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Korpelainen H. The Role of Home Gardens in Promoting Biodiversity and Food Security. PLANTS (BASEL, SWITZERLAND) 2023; 12:2473. [PMID: 37447034 DOI: 10.3390/plants12132473] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Plant genetic resources provide the basis for sustainable agricultural production, adaptation to climate change, and economic development. Many present crop plants are endangered due to extreme environmental conditions induced by climate change or due to the use of a limited selection of plant materials. Changing environmental conditions are a challenge for plant production and food security, emphasizing the urgent need for access to a wider range of plant genetic resources than what are utilized today, for breeding novel crop varieties capable of resilience and adaptation to climate change and other environmental challenges. Besides large-scale agricultural production, it is important to recognize that home gardens have been an integral component of family farming and local food systems for centuries. It is remarkable how home gardens have allowed the adaptation and domestication of plants to extreme or specific ecological conditions, thus contributing to the diversification of cultivated plants. Home gardens can help in reducing hunger and malnutrition and improve food security. In addition, they provide opportunities to broaden the base of cultivated plant materials by harboring underutilized crop plants and crop wild relative species. Crop wild relatives contain a wide range of genetic diversity not available in cultivated crops. Although the importance of home gardens in conserving plant genetic resources is well recognized, there is a risk that local genetic diversity will be lost if traditional plant materials are replaced by high-yielding modern cultivars. This paper provides an overview of home gardens and their present role and future potential in conserving and utilizing plant genetic resources and enhancing food and nutritional security under global challenges.
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Affiliation(s)
- Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014 Helsinki, Finland
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Meziadi C, Blanchet S, Geffroy V, Pflieger S. Genetic resistance against viruses in Phaseolus vulgaris L.: State of the art and future prospects. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:39-50. [PMID: 29223341 DOI: 10.1016/j.plantsci.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/24/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Viruses are obligate parasites that replicate intracellularly in many living organisms, including plants. Consequently, no chemicals are available that target only the virus without impacting host cells or vector organisms. The use of natural resistant varieties appears as the most reliable control strategy and remains the best and cheapest option in managing virus diseases, especially in the current ecological context of preserving biodiversity and environment in which the use of phytosanitary products becomes limited. Common bean is a grain legume cultivated mainly in Africa and Central-South America. Virus diseases of common bean have been extensively studied both by breeders to identify natural resistance genes in existing germplasms and by pathologists to understand the molecular bases of plant-virus interactions. Here we present a critical review in which we synthesize previous and recent information concerning 1) main viruses causing diseases in common bean, 2) genetic resistance to viruses in common bean, 3) the different resistance phenotypes observed and more particularly the effect of temperature, 4) the molecular bases of resistance genes to viruses in common bean, and 5) future prospects using transgenic-engineered resistant lines.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France.
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Bitocchi E, Rau D, Bellucci E, Rodriguez M, Murgia ML, Gioia T, Santo D, Nanni L, Attene G, Papa R. Beans ( Phaseolus ssp.) as a Model for Understanding Crop Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:722. [PMID: 28533789 PMCID: PMC5420584 DOI: 10.3389/fpls.2017.00722] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Domenico Rau
- Department of Agriculture, University of SassariSassari, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | | | - Maria L. Murgia
- Department of Agriculture, University of SassariSassari, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of BasilicataPotenza, Italy
| | - Debora Santo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Giovanna Attene
- Department of Agriculture, University of SassariSassari, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
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De Ron AM, Rodiño AP, Santalla M, González AM, Lema MJ, Martín I, Kigel J. Seedling Emergence and Phenotypic Response of Common Bean Germplasm to Different Temperatures under Controlled Conditions and in Open Field. FRONTIERS IN PLANT SCIENCE 2016; 7:1087. [PMID: 27532005 PMCID: PMC4969293 DOI: 10.3389/fpls.2016.01087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/11/2016] [Indexed: 05/08/2023]
Abstract
Rapid and uniform seed germination and seedling emergence under diverse environmental conditions is a desirable characteristic for crops. Common bean genotypes (Phaseolus vulgaris L.) differ in their low temperature tolerance regarding growth and yield. Cultivars tolerant to low temperature during the germination and emergence stages and carriers of the grain quality standards demanded by consumers are needed for the success of the bean crop. The objectives of this study were (i) to screen the seedling emergence and the phenotypic response of bean germplasm under a range of temperatures in controlled chamber and field conditions to display stress-tolerant genotypes with good agronomic performances and yield potential, and (ii) to compare the emergence of bean seedlings under controlled environment and in open field conditions to assess the efficiency of genebanks standard germination tests for predicting the performance of the seeds in the field. Three trials were conducted with 28 dry bean genotypes in open field and in growth chamber under low, moderate, and warm temperature. Morpho-agronomic data were used to evaluate the phenotypic performance of the different genotypes. Cool temperatures resulted in a reduction of the rate of emergence in the bean genotypes, however, emergence and early growth of bean could be under different genetic control and these processes need further research to be suitably modeled. Nine groups arose from the Principal Component Analysis (PCA) representing variation in emergence time and proportion of emergence in the controlled chamber and in the open field indicating a trend to lower emergence in large and extra-large seeded genotypes. Screening of seedling emergence and phenotypic response of the bean germplasm under a range of temperatures in controlled growth chambers and under field conditions showed several genotypes, as landraces 272, 501, 593, and the cultivar Borlotto, with stress-tolerance at emergence, and high yield potential that could be valuable genetic material for breeding programs. Additionally, the potential genetic erosion in genebanks was assessed. Regarding bean commercial traits, under low temperature at sowing time seed reached larger size, and crop yield was higher compared to warmer temperatures at the sowing time. Therefore, early sowing of bean is strongly recommended.
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Affiliation(s)
- Antonio M. De Ron
- Biology of Agrosystems, Misión Biológica de Galicia, National Spanish Research CouncilPontevedra, Spain
- Sistemas Agroforestales, Unidad Asociada a la Misión Biológica de Galicia (CSIC)Pontevedra, Spain
| | - Ana P. Rodiño
- Biology of Agrosystems, Misión Biológica de Galicia, National Spanish Research CouncilPontevedra, Spain
| | - Marta Santalla
- Biology of Agrosystems, Misión Biológica de Galicia, National Spanish Research CouncilPontevedra, Spain
| | - Ana M. González
- Biology of Agrosystems, Misión Biológica de Galicia, National Spanish Research CouncilPontevedra, Spain
| | - María J. Lema
- Sistemas Agroforestales, Unidad Asociada a la Misión Biológica de Galicia (CSIC)Pontevedra, Spain
- Phytopathological Station do Areeiro, Provincial ChamberPontevedra, Spain
| | - Isaura Martín
- National Center for Plant Genetic Resources, National Institute for Agricultural and Food Research and TechnologyAlcalá de Henares, Spain
| | - Jaime Kigel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of JerusalemRehovot, Israel
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Castro-Guerrero NA, Isidra-Arellano MC, Mendoza-Cozatl DG, Valdés-López O. Common Bean: A Legume Model on the Rise for Unraveling Responses and Adaptations to Iron, Zinc, and Phosphate Deficiencies. FRONTIERS IN PLANT SCIENCE 2016; 7:600. [PMID: 27200068 PMCID: PMC4853408 DOI: 10.3389/fpls.2016.00600] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/18/2016] [Indexed: 05/19/2023]
Abstract
Common bean (Phaseolus vulgaris) was domesticated ∼8000 years ago in the Americas and today is a staple food worldwide. Besides caloric intake, common bean is also an important source of protein and micronutrients and it is widely appreciated in developing countries for their affordability (compared to animal protein) and its long storage life. As a legume, common bean also has the economic and environmental benefit of associating with nitrogen-fixing bacteria, thus reducing the use of synthetic fertilizers, which is key for sustainable agriculture. Despite significant advances in the plant nutrition field, the mechanisms underlying the adaptation of common bean to low nutrient input remains largely unknown. The recent release of the common bean genome offers, for the first time, the possibility of applying techniques and approaches that have been exclusive to model plants to study the adaptive responses of common bean to challenging environments. In this review, we discuss the hallmarks of common bean domestication and subsequent distribution around the globe. We also discuss recent advances in phosphate, iron, and zinc homeostasis, as these nutrients often limit plant growth, development, and yield. In addition, iron and zinc are major targets of crop biofortification to improve human nutrition. Developing common bean varieties able to thrive under nutrient limiting conditions will have a major impact on human nutrition, particularly in countries where dry beans are the main source of carbohydrates, protein and minerals.
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Affiliation(s)
- Norma A. Castro-Guerrero
- Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, ColumbiaMO, USA
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, FES Iztacala, Universidad Nacional Autónoma de MéxicoCiudad de México, México
| | - David G. Mendoza-Cozatl
- Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, ColumbiaMO, USA
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, FES Iztacala, Universidad Nacional Autónoma de MéxicoCiudad de México, México
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Ribeiro IC, Pinheiro C, Ribeiro CM, Veloso MM, Simoes-Costa MC, Evaristo I, Paulo OS, Ricardo CP. Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats. FRONTIERS IN PLANT SCIENCE 2016; 7:1293. [PMID: 27630646 PMCID: PMC5006101 DOI: 10.3389/fpls.2016.01293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 05/20/2023]
Abstract
The establishment of stress resilient sugar beets (Beta vulgaris spp. vulgaris) is an important breeding goal since this cash crop is susceptible to drought and salinity. The genetic diversity in cultivated sugar beets is low and the beet wild relatives are useful genetic resources for tolerance traits. Three wild beet populations (Beta vulgaris spp. maritima) from contrasting environments, Vaiamonte (VMT, dry inland hill), Comporta (CMP, marsh) and Oeiras (OEI, coastland), and one commercial sugar beet (Isella variety, SB), are compared. At the genetic level, the use of six microsatellite allowed to detect a total of seventy six alleles. It was observed that CMP population has the highest value concerning the effective number of alleles and of expected heterozygosity. By contrast, sugar beet has the lowest values for all the parameters considered. Loci analysis with STRUCTURE allows defining three genetic clusters, the sea beet (OEI and CMP), the inland ruderal beet (VMT) and the sugar beet (SB). A screening test for progressive drought and salinity effects demonstrated that: all populations were able to recover from severe stress; drought impact was higher than that from salinity; the impact on biomass (total, shoot, root) was population specific. The distinct strategies were also visible at physiological level. We evaluated the physiological responses of the populations under drought and salt stress, namely at initial stress stages, late stress stages, and early stress recovery. Multivariate analysis showed that the physiological performance can be used to discriminate between genotypes, with a strong contribution of leaf temperature and leaf osmotic adjustment. However, the separation achieved and the groups formed are dependent on the stress type, stress intensity and duration. Each of the wild beet populations evaluated is very rich in genetic terms (allelic richness) and exhibited physiological plasticity, i.e., the capacity to physiologically adjust to changing environments. These characteristics emphasize the importance of the wild beet ecotypes for beet improvement programs. Two striking ecotypes are VMT, which is the best to cope with drought and salinity, and CMP which has the highest root to shoot ratio. These genotypes can supply breeding programs with distinct goals.
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Affiliation(s)
- Isa C. Ribeiro
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
- Faculdade de Ciências e Tecnologia, Universidade NOVA de LisboaCaparica, Portugal
- *Correspondence: Carla Pinheiro,
| | - Carla M. Ribeiro
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Maria M. Veloso
- INIAV, Unidade de Investigação de Biotecnologia e Recursos GenéticosOeiras, Portugal
- Instituto Superior de Agronomia, Linking Landscape, Environment, Agriculture and Food, Universidade de LisboaLisboa, Portugal
| | - Maria C. Simoes-Costa
- Instituto Superior de Agronomia, Linking Landscape, Environment, Agriculture and Food, Universidade de LisboaLisboa, Portugal
| | - Isabel Evaristo
- INIAV, Unidade de Investigação de Sistemas Agrários e Florestais e Sanidade VegetalOeiras, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Cândido P. Ricardo
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
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Song Q, Jia G, Hyten DL, Jenkins J, Hwang EY, Schroeder SG, Osorno JM, Schmutz J, Jackson SA, McClean PE, Cregan PB. SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean. G3 (BETHESDA, MD.) 2015; 5:2285-90. [PMID: 26318155 PMCID: PMC4632048 DOI: 10.1534/g3.115.020594] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/27/2015] [Indexed: 11/28/2022]
Abstract
A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.
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Affiliation(s)
- Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705
| | - Gaofeng Jia
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705
| | - David L Hyten
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Eun-Young Hwang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742
| | - Steven G Schroeder
- USDA-ARS, Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Beltsville, Maryland 20705
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102
| | - Perry B Cregan
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705
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Vahidi SMF, Tarang AR, Naqvi AUN, Falahati Anbaran M, Boettcher P, Joost S, Colli L, Garcia JF, Ajmone-Marsan P. Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran. Genet Sel Evol 2014; 46:27. [PMID: 24742145 PMCID: PMC4044659 DOI: 10.1186/1297-9686-46-27] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 03/05/2014] [Indexed: 11/17/2022] Open
Abstract
Background Iran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10 000 years ago) in the Iranian Zagros Mountains as well as in the high Euphrates valley and southeastern Anatolia. In addition, mitochondrial DNA data of domestic goats and wild ancestors (C. aegagrusor bezoar) suggest a pre-domestication management of wild populations in southern Zagros and central Iranian Plateau. In this study genetic diversity was assessed in seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. A total of 317 animals were characterized using 14 microsatellite loci. Two Pakistani goat populations, Pahari and Teddy, were genotyped for comparison. Results Iranian goats possess a remarkable genetic diversity (average expected heterozygosity of 0.671 across loci, 10.7 alleles per locus) mainly accounted for by the within-breed component (GST = 5.9%). Positive and highly significant FIS values in the Naini, Turki-Ghashghaei, Abadeh and Markhoz breeds indicate some level of inbreeding in these populations. Multivariate analyses cluster Iranian goats into northern, central and western groups, with the western breeds relatively distinct from the others. Pakistani breeds show some relationship with Iranian populations, even if their position is not consistent across analyses. Gene flow was higher within regions (west, north, central) compared to between regions but particularly low between the western and the other two regions, probably due to the isolating topography of the Zagros mountain range. The Turki-Ghashghaei, Najdi and Abadeh breeds are reared in geographic areas where mtDNA provided evidence of early domestication. These breeds are highly variable, located on basal short branches in the neighbor-joining tree, close to the origin of the principal component analysis plot and, although highly admixed, they are quite distinct from those reared on the western side of the Zagros mountain range. Conclusions These observations call for further investigation of the nuclear DNA diversity of these breeds within a much wider geographic context to confirm or re-discuss the current hypothesis (based on maternal lineage data) of an almost exclusive contribution of the eastern Anatolian bezoar to the domestic goat gene pool.
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Gioia T, Logozzo G, Attene G, Bellucci E, Benedettelli S, Negri V, Papa R, Spagnoletti Zeuli P. Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes) hybridization in the European common bean (Phaseolus vulgaris L.) germplasm. PLoS One 2013; 8:e75974. [PMID: 24098412 PMCID: PMC3788063 DOI: 10.1371/journal.pone.0075974] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/19/2013] [Indexed: 11/18/2022] Open
Abstract
Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from "pure" accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with "pure" accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.
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Affiliation(s)
- Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Giuseppina Logozzo
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica, Università degli Studi di Sassari, Sassari, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Stefano Benedettelli
- Dipartimento delle Scienze delle Produzioni Vegetali, del Suolo e dell'Ambiente Agroforestale, Università degli Studi di Firenze, Firenze, Italy
| | - Valeria Negri
- Dipartimento di Biologia Applicata, Università degli Studi di Perugia, Perugia, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), Foggia, Italy
| | - Pierluigi Spagnoletti Zeuli
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
- * E-mail:
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Kim MY, Van K, Kang YJ, Kim KH, Lee SH. Tracing soybean domestication history: From nucleotide to genome. BREEDING SCIENCE 2012; 61:445-52. [PMID: 23136484 PMCID: PMC3406779 DOI: 10.1270/jsbbs.61.445] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 10/14/2011] [Indexed: 05/20/2023]
Abstract
Since the genome sequences of wild species may provide key information about the genetic elements involved in speciation and domestication, the undomesticated soybean (Glycine soja Sieb. and Zucc.), a wild relative of the current cultivated soybean (G. max), was sequenced. In contrast to the current hypothesis of soybean domestication, which holds that the current cultivated soybean was domesticated from G. soja, our previous work has suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. In this review, many structural genomic differences between the two genomes are described and a total of 705 genes are identified as structural variations (SVs) between G. max and G. soja. After protein families database of alignments and hidden Markov models IDs and gene ontology terms were assigned, many interesting genes are discussed in detail using four domestication related traits, such as flowering time, transcriptional factors, carbon metabolism and disease resistance. Soybean domestication history is explored by studying these SVs in genes. Analysis of SVs in genes at the population-level may clarify the domestication history of soybean.
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Affiliation(s)
- Moon Young Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kyujung Van
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Yang Jae Kang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kil Hyun Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
- Corresponding author (e-mail: )
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Küpper Cardoso Perseguini JM, Chioratto AF, Zucchi MI, Colombo CA, Carbonell SAM, Costa Mondego JM, Gazaffi R, Franco Garcia AA, de Campos T, de Souza AP, Rubiano LB. Genetic diversity in cultivated carioca common beans based on molecular marker analysis. Genet Mol Biol 2011; 34:88-102. [PMID: 21637550 PMCID: PMC3085381 DOI: 10.1590/s1415-47572011000100017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 07/29/2010] [Indexed: 01/10/2023] Open
Abstract
A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.
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Affiliation(s)
| | | | - Maria Imaculada Zucchi
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, Campinas, SP, Brazil
| | - Carlos Augusto Colombo
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, Campinas, SP, Brazil
| | | | | | - Rodrigo Gazaffi
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Antonio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Tatiana de Campos
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Anete Pereira de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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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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