be an ideal source of diversity for breeding new varieties, which could potentially grow in diverse habitats shaped by climate change. However, there is still a lack of knowledge about the potential distribution of these species. The aim of the presented work was the understand the impacts of climate change on the potential distribution and habitat fragmentation of Caucasian crab apple (Malus orientalis Uglitzk.) and the designation of areas of high interest according to climatic conditions. We used the MaxEnt models and Morphological-Spatial Analysis (MSPA) to evaluate the potential distribution, suitability changes, habitat fragmentation, and connectivity throughout the species range in Turkey, Armenia, Georgia, Russia, and Iran. The results revealed that the potentially suitable range of M. orientalis encompasses 858,877 km², 635,279 km² and 456,795 km² under the present, RCP4.5 and RCP8.5 scenario, respectively. The range fragmentation analysis demonstrated a notable shift in the edge/core ratio, which increased from 50.95% in the current scenario to even 67.70% in the future. The northern part of the range (Armenia, northern Georgia, southern Russia), as well as the central and western parts of Hyrcania will be a core of the species range with suitable habitats and a high connectivity between M. orientalis populations and could work as major refugia for the studied species. However, in the Zagros and central Turkey, the potential range will shrink due to the lack of suitable climatic conditions, and the edge/core ratio will grow. In the southern part of the range, a decline of M. orientalis habitats is expected due to changing climatic conditions. The future outlook suggests that the Hyrcanian forest and the Caucasus region could serve as important refuges for M. orientalis. This study helps to understand spatial changes in species' range in response to climate change and can help develop conservation strategies. This is all the more important given the species' potential use in future breeding programs aimed at enriching the gene pool of cultivated apple varieties.
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Affiliation(s)
- Łukasz Walas
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, Kórnik, 62-035, Poland.
| | - Shirin Alipour
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, Kórnik, 62-035, Poland.
| | - Shiekh Marifatul Haq
- Department of Ethnobotany, Institute of Botany, Ilia State University, Tbilisi, Georgia
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
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Chen X, Cornille A, An N, Xing L, Ma J, Zhao C, Wang Y, Han M, Zhang D. The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties. Mol Ecol 2023; 32:5125-5139. [PMID: 35510734 DOI: 10.1111/mec.16485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/09/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.
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Affiliation(s)
- Xilong Chen
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Na An
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Libo Xing
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Juanjuan Ma
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Caiping Zhao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Yibin Wang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
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Chen X, Avia K, Forler A, Remoué C, Venon A, Rousselet A, Lucas G, Kwarteng AO, Rover R, Le Guilloux M, Belcram H, Combes V, Corti H, Olverà-Vazquez S, Falque M, Alins G, Kirisits T, Ursu TM, Roman A, Volk GM, Bazot S, Cornille A. Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple. ANNALS OF BOTANY 2023; 131:1025-1037. [PMID: 37148364 PMCID: PMC10332392 DOI: 10.1093/aob/mcad061] [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: 12/30/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations. METHODS Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested. KEY RESULTS A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates. CONCLUSIONS This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.
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Affiliation(s)
- X Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - K Avia
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France
| | - A Forler
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - C Remoué
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Venon
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Rousselet
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Lucas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - A O Kwarteng
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - R Rover
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Le Guilloux
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Belcram
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - V Combes
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Corti
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - S Olverà-Vazquez
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Falque
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Alins
- Institut de Recerca i Tecnologia Agroalimentàries, IRTA-Fruit Production, PCiTAL, Parc 21 de Gardeny, edifici Fruitcentre, 25003 Lleida, Spain
| | - T Kirisits
- Institute of Forest Entomology, Forest Pathology and Forest Protection (IFFF), Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Peter-Jordan-Straße 82 (Franz Schwackhöfer-Haus), A-1190 Vienna, Austria
| | - T M Ursu
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - A Roman
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - G M Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
| | - S Bazot
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris‐Saclay, Orsay, France
| | - A Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
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Sias C, Subramanian N, Hodnett G, Rooney W, Bagavathiannan M. Rate of crop-weed hybridization in Sorghum bicolor × Sorghum halepense is influenced by genetic background, pollen load, and the environment. Evol Appl 2023; 16:781-796. [PMID: 37124087 PMCID: PMC10130556 DOI: 10.1111/eva.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/22/2022] [Accepted: 02/02/2023] [Indexed: 03/29/2023] Open
Abstract
The potential for gene flow between cultivated species and their weedy relatives poses agronomic and environmental concerns, particularly when there are opportunities for the transfer of adaptive or agronomic traits such as herbicide resistance into the weedy forms. Grain sorghum (Sorghum bicolor) is an important crop capable of interspecific hybridization with its weedy relative johnsongrass (Sorghum halepense). Previous findings have shown that triploid progenies resulting from S. bicolor × S. halepense crosses typically collapse with only a few developing into mature seeds, whereas tetraploids often fully develop. The objective of this experiment was to determine the impact of S. bicolor genotype and pollen competition on the frequency of hybridization between S. bicolor and S. halepense. A total of 12 different cytoplasmic male sterile S. bicolor genotypes were compared with their respective male fertile lines across 2 years, to assess the frequency of hybridization and seed set when S. halepense served as the pollinator parent. Results indicate significant differences in the frequency of interspecific hybridization among the S. bicolor genotypes, and pollen fertility in S. bicolor reduced the rate of this interspecific hybridization by up to two orders of magnitude. Further, hybridization rates greatly varied across the two study environments. Results are helpful for developing appropriate gene flow mitigation strategies and indicate that gene flow could be reduced by the selection of appropriate seed parents for sorghum hybrids.
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Affiliation(s)
- Cynthia Sias
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Nithya Subramanian
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
| | - George Hodnett
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
| | - William Rooney
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexasUSA
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5
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Ruhsam M, Bell D, Hart M, Hollingsworth P. The genome sequence of the European crab apple, Malus sylvestris (L.) Mill., 1768. Wellcome Open Res 2022; 7:296. [PMID: 36874569 PMCID: PMC9975420 DOI: 10.12688/wellcomeopenres.18645.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
We present a genome assembly from an individual Malus sylvestris (the European or 'wild' crab apple; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence is 642 megabases in span. Most of the assembly (99.98%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial and chloroplast genomes were also assembled, with respective lengths of 396.9 kilobases and 160.0 kilobases.
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Affiliation(s)
| | - David Bell
- Royal Botanic Garden, Edinburgh, Edinburgh, UK
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6
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Bina H, Yousefzadeh H, Venon A, Remoué C, Rousselet A, Falque M, Faramarzi S, Chen X, Samanchina J, Gill D, Kabaeva A, Giraud T, Hosseinpour B, Abdollahi H, Gabrielyan I, Nersesyan A, Cornille A. Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool. Mol Ecol 2022; 31:5581-5601. [PMID: 35984725 DOI: 10.1111/mec.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/08/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022]
Abstract
Divergence processes in crop-wild fruit tree complexes in pivotal regions for plant domestication such as the Caucasus and Iran remain little studied. We investigated anthropogenic and natural divergence processes in apples in these regions using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two genetically distinct cultivated populations in Iran that are differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences showed that these two cultivated populations originated from specific domestication events of Malus orientalis in Iran. We found evidence of substantial wild-crop and crop-crop gene flow in the Caucasus and Iran, as has been described in apple in Europe. In addition, we identified seven genetically differentiated populations of wild apple (M. orientalis), not introgressed by the cultivated apple. Niche modelling combined with genetic diversity estimates indicated that these wild populations likely resulted from range changes during past glaciations. This study identifies Iran as a key region in the domestication of apple and M. orientalis as an additional contributor to the cultivated apple gene pool. Domestication of the apple tree therefore involved multiple origins of domestication in different geographic locations and substantial crop-wild hybridization, as found in other fruit trees. This study also highlights the impact of climate change on the natural divergence of a wild fruit tree and provides a starting point for apple conservation and breeding programmes in the Caucasus and Iran.
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Affiliation(s)
- Hamid Bina
- Department of Forestry, Tarbiat Modares University, Noor, Iran
| | - Hamed Yousefzadeh
- Department of Environmental Science, Biodiversity Branch, Natural Resources Faculty, Tarbiat Modares University, Noor, Iran
| | - Anthony Venon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Carine Remoué
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Shadab Faramarzi
- Department of Plant Production and Genetics, Faculty of Agriculture, Razi University, Kermanshah, Iran
| | - Xilong Chen
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | | | - David Gill
- Fauna & Flora International, Cambridge, UK
| | | | - Tatiana Giraud
- Ecologie Systematique Evolution, Universite Paris-Saclay, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Batool Hosseinpour
- Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Institute of Agriculture, Tehran, Iran
| | - Hamid Abdollahi
- Temperate Fruits Research Centre, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ivan Gabrielyan
- Department of Palaeobotany, A. Takhtajyan Institute of Botany, Armenian National Academy of Sciences, Yerevan, Armenia
| | - Anush Nersesyan
- Department of Conservation of Genetic Resources of Armenian Flora, A. Takhtajyan Institute of Botany, Armenian National Academy of Sciences, Yerevan, Armenia
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
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7
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Ha YH, Gil HY, Kim SC, Choi K, Kim JH. Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing. Sci Rep 2022; 12:16262. [PMID: 36171257 PMCID: PMC9519971 DOI: 10.1038/s41598-022-20513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
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Wang Z, Cai X, Jiang X, Xia Q, Li L, Lu B. Sympatric genetic divergence between early- and late-season weedy rice populations. THE NEW PHYTOLOGIST 2022; 235:2066-2080. [PMID: 35637631 PMCID: PMC9544748 DOI: 10.1111/nph.18288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Sympatric genetic divergence is the most appealing and controversial pattern in the theory of ecological speciation. Examples that support sympatric genetic divergence in plant species are extremely rare. Solid evidence of sympatric genetic divergence will provide deep insights for revealing the underlying mechanisms of ecological speciation. We analysed the total genomic DNA sequences of 120 weedy rice (WR; Oryza sativa f. spontanea) plants, representing three WR population pairs separately from three early- and late-season rice fields, in comparison with those of the co-occurring rice cultivars and other rice materials. We detected substantial genetic divergence within the pairs of the sympatric early- and late-season WR populations, although genetic divergence was unevenly distributed across the genomes. Restricted gene flow was determined between the sympatric WR populations, resulting in their distinct genetic structures. We also detected relatively low genetic diversity that was likely to be associated with stronger selection in early-season WR populations. Our findings provide strong evidence for sympatric genetic divergence between the WR populations in the same fields but in different seasons. We conclude that temporal isolation plays an important role in creating genetic divergence between sympatric populations/species in plants.
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Affiliation(s)
- Zhi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xingxing Cai
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xiao‐Qi Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Qi‐Yu Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsInstitute of Tropical Bioscience and Biotechnology, CATASHaikou571101China
| | - Lin‐Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
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9
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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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10
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Davies T, Watts S, McClure K, Migicovsky Z, Myles S. Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii). PLoS One 2022; 17:e0250751. [PMID: 35320270 PMCID: PMC8942233 DOI: 10.1371/journal.pone.0250751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada's Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.
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Affiliation(s)
- Thomas Davies
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Sophie Watts
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Kendra McClure
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- * E-mail:
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11
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Wang Y, Paterson AH. Loquat (Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two-staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:942-952. [PMID: 33624402 DOI: 10.1111/tpj.15209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Crop domestication and evolution represent key fields of plant and genetics research. Here, we re-sequenced and analyzed whole genome data from 51 wild accessions and 53 representative cultivars of Eriobotrya japonica, an important semi-subtropical fruit crop. Population genomics analysis suggested that modern cultivated E. japonica experienced a two-staged domestication fitting the "marginality model," being initially domesticated in west-northern Hubei province from a mono-phylogenetic wild progenitor, then refined mainly in Jiangsu, Zhejiang and Fujian provinces of China. Cultivated E. japonica has experienced little reduction in genome-wide nucleotide polymorphism compared with wild forms. Genes responsible for sugar biosynthesis were enriched in regions harboring putative selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes was used to identify convergent/parallel selective sweeps among different crops. Specifically, more than one hundred of orthologs and paralogs undergoing selective sweeps were identified between loquat, apple and peach, among which 14 encoded "UDP glycosyltransferase 1." In sum, the study not only provided valuable information for breeding of E. japonica, but also enriched knowledge of crop domestication.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, Guizhou Province, 556011, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, 30605, USA
- Southwest University, Chongqing, China
- North China University of Science and Technology, Tangshan City, Hebei Province, 063210, China
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12
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Genetic structure of Malus sylvestris and potential link with preference/performance by the rosy apple aphid pest Dysaphis plantaginea. Sci Rep 2021; 11:5732. [PMID: 33707470 PMCID: PMC7970975 DOI: 10.1038/s41598-021-85014-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
The European crabapple Malus sylvestris, a crop wild relative of Malus domestica, is a major contributor to the cultivated apple genome and represents a potential source of interesting alleles or genes, particularly pest resistance traits. An original approach was used to explore the trophic interaction between M. sylvestris populations and its pest, the rosy apple aphid (Dysaphis plantaginea). Using 13 microsatellite markers, population genetic structure and level of crop-to-wild introgressions were inferred between M. sylvestris seedlings from three sites in Europe (Denmark, France, Romania), and M. domestica seedlings. Genetically characterized plants were also used to analyze aphid feeding behavior and fitness parameters. First, aphids submitted to two genetically close M. sylvestris populations (the Danish and French) exhibited similar behavioral parameters, suggesting similar patterns of resistance in these host plants. Second, the Romanian M. sylvestris population was most closely genetically related to M. domestica. Although the two plant genetic backgrounds were significantly differentiated, they showed comparable levels of sensitivity to D. plantaginea infestation. Third, aphid fitness parameters were not significantly impacted by the host plant's genetic background. Finally, crop-to-wild introgression seemed to significantly drive resistance to D. plantaginea independent of host plant population genetic structure, with hybrids being less suitable hosts.
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13
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Ha YH, Oh SH, Lee SR. Genetic Admixture in the Population of Wild Apple ( Malus Sieversii) from the Tien Shan Mountains, Kazakhstan. Genes (Basel) 2021; 12:104. [PMID: 33467767 PMCID: PMC7829876 DOI: 10.3390/genes12010104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/01/2021] [Accepted: 01/12/2021] [Indexed: 01/14/2023] Open
Abstract
There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Diversity, Korea National Arboretum, Pocheon 11186, Korea; (Y.-H.H.); (S.-H.O.)
- Department of Life Sciences, Gachon University, Seongnam 13120, Korea
| | - Seung-Hwan Oh
- Division of Forest Diversity, Korea National Arboretum, Pocheon 11186, Korea; (Y.-H.H.); (S.-H.O.)
| | - Soo-Rang Lee
- Department of Biology Education, College of Natural Sciences, 309 Pilmun-Daero, Dong-Gu, Gwangju 61452, Korea
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14
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Wang X, Shen F, Gao Y, Wang K, Chen R, Luo J, Yang L, Zhang X, Qiu C, Li W, Wu T, Xu X, Wang Y, Cong P, Han Z, Zhang X. Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions. BMC PLANT BIOLOGY 2020; 20:540. [PMID: 33256591 PMCID: PMC7708918 DOI: 10.1186/s12870-020-02744-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars 'Jonathan' and 'Golden Delicious' were used. RESULTS A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7-71.4% of the 331 bud sports derived from 'Fuji', 'Red Delicious', 'Gala', 'Golden Delicious', and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. CONCLUSIONS The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.
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Affiliation(s)
- Xuan Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan Gao
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Kun Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Ruiting Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Present Address: Shaanxi Haisheng Fruit Industry Development Co., Ltd., Shaanxi, Xian, China
| | - Jun Luo
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Lili Yang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Peihua Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China.
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15
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Feurtey A, Guitton E, De Gracia Coquerel M, Duvaux L, Shiller J, Bellanger MN, Expert P, Sannier M, Caffier V, Giraud T, Le Cam B, Lemaire C. Threat to Asian wild apple trees posed by gene flow from domesticated apple trees and their "pestified" pathogens. Mol Ecol 2020; 29:4925-4941. [PMID: 33031644 DOI: 10.1111/mec.15677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022]
Abstract
Secondary contact between crops and their wild relatives poses a threat to wild species, not only through gene flow between plants, but also through the dispersal of crop pathogens and genetic exchanges involving these pathogens, particularly those that have become more virulent by indirect selection on resistant crops, a phenomenon known as "pestification." Joint analyses of wild and domesticated hosts and their pathogens are essential to address this issue, but such analyses remain rare. We used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs of wild or domesticated apple trees from Central Asia and their main fungal pathogen, Venturia inaequalis, which itself has differentiated agricultural and wild-type populations. We confirmed the occurrence of gene flow from cultivated (Malus domestica) to wild (Malus sieversii) apple trees in Asian forests, potentially threatening the persistence of Asian wild apple trees. Pathogenicity tests demonstrated the pestification of V. inaequalis, the agricultural-type population being more virulent on both wild and domesticated trees. Single nucleotide polymorphism (SNP) markers and the demographic modelling of pathogen populations revealed hybridization following secondary contact between agricultural and wild-type fungal populations, and dispersal of the agricultural-type pathogen population in wild forests, increasing the threat of disease in the wild apple species. We detected an SNP potentially involved in pathogen pestification, generating an early stop codon in a gene encoding a small secreted protein in the agricultural-type fungal population. Our findings, based on joint analyses of paired host and pathogen data sets, highlight the threat posed by cultivating a crop near its centre of origin, in terms of pestified pathogen invasions in wild plant populations and introgression in the wild-type pathogen population.
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Affiliation(s)
- Alice Feurtey
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ellen Guitton
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | | | - Ludovic Duvaux
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France.,BIOGECO, INRAE, Université de Bordeaux, Cestas, France
| | - Jason Shiller
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France.,Noble Research Institute, Ardmore, OK, USA
| | | | - Pascale Expert
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Mélanie Sannier
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Valérie Caffier
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Bruno Le Cam
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Christophe Lemaire
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
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16
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Reim S, Lochschmidt F, Proft A, Höfer M. Genetic integrity is still maintained in natural populations of the indigenous wild apple species Malus sylvestris (Mill.) in Saxony as demonstrated with nuclear SSR and chloroplast DNA markers. Ecol Evol 2020; 10:11798-11809. [PMID: 33145002 PMCID: PMC7593173 DOI: 10.1002/ece3.6818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/13/2020] [Accepted: 08/21/2020] [Indexed: 12/25/2022] Open
Abstract
Malus sylvestris (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry, and urbanization increasingly endanger Malus sylvestris natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple Malus × domestica (Borkh.) threaten the genetic integrity of M. sylvestris. The present study investigated the number of hybrids, genetic diversity, and genetic structure of 292 putative M. sylvestris that originate from five different natural M. sylvestris populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony. Eighty-seven percent of the wild apple accessions were identified as pure M. sylvestris. The cpDNA analysis showed six private haplotypes for M. sylvestris, whereas three haplotypes were present in M. sylvestris and M. × domestica. The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure M. sylvestris and M. × domestica individuals indicating a low gene flow between both species. The genetic diversity within the pure M. sylvestris populations was high with a weak genetic structure between the M. sylvestris populations indicating an unrestricted genetic exchange between these M. sylvestris populations. The clear distinguishing of M. sylvestris and M. ×domestica confirms our expectation of the existence of pure M. sylvestris accessions in this area and supports the argument for the implementation of preservation measures to protect the M. sylvestris populations in Saxony.
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Affiliation(s)
- Stefanie Reim
- Federal Research Centre for Cultivated PlantsInstitute for Breeding Research on Fruit CropsJulius Kühn Institute (JKI)DresdenGermany
| | | | - Anke Proft
- Green League Osterzgebirge e.V.DippoldiswaldeGermany
| | - Monika Höfer
- Federal Research Centre for Cultivated PlantsInstitute for Breeding Research on Fruit CropsJulius Kühn Institute (JKI)DresdenGermany
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17
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Spengler RN. Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees. FRONTIERS IN PLANT SCIENCE 2019; 10:617. [PMID: 31191563 PMCID: PMC6545323 DOI: 10.3389/fpls.2019.00617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
The apple (Malus domestica [Suckow] Borkh.) is one of the most economically and culturally significant fruits in the world today, and it is grown in all temperate zones. With over a thousand landraces recognized, the modern apple provides a unique case study for understanding plant evolution under human cultivation. Recent genomic and archaeobotanical studies have illuminated parts of the process of domestication in the Rosaceae family. Interestingly, these data seem to suggest that rosaceous arboreal crops did not follow the same pathway toward domestication as other domesticated, especially annual, plants. Unlike in cereal crops, tree domestication appears to have been rapid and driven by hybridization. Apple domestication also calls into question the concept of centers of domestication and human intentionality. Studies of arboreal domestication also illustrate the importance of fully understanding the seed dispersal processes in the wild progenitors when studying crop origins. Large fruits in Rosaceae evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene. Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers. Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning. Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).
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Affiliation(s)
- Robert Nicholas Spengler
- Paleoethnobotany Laboratories, Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
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18
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Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple. Heredity (Edinb) 2017. [PMID: 28635965 DOI: 10.1038/hdy.2017.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.
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19
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Feurtey A, Cornille A, Shykoff JA, Snirc A, Giraud T. Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe. Evol Appl 2016; 10:180-188. [PMID: 28127394 PMCID: PMC5253423 DOI: 10.1111/eva.12441] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/20/2016] [Indexed: 01/30/2023] Open
Abstract
Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crab-apple fruit tree in particular, is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: (i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crab apples in agrosystems and in forests, (ii) the impact of the level of M. domestica ancestry on individual tree fitness and (iii) pollen dispersal abilities in relation to crop-to-wild gene flow. We found substantial contemporary crop-to-wild gene flow in crab-apple tree populations and superior fitness of hybrids compared to wild seeds and seedlings. Using paternity analyses, we showed that pollen dispersal could occur up to 4 km and decreased with tree density. The seed network furnishing the wild apple reintroduction agroforestry programmes was found to suffer from poor genetic diversity, introgressions and species misidentification. Overall, our findings indicate supported threats for the European wild apple steering us to provide precise recommendations for its conservation.
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Affiliation(s)
- Alice Feurtey
- Ecologie Systématique Evolution Univ. Paris-Sud CNRS AgroParisTech Université Paris-Saclay Orsay France
| | - Amandine Cornille
- Ecologie Systématique Evolution Univ. Paris-Sud CNRS AgroParisTech Université Paris-Saclay Orsay France; Department of Ecology and Genetics Evolutionary Biology Centre Science for Life Laboratory Uppsala University Uppsala Sweden; Adaptation to a Changing Environment ETH Zurich Zurich Switzerland; Present address: Amandine Cornille, Institute of Integrative Biology ETH Zürich Zürich Switzerland
| | - Jacqui A Shykoff
- Ecologie Systématique Evolution Univ. Paris-Sud CNRS AgroParisTech Université Paris-Saclay Orsay France
| | - Alodie Snirc
- Ecologie Systématique Evolution Univ. Paris-Sud CNRS AgroParisTech Université Paris-Saclay Orsay France
| | - Tatiana Giraud
- Ecologie Systématique Evolution Univ. Paris-Sud CNRS AgroParisTech Université Paris-Saclay Orsay France
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20
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Yao JL, Xu J, Cornille A, Tomes S, Karunairetnam S, Luo Z, Bassett H, Whitworth C, Rees-George J, Ranatunga C, Snirc A, Crowhurst R, de Silva N, Warren B, Deng C, Kumar S, Chagné D, Bus VGM, Volz RK, Rikkerink EHA, Gardiner SE, Giraud T, MacDiarmid R, Gleave AP. A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:417-27. [PMID: 26358530 DOI: 10.1111/tpj.13021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 05/20/2023]
Abstract
The molecular genetic mechanisms underlying fruit size remain poorly understood in perennial crops, despite size being an important agronomic trait. Here we show that the expression level of a microRNA gene (miRNA172) influences fruit size in apple. A transposon insertional allele of miRNA172 showing reduced expression associates with large fruit in an apple breeding population, whereas over-expression of miRNA172 in transgenic apple significantly reduces fruit size. The transposon insertional allele was found to be co-located with a major fruit size quantitative trait locus, fixed in cultivated apples and their wild progenitor species with relatively large fruit. This finding supports the view that the selection for large size in apple fruit was initiated prior to apple domestication, likely by large mammals, before being subsequently strengthened by humans, and also helps to explain why signatures of genetic bottlenecks and selective sweeps are normally weaker in perennial crops than in annual crops.
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Affiliation(s)
- Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Juan Xu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud, Bâtiment 360, F-91405, Orsay, France
- CNRS, F-91405, Orsay, France
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Sakuntala Karunairetnam
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Heather Bassett
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, 4442, New Zealand
| | - Claire Whitworth
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Jonathan Rees-George
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Chandra Ranatunga
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Alodie Snirc
- Ecologie, Systématique et Evolution, Université Paris-Sud, Bâtiment 360, F-91405, Orsay, France
- CNRS, F-91405, Orsay, France
| | - Ross Crowhurst
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Nihal de Silva
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Satish Kumar
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, 4442, New Zealand
| | - Vincent G M Bus
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Richard K Volz
- The New Zealand Institute for Plant & Food Research Limited, Havelock North, 4157, New Zealand
| | - Erik H A Rikkerink
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, 4442, New Zealand
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud, Bâtiment 360, F-91405, Orsay, France
- CNRS, F-91405, Orsay, France
| | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew P Gleave
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
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21
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Cornille A, Feurtey A, Gélin U, Ropars J, Misvanderbrugge K, Gladieux P, Giraud T. Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evol Appl 2015; 8:373-84. [PMID: 25926882 PMCID: PMC4408148 DOI: 10.1111/eva.12250] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/09/2014] [Indexed: 02/04/2023] Open
Abstract
Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.
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Affiliation(s)
- Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France ; Department of Plant Ecology and Evolution, Uppsala University Uppsala, Sweden
| | - Alice Feurtey
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| | - Uriel Gélin
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| | | | - Pierre Gladieux
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
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Henry RJ, Nevo E. Exploring natural selection to guide breeding for agriculture. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:655-62. [PMID: 24975385 DOI: 10.1111/pbi.12215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/13/2014] [Accepted: 05/15/2014] [Indexed: 05/02/2023]
Abstract
Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate-resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.
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Affiliation(s)
- Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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23
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The domestication and evolutionary ecology of apples. Trends Genet 2013; 30:57-65. [PMID: 24290193 DOI: 10.1016/j.tig.2013.10.002] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 11/20/2022]
Abstract
The cultivated apple is a major fruit crop in temperate zones. Its wild relatives, distributed across temperate Eurasia and growing in diverse habitats, represent potentially useful sources of diversity for apple breeding. We review here the most recent findings on the genetics and ecology of apple domestication and its impact on wild apples. Genetic analyses have revealed a Central Asian origin for cultivated apple, together with an unexpectedly large secondary contribution from the European crabapple. Wild apple species display strong population structures and high levels of introgression from domesticated apple, and this may threaten their genetic integrity. Recent research has revealed a major role of hybridization in the domestication of the cultivated apple and has highlighted the value of apple as an ideal model for unraveling adaptive diversification processes in perennial fruit crops. We discuss the implications of this knowledge for apple breeding and for the conservation of wild apples.
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