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Donhouedé JCF, Marques I, Salako KV, Assogbadjo AE, Ribeiro N, Ribeiro-Barros AIF. Genetic and morphological diversity in populations of Annona senegalensis Pers. occurring in Western (Benin) and Southern (Mozambique) Africa. PeerJ 2023; 11:e15767. [PMID: 37576509 PMCID: PMC10416773 DOI: 10.7717/peerj.15767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/27/2023] [Indexed: 08/15/2023] Open
Abstract
Background Understanding morpho-genetic diversity and differentiation of species with relatively large distributions is crucial for the conservation and sustainable management of their genetic resources. The present study focused on Annona senegalensis Pers., an important multipurpose wild plant, distributed exclusively in natural ecosystems but facing several threats. The study assessed the genetic and morphological diversity, structure, and differentiation of the species in populations from Western (Benin) and Southern (Mozambique) Africa. The material was evaluated to ascertain the environmental (climatic) determinants of the variation within this species. Methods Four sub-populations comprised of 154 individuals were phenotyped based on nineteen plant, fruit, and leaf morphological traits and further genotyped using ten polymorphic nuclear microsatellite (nSSR) markers. Results The results indicated strong differences in plant, fruit, and leaf morphological traits between Western and Southern populations. Furthermore, the studied populations were characterized by high genetic diversity, with an average genetic diversity index of 1.02. Western populations showed higher heterozygosity values (0.61-0.71) than Southern populations (0.41-0.49). Western and Southern populations were clearly differentiated into two different genetic groups, with further genetic subdivisions reflecting four sub-populations. Genetic variation between regions (populations) was higher (69.1%) than among (21.3%) and within (9.6%) sub-populations. Four distinct morphological clusters were obtained, which were strongly associated with the four genetic groups representing each sub-population. Climate, mainly precipitation and temperature indexes, explained the relatively higher variation found in morphological traits from Western (40.47%) in relation to Southern (27.98%) populations. Our study suggests that both environmental and genetic dynamics play an important role in the development of morphological variation in A. senegalensis.
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Affiliation(s)
- Janine Conforte Fifonssi Donhouedé
- Laboratoire d’Écologie Appliquée, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
- Department of Forest Engineering, Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo, Mozambique
- Laboratoire de Biomathématiques et d’Estimations Forestières, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Bénin
| | - Isabel Marques
- Forest Research Center (CEF), School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Kolawolé Valère Salako
- Laboratoire de Biomathématiques et d’Estimations Forestières, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Bénin
| | - Achille Ephrem Assogbadjo
- Laboratoire d’Écologie Appliquée, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
- Laboratoire de Biomathématiques et d’Estimations Forestières, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Bénin
| | - Natasha Ribeiro
- Department of Forest Engineering, Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo, Mozambique
| | - Ana IF Ribeiro-Barros
- Forest Research Center (CEF), School of Agriculture, University of Lisbon, Lisbon, Portugal
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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Catarino S, Brilhante M, Essoh AP, Charrua AB, Rangel J, Roxo G, Varela E, Moldão M, Ribeiro-Barros A, Bandeira S, Moura M, Talhinhas P, Romeiras MM. Exploring physicochemical and cytogenomic diversity of African cowpea and common bean. Sci Rep 2021; 11:12838. [PMID: 34145302 PMCID: PMC8213759 DOI: 10.1038/s41598-021-91929-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
In sub-Saharan Africa, grain legumes (pulses) are essential food sources and play an important role in sustainable agriculture. Among the major pulse crops, the native cowpea (Vigna unguiculata) and introduced common bean (Phaseolus vulgaris) stand out. This paper has two main goals. First, we provide a comprehensive view of the available genetic resources of these genera in Africa, including data on germplasm collections and mapping biodiversity-rich areas. Second, we investigate patterns of physicochemical and cytogenomic variation across Africa to explore the geographical structuring of variation between native and introduced beans. Our results revealed that 73 Vigna and 5 Phaseolus species occur in tropical regions of Africa, with 8 countries accounting for more than 20 native species. Conversely, germplasm collections are poorly represented when compared to the worldwide collections. Regarding the nuclear DNA content, on average, V. unguiculata presents significantly higher values than P. vulgaris. Also, V. unguiculata is enriched in B, Mg, S, and Zn, while P. vulgaris has more Fe, Ca, and Cu. Overall, our study suggests that the physicochemical and cytogenomic diversity of native Vigna species is higher than previously thought, representing valuable food resources to reduce food insecurity and hunger, particularly of people living in African developing countries.
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Affiliation(s)
- Sílvia Catarino
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Miguel Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Anyse Pereira Essoh
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Research Centre in Biodiversity and Genetic Resources (CIBIO), InBIO Associate Laboratory, Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
- Nova School of Business and Economics, Universidade Nova de Lisboa, Campus de Carcavelos, Rua da Holanda, n.1, Carcavelos, 2775-405, Cascais, Portugal
| | - Alberto B Charrua
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Nova School of Business and Economics, Universidade Nova de Lisboa, Campus de Carcavelos, Rua da Holanda, n.1, Carcavelos, 2775-405, Cascais, Portugal
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Licungo University, P.O. Box 2025, 2100, Beira, Mozambique
| | - Josefa Rangel
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Centro de Botânica, Universidade Agostinho Neto, Luanda, Angola
| | - Guilherme Roxo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Eromise Varela
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Margarida Moldão
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Ana Ribeiro-Barros
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Salomão Bandeira
- Department of Biological Sciences, Eduardo Mondlane University, PO Box 257, 1100, Maputo, Mozambique
| | - Mónica Moura
- Research Centre in Biodiversity and Genetic Resources (CIBIO), InBIO Associate Laboratory, Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Maria M Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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Hoque A, Fiedler JD, Rahman M. Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection. BMC Genomics 2020; 21:557. [PMID: 32795254 PMCID: PMC7430851 DOI: 10.1186/s12864-020-06922-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/17/2020] [Indexed: 11/25/2022] Open
Abstract
Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest (Fst > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.
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Affiliation(s)
- Ahasanul Hoque
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Jason D Fiedler
- Cereal Crops Research, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lupinus mutabilis (tarwi) is a species of Andean origin with high protein and oil content and regarded as a potential crop in Europe. The success in the introduction of this crop depends in part on in depth knowledge of the intra-specific genetic variability of the collections, enabling the establishment of breeding and conservation programs. In this study, we used morphological traits, Inter-Simple Sequence Repeat markers and genome size to assess genetic and genomic diversity of 23 tarwi accessions under Mediterranean conditions. Phenotypic analyses and yield component studies point out accession LM268 as that achieving the highest seed production, producing large seeds and efficiently using primary branches as an important component of total yield, similar to the L. albus cultivars used as controls. By contrast, accession JKI-L295 presents high yield concentrated on the main stem, suggesting a semi-determinate development pattern. Genetic and genomic analyses revealed important levels of diversity, however not relatable to phenotypic diversity, reflecting the recent domestication of this crop. This is the first study of genome size diversity within L. mutabilis, revealing an average size of 2.05 pg/2C (2001 Mbp) with 9.2% variation (1897–2003 Mbp), prompting further studies for the exploitation of this diversity.
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Akbar A, Hussain S, Ullah K, Fahim M, Ali GS. Detection, virulence and genetic diversity of Fusarium species infecting tomato in Northern Pakistan. PLoS One 2018; 13:e0203613. [PMID: 30235252 PMCID: PMC6147440 DOI: 10.1371/journal.pone.0203613] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022] Open
Abstract
In addition to the well-known Fusarium oxysporum f.sp. lycopersici, several other Fusarium species are known to cause extensive worldwide crop losses in tomatoes. Prevalence and identities of Fusarium species infecting tomatoes in Northwest Pakistan is currently not known. In this study, we surveyed and characterized Fusarium species associated with symptomatic tomatoes in Northwest Pakistan using morphological and molecular analyses. Pathogenicity tests revealed varying degrees of virulence with some Fusarium sp. causing severe disease symptoms whereas others displaying mild symptoms. Molecular identification based on Internal Transcribed Spacer (ITS) region and TEF-1α gene sequencing classified all isolates into four major species with a majority (68.9%) belonging to Fusarium incarnatum-equiseti species complex (FIESC), followed by F. graminearum (20.7%), F. acuminatum (6.8%), and F. solani (6.8%). ISSR analyses revealed substantial genetic variability among all the Fusarium population infecting tomatoes. Genetic distance between populations from the central region and the type strain F.o. f.sp. lycopersici from Florida was the highest (0.3662), whereas between the south and central region was the lowest (0.0298), which showed that genetic exchange is negatively effected by distance. High genetic variability suggests that these Fusarium species have the potential to become a major production constraint for tomato growers. Findings in this report would greatly facilitate identification of Fusarium species in developing countries and would provide groundwork for devising and implementing disease management measures for minimizing losses caused by Fusarium species in tomatoes.
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Affiliation(s)
- Asma Akbar
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, Institute of Food and Agricultural Sciences, Apopka, FL, United States of America
| | - Shaukat Hussain
- Khyber-Pakhtumkhwa Agriculture University, Peshawar, Pakistan
| | - Kaleem Ullah
- Khyber-Pakhtumkhwa Agriculture University, Peshawar, Pakistan
| | - Muhammad Fahim
- Khyber-Pakhtumkhwa Agriculture University, Peshawar, Pakistan
| | - Gul Shad Ali
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, Institute of Food and Agricultural Sciences, Apopka, FL, United States of America
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