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Bosmali I, Lagiotis G, Ganopoulos I, Stefanidou E, Madesis P, Biliaderis CG. Phaseolus coccineus L. Landraces in Greece: Microsatellite Genotyping and Molecular Characterization for Landrace Authenticity and Discrimination. BIOTECH 2024; 13:18. [PMID: 38921050 PMCID: PMC11201852 DOI: 10.3390/biotech13020018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Phaseolus coccineus L. is a highly valuable crop for human consumption with a high protein content and other associated health benefits. Herein, 14 P. coccineus L. landraces were selected for genetic characterization: two Protected Geographical Indication (PGI) landraces from the Prespon area, namely "Gigantes" ("G") and "Elephantes" ("E"), and 12 additional landraces from the Greek Gene Bank collection of beans (PC1-PC12). The genetic diversity among these landraces was assessed using capillary electrophoresis utilizing fluorescence-labeled Simple Sequence Repeat (SSR) and Expressed Sequence Tag (EST); Simple Sequence Repeat (SSR) is a molecular marker technology. The "G" and "E" Prespon landraces were clearly distinguished among them, as well as from the PC1 to PC12 landraces, indicating the unique genetic identity of the Prespon beans. Overall, the genetic characterization of the abundant Greek bean germplasm using molecular markers can aid in the genetic identification of "G" and "E" Prespon beans, thus preventing any form of fraudulent practices as well as supporting traceability management strategies for the identification of authenticity, and protection of the origin of local certified products.
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Affiliation(s)
- Irene Bosmali
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece;
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis, 57001 Thessaloniki, Greece; (G.L.); (E.S.)
| | - Georgios Lagiotis
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis, 57001 Thessaloniki, Greece; (G.L.); (E.S.)
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou St., 38446 Volos, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA (ex NAGREF), 1st District Road of Thessalonikis-Polygyrou, 57001 Thermi, Greece;
| | - Eleni Stefanidou
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis, 57001 Thessaloniki, Greece; (G.L.); (E.S.)
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou St., 38446 Volos, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis, 57001 Thessaloniki, Greece; (G.L.); (E.S.)
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou St., 38446 Volos, Greece
| | - Costas G. Biliaderis
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece;
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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:ETLS20230067. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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Ruiz Mondragon KY, Aguirre-Planter E, Gasca-Pineda J, Klimova A, Trejo-Salazar RE, Reyes Guerra MA, Medellin RA, Piñero D, Lira R, Eguiarte LE. Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico. PeerJ 2022; 10:e14398. [PMID: 36415865 PMCID: PMC9676017 DOI: 10.7717/peerj.14398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background Genetic diversity is fundamental for the survival of species. In particular, in a climate change scenario, it is crucial that populations maintain genetic diversity so they can adapt to novel environmental conditions. Genetic diversity in wild agaves is usually high, with low genetic differentiation among populations, in part maintained by the agave pollinators such as the nectarivorous bats. In cultivated agaves, patterns of genetic diversity vary according to the intensity of use, management, and domestication stage. In Agave tequilana Weber var. azul (A. tequilana thereafter), the plant used for tequila production, clonal propagation has been strongly encouraged. These practices may lead to a reduction in genetic diversity. Methods We studied the diversity patterns with genome-wide SNPs, using restriction site associated DNA sequencing in cultivated samples of A. tequilana from three sites of Jalisco, Mexico. For one locality, seeds were collected and germinated in a greenhouse. We compared the genomic diversity, levels of inbreeding, genetic differentiation, and connectivity among studied sites and between adults and juvenile plants. Results Agave tequilana presented a genomic diversity of HT = 0.12. The observed heterozygosity was higher than the expected heterozygosity. Adults were more heterozygous than juveniles. This could be a consequence of heterosis or hybrid vigor. We found a shallow genetic structure (average paired FST = 0.0044). In the analysis of recent gene flow, we estimated an average migration rate among the different populations of m = 0.25. In particular, we found a population that was the primary source of gene flow and had greater genomic diversity (HE and HO ), so we propose that this population should continue to be monitored as a potential genetic reservoir. Discussion Our results may be the consequence of more traditional management in the studied specific region of Jalisco. Also, the exchange of seeds or propagules by producers and the existence of gene flow due to occasional sexual reproduction may play an important role in maintaining diversity in A. tequilana. For populations to resist pests, to continue evolving and reduce their risk of extinction under a climate change scenario, it is necessary to maintain genetic diversity. Under this premise we encourage to continue acting in conservation programs for this species and its pollinators.
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Affiliation(s)
| | - Erika Aguirre-Planter
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jaime Gasca-Pineda
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anastasia Klimova
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | | | - Rodrigo A. Medellin
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Daniel Piñero
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Pérez-Martínez AL, Eguiarte LE, Mercer KL, Martínez-Ainsworth NE, McHale L, van der Knaap E, Jardón-Barbolla L. Genetic diversity, gene flow, and differentiation among wild, semiwild, and landrace chile pepper (Capsicum annuum) populations in Oaxaca, Mexico. AMERICAN JOURNAL OF BOTANY 2022; 109:1157-1176. [PMID: 35694731 DOI: 10.1002/ajb2.16019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. METHODS We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. RESULTS Genetic diversity (HE ) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. CONCLUSIONS Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.
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Affiliation(s)
- Ana L Pérez-Martínez
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México; Circuito exterior s/n anexo al Jardín Botánico. C.P. 04510. Ciudad Universitaria, Ciudad de México, México
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - Natalia E Martínez-Ainsworth
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
| | - Leah McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - Esther van der Knaap
- Department of Horticulture, Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Lev Jardón-Barbolla
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (
Phaseolus coccineus
L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Department of Plant Sciences University of Saskatchewan Saskatoon SK S7N 5A2 Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Environmental Genomics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center University of California, Davis Davis California 95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali Università Politecnica delle Marche Ancona 60131 Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
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The Household Context of In Situ Conservation in a Center of Crop Diversity: Self-Reported Practices and Perceptions of Maize and Phaseolus Bean Farmers in Oaxaca, Mexico. SUSTAINABILITY 2022. [DOI: 10.3390/su14127148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Crop diversity conservation in situ is an ecosystem service with benefits at household, community, and global scales. These include risk reduction and adaptation to changing physical and sociocultural environments—both important given the accelerating changes in climate, human migration, and the industrialization of agriculture. In situ conservation typically occurs as part of small-scale, traditionally based agriculture and can support cultural identity and values. Although decisions regarding crop diversity occur at the household level, few data detail the household context of in situ crop diversity management. Our research addressed this data gap for maize and Phaseolus bean in Oaxaca, Mexico, a major center of diversity for those crops. We defined diversity as farmer-named varieties and interviewed 400 farming households across eight communities in two contrasting socioecological regions. Our research asked, “In a major center of maize and Phaseolus diversity, what are the demographic, production, and consumption characteristics of the households that are stewarding this diversity?” We describe the context of conservation and its variation within and between communities and regions and significant associations between diversity and various independent variables, including direct maize consumption, region, and marketing of crops. These results provide a benchmark for communities to understand and strengthen their maize and bean systems in ways they value and for scientists to support those communities in dynamically stewarding locally and globally significant diversity.
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Nasar S, Ostevik K, Murtaza G, Rausher MD. Morphological and molecular characterization of variation in common bean (Phaseolus vulgaris L.) germplasm from Azad Jammu and Kashmir, Pakistan. PLoS One 2022; 17:e0265817. [PMID: 35472209 PMCID: PMC9041810 DOI: 10.1371/journal.pone.0265817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/08/2022] [Indexed: 11/18/2022] Open
Abstract
Phaseolus vulgaris, an essential food and source of protein, is cultivated across the world. This study was carried out to investigate the diversity and population structure of 34 P. vulgaris landrace accessions collected from the Azad Jammu and Kashmir (AJ&K) regions of Pakistan. The samples were analyzed both morphologically and using genetic variation identified through RNA sequencing. Our results indicated that most genetic variation occurs among local accessions, with little genetic variation occurring between geographical regions. In addition, the accessions fell into two major genetic groups. Morphological analysis revealed that these two genetic groups differ in a number of quantitative traits, including seed length, seed width, and seed weight. One accession, DUD-11, appears to be a mixture of the two major groups genetically as well as morphologically. Among the other accessions, DUD-8, RWK-2, and NGD-1 depicted particularly high seed weight along with higher seed length, seed width, and seed yield per plant. We suggest focusing on these accessions in future breeding programs. More generally, our results provide baseline data that will be useful for crop improvement and effective cultivation practices in Pakistan.
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Affiliation(s)
- Sidra Nasar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Kate Ostevik
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California, United States of America
| | - Ghulam Murtaza
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Mark D. Rausher
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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8
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Oliveira GCX, Vieira ICG, Tremblay RL. Editorial: Gene Flow Among Wild and Domesticated Plant Species in the Neotropical Region. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.799071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Arriagada O, Schwember AR, Greve MJ, Urban MO, Cabeza RA, Carrasco B. Morphological and Molecular Characterization of Selected Chilean Runner Bean ( Phaseolus coccineus L.) Genotypes Shows Moderate Agronomic and Genetic Variability. PLANTS (BASEL, SWITZERLAND) 2021; 10:1688. [PMID: 34451733 PMCID: PMC8400864 DOI: 10.3390/plants10081688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/02/2022]
Abstract
The runner bean is the third most economically important Phaseolus species, which is cultivated on small-scale agriculture for the production of immature pods or to obtain dry seeds. However, despite the economic importance and agronomic potential of this species, the runner bean has been little studied from the genetic standpoint. Therefore, the main objective of this study was to characterize ten selected lines of runner bean obtained from Central (Santiago) and Southern (Valdivia and Villarica) Chile based on morphological and agronomic traits. In addition, the genetic variability of these lines was determined using 12 Inter-Simple Sequence Repeat (ISSR) markers to evaluate the potential of this germplasm for breeding and commercial purposes. As a result, the lines from Central Chile were characterized, and had a higher number of pods per plant compared to the Southern lines, although the size and weight of their seeds were lower. Moreover, a low level of genetic diversity (He = 0.251) was encountered in this population. Finally, this is one of the first studies that generate relevant and novel information on the morphological, agronomic and genetic characterization of the P. coccineus germplasm present in Chile.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (A.R.S.); (M.J.G.)
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (A.R.S.); (M.J.G.)
| | - María Jesús Greve
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (A.R.S.); (M.J.G.)
| | - Milan O. Urban
- Bean Physiology Team, International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia;
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Basilio Carrasco
- Scientific Director at Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3460000, Chile
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Chacón-Sánchez MI, Martínez-Castillo J, Duitama J, Debouck DG. Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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11
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Chen M, Lin JY, Wu X, Apuya NR, Henry KF, Le BH, Bui AQ, Pelletier JM, Cokus S, Pellegrini M, Harada JJ, Goldberg RB. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proc Natl Acad Sci U S A 2021; 118:e2024704118. [PMID: 33536344 PMCID: PMC8017943 DOI: 10.1073/pnas.2024704118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An important question is what genes govern the differentiation of plant embryos into suspensor and embryo proper regions following fertilization and division of the zygote. We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region. We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones, such as gibberellic acid, and other metabolites are up-regulated in giant scarlet runner bean and common bean suspensors. Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well, strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper. By contrast, genes controlling transcriptional regulation, development, and cell division are up-regulated primarily within the embryo proper. Transcriptomes from less specialized soybean and Arabidopsis suspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated. Genes active in the embryo proper, however, are functionally similar to those active in scarlet runner bean and common bean embryo proper regions. We uncovered a set of suspensor- and embryo proper-specific transcription factors (TFs) that are shared by all embryos irrespective of morphology, suggesting that they are involved in early differentiation processes common to all plants. Chromatin immunoprecipitation sequencing (ChIP-Seq) experiments with scarlet runner bean and soybean WOX9, an up-regulated suspensor TF, gained entry into a regulatory network important for suspensor development irrespective of morphology.
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Affiliation(s)
- Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Xiaomeng Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Nestor R Apuya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Julie M Pelletier
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Shawn Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - John J Harada
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
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Quintero-Corrales C, Ángeles-Argáiz R, Jaramillo-Correa JP, Piñero D, Garibay-Orijel R, Mastretta-Yanes A. Allopatric instead of parapatric divergence in an ectomycorrhizal fungus (Laccaria trichodermophora) in tropical sky-islands. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Corzo-Ríos LJ, Sánchez-Chino XM, Cardador-Martínez A, Martínez-Herrera J, Jiménez-Martínez C. Effect of cooking on nutritional and non-nutritional compounds in two species of Phaseolus (P. vulgaris and P. coccineus) cultivated in Mexico. Int J Gastron Food Sci 2020. [DOI: 10.1016/j.ijgfs.2020.100206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Herron SA, Rubin MJ, Ciotir C, Crews TE, Van Tassel DL, Miller AJ. Comparative Analysis of Early Life Stage Traits in Annual and Perennial Phaseolus Crops and Their Wild Relatives. FRONTIERS IN PLANT SCIENCE 2020; 11:34. [PMID: 32210978 PMCID: PMC7076113 DOI: 10.3389/fpls.2020.00034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/13/2020] [Indexed: 05/27/2023]
Abstract
Herbaceous perennial species are receiving increased attention for their potential to provide both edible products and ecosystem services in agricultural systems. Many legumes (Fabaceae Lindl.) are of special interest due to nitrogen fixation carried out by bacteria in their roots and their production of protein-rich, edible seeds. However, herbaceous perennial legumes have yet to enter widespread use as pulse crops, and the response of wild, herbaceous perennial species to artificial selection for increased seed yield remains under investigation. Here we compare cultivated and wild accessions of congeneric annual and herbaceous perennial legume species to investigate associations of lifespan and cultivation with early life stage traits including seed size, germination, and first year vegetative growth patterns, and to assess variation and covariation in these traits. We use "cultivated" to describe accessions with a history of human planting and use, which encompasses a continuum of domestication. Analyses focused on three annual and four perennial species of the economically important genus Phaseolus. We found a significant association of both lifespan and cultivation status with seed size (weight, two-dimensional lateral area, length), node number, and most biomass traits (with cultivation alone showing additional significant associations). Wild annual and perennial accessions primarily showed only slight differences in trait values. Relative to wild forms, both cultivated annual and cultivated perennial accessions exhibited greater seed size and larger overall vegetative size, with cultivated perennials showing greater mean trait differences relative to wild accessions than cultivated annuals. Germination proportion was significantly lower in cultivated relative to wild annual accessions, while no significant difference was observed between cultivated and wild perennial germination. Regardless of lifespan and cultivation status, seed size traits were positively correlated with most vegetative traits, and all biomass traits examined here were positively correlated. This study highlights some fundamental similarities and differences between annual and herbaceous perennial legumes and provides insights into how perennial legumes might respond to artificial selection compared to annual species.
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Affiliation(s)
- Sterling A. Herron
- Department of Biology, Saint Louis University, St. Louis, MO, United States
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Matthew J. Rubin
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Claudia Ciotir
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | | | | | - Allison J. Miller
- Department of Biology, Saint Louis University, St. Louis, MO, United States
- Donald Danforth Plant Science Center, St. Louis, MO, United States
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Sahruzaini NA, Rejab NA, Harikrishna JA, Khairul Ikram NK, Ismail I, Kugan HM, Cheng A. Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading. FRONTIERS IN PLANT SCIENCE 2020; 11:531. [PMID: 32431724 PMCID: PMC7212832 DOI: 10.3389/fpls.2020.00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/07/2020] [Indexed: 05/12/2023]
Abstract
The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.
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Affiliation(s)
- Nurul Amylia Sahruzaini
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Kusaira Khairul Ikram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Hazel Marie Kugan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Acga Cheng,
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Capistrán-Carabarin A, Aquino-Bolaños EN, García-Díaz YD, Chávez-Servia JL, Vera-Guzmán AM, Carrillo-Rodríguez JC. Complementarity in Phenolic Compounds and the Antioxidant Activities of Phaseolus coccineus L. and P. vulgaris L. Landraces. Foods 2019; 8:foods8080295. [PMID: 31357736 PMCID: PMC6723271 DOI: 10.3390/foods8080295] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 01/25/2023] Open
Abstract
Phaseolus vulgaris L. is one of the most consumed and documented legumes in regard to its grain composition, but little is known about P. coccineus L. To evaluate and compare the phenolic compound content and antioxidant activity between landraces of P. coccineus and P. vulgaris, a total of 14 accessions of P. coccineus and P. vulgaris were collected from farmers in Oaxaca, Mexico. Based on reference standards and spectrophotometry, the polyphenol, flavonoid and anthocyanin contents were quantified, and the antioxidant activity was determined by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. The results showed significant differences (p ≤ 0.05) between species and accessions, where P. coccineus and P. vulgaris significantly differed in their contents of polyphenols, flavonoids, and anthocyanins, as well as their antioxidant activity in the seed coat and cotyledons. Higher concentrations were found in the seed coat than in the cotyledons for both species. P. vulgaris had a higher anthocyanin content in the seed coat and a higher flavonoid content in the cotyledons than P. coccineus, but it did not for the other compounds tested. There was high variability among the accessions that were classified into four phenotypic groups: Two of P. coccineus, one of a P. coccineus–vulgaris mixed group, and one group of P. vulgaris.
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Affiliation(s)
| | | | | | - José Luis Chávez-Servia
- CIIDIR-Oaxaca, Instituto Politécnico Nacional, Santa Cruz Xoxocotlán, Oaxaca 71230, Mexico
- Correspondence: ; Tel.: +52-951-517-0610
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Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation. Biochem Genet 2019; 57:747-766. [PMID: 30997627 DOI: 10.1007/s10528-019-09920-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, 'Gigantes' and 'Elephantes' phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for 'Gigantes' and 'Elephantes,' respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in 'Elephantes' and 648 upregulated in 'Gigantes.' A significant upregulation of defense-related genes was observed in 'Elephantes,' among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in 'Gigantes' and 'Elephantes,' respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in 'Gigantes' and 40.1% in 'Elephantes' of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.
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Cortés AJ, Skeen P, Blair MW, Chacón-Sánchez MI. Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication? FRONTIERS IN PLANT SCIENCE 2018; 9:1816. [PMID: 30619396 PMCID: PMC6306030 DOI: 10.3389/fpls.2018.01816] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/22/2018] [Indexed: 05/10/2023]
Abstract
Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more prone to harbor within-species differentiation due to genomic features, suppressed recombination, smaller effective population size or increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure produced by multiple independent domestications each especially in Andean and Mesoamerican / Middle American geographies. We genotyped 22,531 GBS-derived SNP markers in 209 individuals of wild and cultivated Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepool comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, genomic regions with overall high relative differentiation (measured by FST) coincided with regions of low SNP density and regions of elevated delta divergence between-genepools (ΔDiv), independent of the scale of divergence. The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggest that shared variants are being recurrently fixed at replicated regions of the genome, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation and within-species divergence. In summary, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue to fortuitously shape genomic differentiation at various others scales of divergence.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia) – Centro de Investigación La Selva, Rionegro, Colombia
- Universidad Nacional de Colombia – Sede Medellín, Facultad de Ciencias Agrarias – Departamento de Ciencias
Forestales, Medellín, Colombia
| | - Paola Skeen
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Matthew W. Blair
- Department of Agricultural and Environmental Science, Tennessee State University, Nashville, TN, United States
| | - María I. Chacón-Sánchez
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
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Abstract
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.
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