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Hernández F, Palmieri L, Brunet J. Introgression and persistence of cultivar alleles in wild carrot (Daucus carota) populations in the United States. AMERICAN JOURNAL OF BOTANY 2023; 110:e16242. [PMID: 37681637 DOI: 10.1002/ajb2.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
PREMISE Cultivated species and their wild relatives often hybridize in the wild, and the hybrids can survive and reproduce in some environments. However, it is unclear whether cultivar alleles are permanently incorporated into the wild genomes or whether they are purged by natural selection. This question is key to accurately assessing the risk of escape and spread of cultivar genes into wild populations. METHODS We used genomic data and population genomic methods to study hybridization and introgression between cultivated and wild carrot (Daucus carota) in the United States. We used single nucleotide polymorphisms (SNPs) obtained via genotyping by sequencing for 450 wild individuals from 29 wild georeferenced populations in seven states and 144 cultivars from the United States, Europe, and Asia. RESULTS Cultivated and wild carrot formed two genetically differentiated groups, and evidence of crop-wild admixture was detected in several but not all wild carrot populations in the United States. Two regions were identified where cultivar alleles were present in wild carrots: California and Nantucket Island (Massachusetts). Surprisingly, there was no evidence of introgression in some populations with a long-known history of sympatry with the crop, suggesting that post-hybridization barriers might prevent introgression in some areas. CONCLUSIONS Our results provide support for the introgression and long-term persistence of cultivar alleles in wild carrots populations. We thus anticipate that the release of genetically engineered (GE) cultivars would lead to the introduction and spread of GE alleles in wild carrot populations.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina
- CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Luciano Palmieri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Madison, WI, USA
| | - Johanne Brunet
- Vegetable Crops Research Unit, USDA-ARS, Madison, WI, USA
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2
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Wu Q, Dong S, Zhao Y, Yang L, Qi X, Ren Z, Dong S, Cheng J. Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:254. [PMID: 37189068 DOI: 10.1186/s12870-023-04212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. RESULTS Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant "Isolation by Distance" between populations. CONCLUSIONS Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.
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Affiliation(s)
- Qi Wu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shang Dong
- Department of Yichun, Heilongjiang Academy of Forestry, Yichun, Heilongjiang, China
| | - Yuxin Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Yang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiujin Qi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhihe Ren
- Management Office of Hebei Dahaituo National Nature Reserve, Chicheng, Hebei, China
| | - Shubin Dong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
| | - Jin Cheng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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3
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Vercellino RB, Hernández F, Pandolfo C, Ureta S, Presotto A. Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds. PEST MANAGEMENT SCIENCE 2023; 79:922-934. [PMID: 36507604 DOI: 10.1002/ps.7321] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/04/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Román B Vercellino
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Fernando Hernández
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Claudio Pandolfo
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Soledad Ureta
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Alejandro Presotto
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
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4
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Owens GL, Huang K, Todesco M, Rieseberg LH. Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers. Mol Biol Evol 2023; 40:6989481. [PMID: 36648104 PMCID: PMC9907532 DOI: 10.1093/molbev/msad013] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best-studied examples of homoploid hybrid speciation. To understand a broader picture of hybridization within the annual sunflowers, we used whole-genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with increasing recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. This means our results are consistent with, but not definitive proof of, two ancient independent homoploid hybrid speciation events in the genus. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.
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Affiliation(s)
| | - Kaichi Huang
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Marco Todesco
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
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5
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Hernández F, Vercellino RB, Pandolfo C, Mandel JR, Presotto A. Rapid evolution of seed dormancy during sunflower de-domestication. J Hered 2022; 113:288-297. [PMID: 35192723 DOI: 10.1093/jhered/esac009] [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: 08/27/2021] [Accepted: 02/21/2022] [Indexed: 11/14/2022] Open
Abstract
Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus annuus L.) is typically found in ruderal environments, but crop-wild hybridization may facilitate the evolution of weedy populations. Using one crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of a recently discovered weedy population of sunflower (named BRW). Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild populations 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines and low differentiation with one wild population, suggesting that wild hybridization increased their genetic diversity. We found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Our results highlight the importance of seed dormancy during the earliest stages of adaptation and show that crop-wild hybrids can evolve quickly in agricultural environments.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
| | - Roman B Vercellino
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
| | - Claudio Pandolfo
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN
| | - Alejandro Presotto
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
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6
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Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
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Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
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7
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Hübner S, Sisou D, Mandel T, Todesco M, Matzrafi M, Eizenberg H. Wild sunflower goes viral: citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant. Mol Ecol 2022; 31:2061-2072. [PMID: 35106854 PMCID: PMC9542508 DOI: 10.1111/mec.16380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Globalization and intensified volume of trade and transport around the world are accelerating the rate of biological invasions. It is therefore increasingly important to understand the processes through which invasive species colonize new habitats, often to the detriment of native flora. The initial steps of an invasion are particularly critical, as the introduced species relies on limited genetic diversity to adapt to a new environment. However, our understanding of this critical stage of the invasion is currently limited. We used a citizen science approach and social media to survey the distribution of invasive sunflower in Israel. We then sampled and sequenced a representative collection and compared it with available genomic data sets of North American wild sunflower, landraces and cultivars. We show that invasive wild sunflower is rapidly establishing throughout Israel, probably from a single, recent introduction from Texas, while maintaining high genetic diversity through ongoing gene flow. Since its introduction, invasive sunflower has spread quickly to most regions, and differentiation was detected despite extensive gene flow between clusters. Our findings suggest that rapid spread followed by continuous gene flow between diverging populations can serve as an efficient mechanism for maintaining sufficient genetic diversity at the early stages of invasion, promoting rapid adaptation and establishment in the new territory.
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Affiliation(s)
- Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai Academic College, Upper Galilee, 11016, Israel
| | - Dana Sisou
- Galilee Research Institute (MIGAL), Tel-Hai Academic College, Upper Galilee, 11016, Israel.,Department of Phytopathology and Weed Research, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel.,The Robert H. Smith Institute of Plant Sciences and Genetics, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tali Mandel
- Galilee Research Institute (MIGAL), Tel-Hai Academic College, Upper Galilee, 11016, Israel
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Maor Matzrafi
- Department of Phytopathology and Weed Research, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Hanan Eizenberg
- Department of Phytopathology and Weed Research, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel
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8
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Cheng J, Kao H, Dong S. Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing. BMC PLANT BIOLOGY 2020; 20:391. [PMID: 32842966 PMCID: PMC7448513 DOI: 10.1186/s12870-020-02594-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/12/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. RESULTS In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. CONCLUSIONS This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.
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Affiliation(s)
- Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huixia Kao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shubin Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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9
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McGoey BV, Hodgins KA, Stinchcombe JR. Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation. Ecol Evol 2020; 10:4595-4608. [PMID: 32551046 PMCID: PMC7297792 DOI: 10.1002/ece3.6163] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 01/06/2023] Open
Abstract
As introduced species expand their ranges, they often encounter differences in climate which are often correlated with geography. For introduced species, encountering a geographically variable climate sometimes leads to the re-establishment of clines seen in the native range. However, clines can also be caused by neutral processes, and so it is important to gather additional evidence that population differentiation is the result of selection as opposed to nonadaptive processes. Here, we examine phenotypic and genetic differences in ragweed from the native (North America) and introduced (European) ranges. We used a common garden to assess phenotypic differentiation in size and flowering time in ragweed populations. We found significant parallel clines in flowering time in both North America and Europe. Height and branch number had significant clines in North America, and, while not statistically significant, the patterns in Europe were the same. We used SNP data to assess population structure in both ranges and to compare phenotypic differentiation to neutral genetic variation. We failed to detect significant patterns of isolation by distance, geographic patterns in population structure, or correlations between the major axes of SNP variation and phenotypes or latitude of origin. We conclude that the North American clines in size and the parallel clines seen for flowering time are most likely the result of adaptation.
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Affiliation(s)
- Brechann V. McGoey
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | | | - John R. Stinchcombe
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Koffler Scientific ReserveUniversity of TorontoTorontoONCanada
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10
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Filippi CV, Merino GA, Montecchia JF, Aguirre NC, Rivarola M, Naamati G, Fass MI, Álvarez D, Di Rienzo J, Heinz RA, Contreras Moreira B, Lia VV, Paniego NB. Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections. Genes (Basel) 2020; 11:E283. [PMID: 32155892 PMCID: PMC7140877 DOI: 10.3390/genes11030283] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/20/2022] Open
Abstract
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America-Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.
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Affiliation(s)
- Carla V. Filippi
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
- Programa Académico para la Investigación e Innovación en Biotecnología, Universidad Nacional de Moreno–UNM, Moreno 1744, Argentina
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gabriela A. Merino
- Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática–IBB, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Entre Ríos, Oro Verde 3100, Argentina
- Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional-sinc(i), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Juan F. Montecchia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Natalia C. Aguirre
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mónica I. Fass
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Daniel Álvarez
- Estación Experimental Agropecuaria INTA Manfredi, Manfredi 5988, Argentina
| | - Julio Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Ruth A. Heinz
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Bruno Contreras Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Verónica V. Lia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Norma B. Paniego
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
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11
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Hernández F, Presotto A, Poverene M, Mandel JR. Genetic Diversity and Population Structure of Wild Sunflower (Helianthus annuus L.) in Argentina: Reconstructing Its Invasion History. J Hered 2019; 110:746-759. [PMID: 31353398 DOI: 10.1093/jhered/esz047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/27/2019] [Indexed: 11/13/2022] Open
Abstract
Studying the levels and patterns of genetic diversity of invasive populations is important to understand the evolutionary and ecological factors promoting invasions and for better designing preventive and control strategies. Wild sunflower (Helianthus annuus L.) is native to North America and was introduced, and has become invasive, in several countries, including Argentina (ARG). Here, using classical population genetic analyses and approximate Bayesian computation (ABC) modeling, we studied the invasion history of wild sunflower in ARG. We analyzed 115 individuals belonging to 15 populations from ARG (invasive range) and United States (US, native range) at 14 nuclear and 3 chloroplast simple sequence repeat markers along with 23 phenotypic variables. Populations from ARG showed similar levels of nuclear genetic diversity to US populations and higher genetic diversity in the chloroplast genome, indicating no severe genetic bottlenecks during the invasion process. Bayesian clustering analysis, based on nuclear markers, suggests the presence of 3 genetic clusters, all present in both US and ARG. Discriminant analysis of principal components (DAPC) detected an overall low population structure between central US and ARG populations but separated 2 invasive populations from the rest. ABC modeling supports multiple introductions but also a southward dispersal within ARG. Genetic and phenotypic data support the central US as a source of introduction while the source of secondary introductions could not be resolved. Finally, using genetic markers from the chloroplast genome, we found lower population structure in ARG when compared with US populations, suggesting a role for seed-mediated gene flow in Argentina.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca, Argentina.,Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), CONICET-Bahía Blanca, Bahía Blanca, Argentina
| | - Alejandro Presotto
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca, Argentina.,Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), CONICET-Bahía Blanca, Bahía Blanca, Argentina
| | - Mónica Poverene
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca, Argentina.,Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), CONICET-Bahía Blanca, Bahía Blanca, Argentina
| | - Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, TN
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12
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Re-establishment of latitudinal clines and local adaptation within the invaded area suggest rapid evolution of seed traits in Argentinean sunflower (Helianthus annuus L.). Biol Invasions 2019. [DOI: 10.1007/s10530-019-01998-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Abstract
Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools has made it possible to conduct genetic mapping and population genetic studies to unravel the molecular underpinnings of domestication and crop evolution in diverse crop species. We propose three future avenues for the study of crop evolution: establishment of high-quality reference genomes for crops and their wild relatives; genomic characterization of germplasm collections; and the adoption of novel methodologies such as archaeogenetics, epigenomics, and genome editing.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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14
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Mondon A, Owens GL, Poverene M, Cantamutto M, Rieseberg LH. Gene flow in Argentinian sunflowers as revealed by genotyping-by-sequencing data. Evol Appl 2017; 11:193-204. [PMID: 29387155 PMCID: PMC5775495 DOI: 10.1111/eva.12527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/26/2017] [Indexed: 01/04/2023] Open
Abstract
Gene flow can have several different applied consequences, ranging from extinction to the escape of transgenes to the evolution of weedy or invasive lineages. Here, we describe patterns of hybridization and gene flow involving domesticated and wild sunflowers in Argentina. To address the risks of introgression of variants from the cultivated sunflower into invasive wild Helianthus, we used genotyping‐by‐sequencing (GBS) to genotype 182 samples from 11 sites in Argentina, along with previously published data from samples from the native range (North America), to determine the native source populations of the Argentinian samples and to detect admixture. We unexpectedly discovered two distinctive forms of H. petiolaris in Argentina, one from H. petiolaris subsp. petiolaris as expected, but the other from an unknown source. Extensive admixture was observed among Argentinian sunflowers, largely confirming phenotypic predictions. While many hybrids are F1s, there were signals consistent with introgression from the domesticated sunflower into H. petiolaris. Whether this introgression is incidental or a causal driver of invasiveness is not yet clear, but it seems likely that genes found in the domesticated sunflower genome (whether engineered or not) will quickly find their way into wild Argentinian sunflower populations.
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Affiliation(s)
- Ana Mondon
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) CCT Bahía Blanca Provincia de Buenos Aires Argentina
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Mónica Poverene
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) CCT Bahía Blanca Provincia de Buenos Aires Argentina.,Dpto. Agronomía Universidad Nacional del Sur (UNS) Bahía Blanca Argentina
| | - Miguel Cantamutto
- Estación Experimental Agropecuaria Instituto Nacional de Tecnología Agropecuaria (INTA) Hilario Ascasubi Argentina
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
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