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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Khoury CK, Brush S, Costich DE, Curry HA, de Haan S, Engels JMM, Guarino L, Hoban S, Mercer KL, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. Crop genetic erosion: understanding and responding to loss of crop diversity. THE NEW PHYTOLOGIST 2022; 233:84-118. [PMID: 34515358 DOI: 10.1111/nph.17733] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.
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Affiliation(s)
- Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537, Cali, Colombia
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- San Diego Botanic Garden, 230 Quail Gardens Dr., Encinitas, CA, 92024, USA
| | - Stephen Brush
- University of California Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, México
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH, UK
| | - Stef de Haan
- International Potato Center (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru
| | | | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Sean Hoban
- The Morton Arboretum, The Center for Tree Science, 4100 IL-53, Lisle, IL, 60532, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Gary P Nabhan
- Southwest Center and Institute of the Environment, University of Arizona, 1401 E. First St., PO Box 210185, Tucson, AZ, 85721-0185, USA
| | - Hugo R Perales
- Departamento de Agroecología, El Colegio de la Frontera Sur, San Cristóbal, Chiapas, 29290, México
| | - Chris Richards
- National Laboratory for Genetic Resources Preservation, United States Department of Agriculture, Agricultural Research Service, 1111 South Mason Street, Fort Collins, CO, 80521, USA
| | - Chance Riggins
- Department of Crop Sciences, University of Illinois, 331 Edward R. Madigan Lab, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Imke Thormann
- Federal Office for Agriculture and Food (BLE), Information and Coordination Centre for Biological Diversity (IBV), Deichmanns Aue 29, 53179, Bonn, Germany
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Importance of Landraces in Cereal Breeding for Stress Tolerance. PLANTS 2021; 10:plants10071267. [PMID: 34206299 PMCID: PMC8309184 DOI: 10.3390/plants10071267] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]
Abstract
The renewed focus on cereal landraces is a response to some negative consequences of modern agriculture and conventional breeding which led to a reduction of genetic diversity. Cereal landraces are still cultivated on marginal lands due to their adaptability to unfavourable conditions, constituting an important source of genetic diversity usable in modern plant breeding to improve the adaptation to abiotic or biotic stresses, yield performance and quality traits in limiting environments. Traditional agricultural production systems have played an important role in the evolution and conservation of wide variability in gene pools within species. Today, on-farm and ex situ conservation in gene bank collections, together with data sharing among researchers and breeders, will greatly benefit cereal improvement. Many efforts are usually made to collect, organize and phenotypically and genotypically analyse cereal landrace collections, which also utilize genomic approaches. Their use in breeding programs based on genomic selection, and the discovery of beneficial untapped QTL/genes/alleles which could be introgressed into modern varieties by MAS, pyramiding or biotechnological tools, increase the potential for their better deployment and exploitation in breeding for a more sustainable agricultural production, particularly enhancing adaptation and productivity in stress-prone environments to cope with current climate changes.
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Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation. Heredity (Edinb) 2021; 126:913-928. [PMID: 33785893 PMCID: PMC8178342 DOI: 10.1038/s41437-021-00423-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 02/01/2023] Open
Abstract
Genomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50-year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (Fst 0.008-0.113) than ex situ samples (Fst 0.031-0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers' selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces.
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Diaw Y, Tollon-Cordet C, Charcosset A, Nicolas SD, Madur D, Ronfort J, David J, Gouesnard B. Genetic diversity of maize landraces from the South-West of France. PLoS One 2021; 16:e0238334. [PMID: 33524023 PMCID: PMC7850504 DOI: 10.1371/journal.pone.0238334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/15/2021] [Indexed: 11/30/2022] Open
Abstract
From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France (SWF), a traditional region for maize cultivation. A set of landraces were collected in this area between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces from this region suggested that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridizations between Caribbean and Northern Flint germplasms introduced to Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to better elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part of the studied region. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found in landraces from the East part of the region significant cases of admixture between landraces from the Northern Flint group and landraces from either the Caribbean, Andean or Italian groups. We then assumed that SWF landraces had a multiple origin with a predonderance of Northern Flint germplasm for the two SWF groups, notably for the East part.
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Affiliation(s)
- Yacine Diaw
- Institut Sénégalais de Recherches Agricoles, ISRA-CNRA de Bambey, Dakar, Sénégal
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | | | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D. Nicolas
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Joëlle Ronfort
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Jacques David
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Brigitte Gouesnard
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
- * E-mail:
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Lafarga T, Villaró S, Rivera A, Bobo G, Aguiló-Aguayo I. Bioaccessibility of polyphenols and antioxidant capacity of fresh or minimally processed modern or traditional lettuce ( Lactuca sativa L.) varieties. Journal of Food Science and Technology 2020; 57:754-763. [PMID: 32116384 DOI: 10.1007/s13197-019-04108-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 12/01/2022]
Abstract
Modern city lifestyle is characterized by an increased demand for fresh or minimally processed foods. Lettuce (Lactuca sativa L.), mainly iceberg lettuce, is the main vegetable used during the manufacture of fresh-cut salads. The current study evaluated the phenolic content and antioxidant activity of ten fresh and minimally processed lettuce varieties. The phenolic content of selected lettuce samples varied significantly among varieties. Although a higher phenolic content was observed in modern lettuce varieties, when compared to the traditional ones (except for the landrace Francès 219/855), the antioxidant capacity of modern and traditional lettuce varieties was similar. Minimal processing followed by storage for a 7-day period led to an increased phenolic content in varieties Rutilaï RZ, Abago RZ, Maravilla LS044, Francès 219/855, Negre borratger 386/935, and D'hivern LS008, supporting the hypothesis that wounding can induce the accumulation of phenolic compounds in lettuce leaves. For example, the total phenolic content of Francès 219/855 after processing and storage increased from 8.3 to 11.3 mg/100 g (p < 0.05). Accumulation of phenolic compounds after minimal processing was not observed in all the studied samples, suggesting that this effect could be matrix-dependant. The amount of bioaccessible polyphenols was higher after minimal processing and storage. Indeed, the amount of bioaccessible polyphenols after a simulated gastrointestinal digestion of fresh or minimally processed Pelikan lettuce was calculated as 32.6 or 43.3 mg/100 g respectively (p < 0.05), suggesting that the increased amount of polyphenols caused by processing and storage can also lead to a higher amount of bioaccessible phenolic compounds.
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Affiliation(s)
- Tomás Lafarga
- Postharvest Programme, Institute of Agrifood Research and Technology (IRTA), 25003 Lleida, Spain
| | - Silvia Villaró
- Postharvest Programme, Institute of Agrifood Research and Technology (IRTA), 25003 Lleida, Spain
| | - Ana Rivera
- Fundació Miquel Agustí, Campus del Baix Llobregat, 08860 Castelldefels, Spain
| | - Gloria Bobo
- Postharvest Programme, Institute of Agrifood Research and Technology (IRTA), 25003 Lleida, Spain
| | - Ingrid Aguiló-Aguayo
- Postharvest Programme, Institute of Agrifood Research and Technology (IRTA), 25003 Lleida, Spain
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Lanzanova C, Arrigoni A, Valoti P, Alfieri M, Locatelli S. Agronomic performance, chemical composition and Fusarium verticillioides resistance of Italian white maize varieties. QUALITY ASSURANCE AND SAFETY OF CROPS & FOODS 2019. [DOI: 10.3920/qas2018.1451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- C. Lanzanova
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy
| | - A. Arrigoni
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy
| | - P. Valoti
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy
| | - M. Alfieri
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy
| | - S. Locatelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy
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Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties. Proc Natl Acad Sci U S A 2019; 116:21302-21311. [PMID: 31570572 DOI: 10.1073/pnas.1817664116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mexico is recognized as the center of origin and domestication of maize. Introduction of modern maize varieties (MVs) into Mexico raised concerns regarding the possible effects of gene flow from MVs into maize landraces (LRs) and their wild relatives (WRs), teosintes. However, after more than 60 y from the release of the first MVs, the impact of the sympatry with LRs and their WRs has not been explored with genetic data. In this work, we assessed changes in the genomes of 7 maize LRs and 2 WR subspecies from collections spanning over 70 y. We compared the genotypes obtained by genotyping by sequencing (GBS) for LRs and WRs before and after the adoption of MVs, and observed introgression from sympatric MVs into LRs and into the WR Zea mays ssp. mexicana sampled after the year 2000. We also found a decrease in the paired divergence index (F ST ) between MV-LR and MV-WR over the same time frame. Moreover, we determined that LR genetic diversity increased after 2000, probably as a result of gene flow from MVs introduced in the 1990s. Our findings allowed us to identify ongoing changes in the domesticated and wild maize genetic pools, and concur with previous works that have evaluated short-term gene flow from MVs into LRs in other crops. Our approach represents a useful tool for tracking evolutionary change in wild and domesticated genetic resources, as well as for developing strategies for their conservation.
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Ardenghi NMG, Rossi G, Guzzon F. Back to beaked: Zea mays subsp. mays Rostrata Group in northern Italy, refugia and revival of open-pollinated maize landraces in an intensive cropping system. PeerJ 2018; 6:e5123. [PMID: 30013830 PMCID: PMC6035727 DOI: 10.7717/peerj.5123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/06/2018] [Indexed: 11/25/2022] Open
Abstract
Crop landraces are fundamental resources to increase the eroded genepool of modern crops in order to adapt agriculture to future challenges; plus, they are of immeasurable heritage and cultural value. Between the 1940s and the 1960s open-pollinated varieties (OPVs) of flint and semi-flint maize in Europe were almost completely replaced by high-yielding hybrid dent cultivars selected in North America. No comprehensive assessment was performed after the 1950s to understand which maize genetic resources survived genetic erosion in northern Italy, an area characterized by a high degree of landraces extinction and introgression, intensive hybrid dent monocultures, as well as being one of the hotspots of maize cultivation at a continental level. Among these landraces, beaked maize represents a peculiar case study for assessing the survival of OPVs in intensive cropping systems. By means of ethnobotanical and literature surveys, the history of Zea mays subsp. mays Rostrata Group and its current distribution were reconstructed. It emerged that beaked maize originated in the study area and it is one of the oldest genepools available not subjected to formal crop improvement. We identified 28 landraces of beaked maize currently cultivated, 18 here recorded for the first time. The cultivation of more than half of the 28 landraces has continued throughout the last 80 years in a few fragmented localities that can be regarded as “refugia”. The survival of these landraces from substitution with high-yielding cultivars and unidirectional introgression has been mainly due to active on-farm conservation performed by custodian farmers and secondarily to cultivation in isolated areas (e.g., mountain valleys). After decades of genetic erosion, beaked maize has since the late 1990s experienced a revival, in terms of an increasing number of cultivation localities and the level of product commercialization. This process is mostly spontaneous and only occasionally mediated by governmental institutions; it is linked to the rediscovery of local food products, in this case mainly polenta, a dish made of corn flour, which used to be the staple food across northern Italy. The ex situ conservation of beaked maize and on-farm measures put in place by the farmers to prevent introgression are also assessed. Further research and collecting missions are needed to provide an inventory of open-pollinated landraces of other landrace groups that have survived genetic erosion in Europe. To meet this aim, extensive ethnobotanical surveys, such as the one performed here, are very powerful tools in detecting these genetic resources.
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Affiliation(s)
| | - Graziano Rossi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Lombardia, Italy
| | - Filippo Guzzon
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Lombardia, Italy
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Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.
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11
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Casañas F, Simó J, Casals J, Prohens J. Toward an Evolved Concept of Landrace. FRONTIERS IN PLANT SCIENCE 2017; 8:145. [PMID: 28228769 PMCID: PMC5296298 DOI: 10.3389/fpls.2017.00145] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/24/2017] [Indexed: 05/21/2023]
Abstract
The term "landrace" has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities.
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Affiliation(s)
| | - Joan Simó
- Fundació Miquel Agustí/BarcelonatechBarcelona, Spain
| | - Joan Casals
- Fundació Miquel Agustí/BarcelonatechBarcelona, Spain
| | - Jaime Prohens
- Institut de Conservació i Millora de l’Agrodiversitat Valenciana, Universitat Politècnica de ValènciaValència, Spain
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12
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Bitocchi E, Bellucci E, Rau D, Albertini E, Rodriguez M, Veronesi F, Attene G, Nanni L. European flint landraces grown in situ reveal adaptive introgression from modern maize. PLoS One 2015; 10:e0121381. [PMID: 25853809 PMCID: PMC4390310 DOI: 10.1371/journal.pone.0121381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/31/2015] [Indexed: 12/23/2022] Open
Abstract
We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Domenico Rau
- Department of Agriculture, Università degli Studi di Sassari, Sassari, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Monica Rodriguez
- Department of Agriculture, Università degli Studi di Sassari, Sassari, Italy
| | - Fabio Veronesi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Giovanna Attene
- Department of Agriculture, Università degli Studi di Sassari, Sassari, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Chentoufi L, Sahri A, Arbaoui M, Belqadi L, Birouk A, Roumet P, Muller MH. Anchoring durum wheat diversity in the reality of traditional agricultural systems: varieties, seed management, and farmers' perception in two Moroccan regions. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2014; 10:58. [PMID: 25027694 PMCID: PMC4132198 DOI: 10.1186/1746-4269-10-58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/03/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Traditional agrosystems are the places were crop species have evolved and continue to evolve under a combination of human and environmental pressures. A better knowledge of the mechanisms underlying the dynamics of crop diversity in these agrosystems is crucial to sustain food security and farmers' self-reliance. It requires as a first step, anchoring a description of the available diversity in its geographical, environmental, cultural and socio-economic context. METHODS We conducted interviews with farmers cultivating durum wheat in two contrasted traditional agrosystems of Morocco in the Pre-Rif (163 farmers) and in the oases of the Atlas Mountains (110 farmers). We documented the varietal diversity of durum wheat, the main characteristics of the farms, the farming and seed management practices applied to durum wheat, and the farmers' perception of their varieties. RESULTS As expected in traditional agrosystems, farmers largely practiced diversified subsistence agriculture on small plots and relied on on-farm seed production or informal seed exchange networks. Heterogeneity nevertheless prevailed on many variables, especially on the modernization of practices in the Pre-Rif region. Fourteen (resp. 11) traditional and 5 (resp. 3) modern varieties were identified in the Pre-Rif region (resp. in the Atlas Mountains). The majority of farmers grew a single variety, and most traditional varieties were distributed in restricted geographical areas. At the farm level, more than half of the varieties were renewed in the last decade in the Pre-Rif, a more rapid renewal than in the Atlas Mountain. Modern varieties were more prevalent in the Pre-Rif region and were integrated in the traditional practices of seed production, selection and exchange. They were clearly distinguished by the farmers from the landraces, the last ones being appreciated for their quality traits. CONCLUSIONS The surveyed traditional agrosystems constitute open, dynamic and heterogeneous entities. We suggest that competing factors could favour or limit the cultivation of improved varieties and the erosion of original durum wheat diversity. This first description opens the way to focused further investigations, including complementing variety names with cultural, genetic and phenotypic information and unravelling the multidimensional factors and consequences of modern variety adoption.
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Affiliation(s)
- Lamyae Chentoufi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Ali Sahri
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Mustapha Arbaoui
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Loubna Belqadi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Ahmed Birouk
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco
| | - Pierre Roumet
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060 Montpellier Cedex 1, France
| | - Marie-Hélène Muller
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060 Montpellier Cedex 1, France
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Șuteu D, Băcilă I, Haș V, Haș I, Miclăuș M. Romanian maize (Zea mays) inbred lines as a source of genetic diversity in SE Europe, and their potential in future breeding efforts. PLoS One 2014; 8:e85501. [PMID: 24392016 PMCID: PMC3877385 DOI: 10.1371/journal.pone.0085501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 11/27/2013] [Indexed: 11/24/2022] Open
Abstract
Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm.
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Affiliation(s)
- Dana Șuteu
- National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania
| | - Ioan Băcilă
- National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania
| | - Voichița Haș
- Agricultural Research and Development Station, Turda, Romania
| | - Ioan Haș
- Agricultural Research and Development Station, Turda, Romania
- University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Mihai Miclăuș
- National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania
- * E-mail:
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Bellucci E, Bitocchi E, Rau D, Nanni L, Ferradini N, Giardini A, Rodriguez M, Attene G, Papa R. Population structure of barley landrace populations and gene-flow with modern varieties. PLoS One 2013; 8:e83891. [PMID: 24386303 PMCID: PMC3873955 DOI: 10.1371/journal.pone.0083891] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/16/2013] [Indexed: 11/18/2022] Open
Abstract
Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.
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Affiliation(s)
- Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Nicoletta Ferradini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Alessandro Giardini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
- Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), Foggia, Italy
- * E-mail:
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Scientific Opinion on an application from Pioneer Hi‐Bred International and Dow AgroSciences LLC (EFSA‐GMO‐NL‐2005‐23) for placing on the market of genetically modified maize 59122 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Westengen OT, Berg PR, Kent MP, Brysting AK. Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels. PLoS One 2012; 7:e47832. [PMID: 23091649 PMCID: PMC3472975 DOI: 10.1371/journal.pone.0047832] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/17/2012] [Indexed: 01/11/2023] Open
Abstract
Background Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited. Methodology A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset. Conclusions The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.
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Affiliation(s)
- Ola T Westengen
- Centre for Development and the Environment, SUM, University of Oslo, Oslo, Norway.
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Aerts R, Berecha G, Gijbels P, Hundera K, Glabeke S, Vandepitte K, Muys B, Roldán-Ruiz I, Honnay O. Genetic variation and risks of introgression in the wild Coffea arabica gene pool in south-western Ethiopian montane rainforests. Evol Appl 2012; 6:243-52. [PMID: 23798974 PMCID: PMC3689350 DOI: 10.1111/j.1752-4571.2012.00285.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/19/2012] [Indexed: 12/05/2022] Open
Abstract
The montane rainforests of SW Ethiopia are the primary centre of diversity of Coffea arabica and the origin of all Arabica coffee cultivated worldwide. This wild gene pool is potentially threatened by forest fragmentation and degradation, and by introgressive hybridization with locally improved coffee varieties. We genotyped 703 coffee shrubs from unmanaged and managed coffee populations, using 24 microsatellite loci. Additionally, we genotyped 90 individuals representing 23 Ethiopian cultivars resistant to coffee berry disease (CBD). We determined population genetic diversity, genetic structure, and admixture of cultivar alleles in the in situ gene pool. We found strong genetic differentiation between managed and unmanaged coffee populations, but without significant differences in within-population genetic diversity. The widespread planting of coffee seedlings including CBD-resistant cultivars most likely offsets losses of genetic variation attributable to genetic drift and inbreeding. Mixing cultivars with original coffee genotypes, however, leaves ample opportunity for hybridization and replacement of the original coffee gene pool, which already shows signs of admixture. In situ conservation of the wild gene pool of C. arabica must therefore focus on limiting coffee production in the remaining wild populations, as intensification threatens the genetic integrity of the gene pool by exposing wild genotypes to cultivars.
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Affiliation(s)
- Raf Aerts
- Division Forest, Nature and Landscape, University of Leuven Leuven, Belgium
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Rodriguez M, Rau D, O'Sullivan D, Brown AHD, Papa R, Attene G. Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:171-84. [PMID: 22411093 DOI: 10.1007/s00122-012-1824-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 02/11/2012] [Indexed: 05/14/2023]
Abstract
Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F(ST) = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13% of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.
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Affiliation(s)
- Monica Rodriguez
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy.
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Tesio F, Follis F. Adaptability of old Italian flint maize (Zea maysL.) varieties to different weed control systems. INTERNATIONAL JOURNAL OF BIODIVERSITY SCIENCE, ECOSYSTEM SERVICES & MANAGEMENT 2012. [DOI: 10.1080/21513732.2012.655779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Franco Tesio
- a Dipartimento di Agronomia, Selvicoltura e Gestione del Territorio , Università degli Studi di Torino , Grugliasco , Italy
| | - Francesca Follis
- a Dipartimento di Agronomia, Selvicoltura e Gestione del Territorio , Università degli Studi di Torino , Grugliasco , Italy
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Scientific Opinion on application (EFSA-GMO-UK-2008-60) for placing on the market of genetically modified herbicide tolerant maize GA21 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003 from Syngenta Seeds. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2480] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Scientific Opinion on application (EFSA-GMO-CZ-2008-54) for placing on the market of genetically modified insect resistant and herbicide tolerant maize MON 88017 for cultivation under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2428] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Ryffel GU. Dismay with GM maize. A science-based solution to public resistance against genetically modified crops that could be compatible with organic farming. EMBO Rep 2011; 12:996-9. [PMID: 21909075 DOI: 10.1038/embor.2011.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 08/24/2011] [Indexed: 01/20/2023] Open
Affiliation(s)
- Gerhart U Ryffel
- Institute for Cell Biology, University Hospital Essen, University Duisburg-Essen, Germany.
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Kwit C, Moon HS, Warwick SI, Stewart CN. Transgene introgression in crop relatives: molecular evidence and mitigation strategies. Trends Biotechnol 2011; 29:284-93. [PMID: 21388698 DOI: 10.1016/j.tibtech.2011.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 01/31/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
Abstract
Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided.
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Affiliation(s)
- Charles Kwit
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA.
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PÉREZ-FIGUEROA A, GARCÍA-PEREIRA MJ, SAURA M, ROLÁN-ALVAREZ E, CABALLERO A. Comparing three different methods to detect selective loci using dominant markers. J Evol Biol 2010; 23:2267-2276. [DOI: 10.1111/j.1420-9101.2010.02093.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Tanto Hadado T, Rau D, Bitocchi E, Papa R. Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L.) landraces revealed by molecular analysis. BMC PLANT BIOLOGY 2010; 10:121. [PMID: 20565982 PMCID: PMC3095281 DOI: 10.1186/1471-2229-10-121] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 06/21/2010] [Indexed: 05/27/2023]
Abstract
BACKGROUND Among the cereal crops, barley is the species with the greatest adaptability to a wide range of environments. To determine the level and structure of genetic diversity in barley (Hordeum vulgare L.) landraces from the central highlands of Ethiopia, we have examined the molecular variation at seven nuclear microsatellite loci. RESULTS A total of 106 landrace populations were sampled in the two growing seasons (Meher and Belg; the long and short rainy seasons, respectively), across three districts (Ankober, Mojanawadera and Tarmaber), and within each district along an altitudinal gradient (from 1,798 to 3,324 m a.s.l). Overall, although significant, the divergence (e.g. FST) is very low between seasons and geographical districts, while it is high between different classes of altitude. Selection for adaptation to different altitudes appears to be the main factor that has determined the observed clinal variation, along with population-size effects. CONCLUSIONS Our data show that barley landraces from Ethiopia are constituted by highly variable local populations (farmer's fields) that have large within-population diversity. These landraces are also shown to be locally adapted, with the major driving force that has shaped their population structure being consistent with selection for adaptation along an altitudinal gradient. Overall, our study highlights the potential of such landraces as a source of useful alleles. Furthermore, these landraces also represent an ideal system to study the processes of adaptation and for the identification of genes and genomic regions that have adaptive roles in crop species.
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Affiliation(s)
- Tesema Tanto Hadado
- Dipartimento di Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Institute of Biodiversity Conservation, P.O. Box 30726, Addis Ababa, Ethiopia
| | - Domenico Rau
- Dipartimento di Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Arnaud JF, Fénart S, Godé C, Deledicque S, Touzet P, Cuguen J. Fine-scale geographical structure of genetic diversity in inland wild beet populations. Mol Ecol 2009; 18:3201-15. [PMID: 19627487 DOI: 10.1111/j.1365-294x.2009.04279.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Introgression arising from crop-to-wild gene flow provides novel sources of genetic variation in plant species complexes. Hybridization within the Beta vulgaris species complex is of immediate concern; crop lineages (B. vulgaris ssp. vulgaris) hybridize easily with their wild relatives (B. vulgaris ssp. maritima) thereby threatening wild beet gene diversity with genetic swamping. Hybridization 'hotspots' occur in European seed production areas because inland ruderal wild beets occur and reproduce in sympatry with cultivated beets. We studied gene flow occurring between seed-producing cultivars and ruderal wild B. vulgaris in southwestern France to determine whether feral beets, arising from unharvested cultivated seed, represent an opportunity for crop-to-wild gene flow. We surveyed 42 inland ruderal beet populations located near seed production fields for nucleo-cytoplasmic variation and used a cytoplasmic marker diagnostic of cultivated lines. Occurrence of cultivated-type cytoplasm within ruderal populations clearly reflected events of crop seed escape. However, we found no genetic signatures of nuclear cultivated gene introgression, which suggests past introgression of cultivated cytoplasm into a wild nuclear background through seed escape rather than recent direct pollen flow. Overall, patterns of genetic structure suggested that inland ruderal wild beet populations act as a metapopulation, with founding events involving a few sib groups, followed by low rates of seed or pollen gene flow after populations are established. Altogether, our results indicate that a long-lived seed bank plays a key role in maintaining cultivated-type cytoplasm in the wild and highlight the need for careful management of seed production areas where wild and cultivated relatives co-occur.
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Affiliation(s)
- Jean-François Arnaud
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Bâtiment SN2, Université des Sciences et Technologies de Lille - Lille 1, F-59655 Villeneuve d'Ascq Cedex, France.
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Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R. Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2009; 2:504-22. [PMID: 25567895 PMCID: PMC3352449 DOI: 10.1111/j.1752-4571.2009.00082.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 05/24/2009] [Indexed: 01/07/2023] Open
Abstract
Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes.
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Affiliation(s)
- Monica Rossi
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Elena Bitocchi
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Elisa Bellucci
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Laura Nanni
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Domenico Rau
- Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari Sassari, Italy
| | - Giovanna Attene
- Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari Sassari, Italy
| | - Roberto Papa
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
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Applications (EFSA‐GMO‐RX‐MON810) for renewal of authorisation for the continued marketing of (1) existing food and food ingredients produced from genetically modified insect resistant maize MON810; (2) feed consisting of and/or containing maize MON810, including the use of seed for cultivation; and of (3) food and feed additives, and feed materials produced from maize MON810, all under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2009. [DOI: 10.2903/j.efsa.2009.1149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Applications (references EFSA‐GMO‐NL‐2005‐22, EFSA‐GMO‐RX‐NK603) for the placing on the market of the genetically modified glyphosate tolerant maize NK603 for cultivation, food and feed uses, import and processing and for renewal of the authorisation of maize NK603 as existing products, both under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2009. [DOI: 10.2903/j.efsa.2009.1137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Affiliation(s)
- Allison Snow
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA.
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