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Zheng H, Dang Y, Sui N. Sorghum: A Multipurpose Crop. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17570-17583. [PMID: 37933850 DOI: 10.1021/acs.jafc.3c04942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Sorghum (Sorghum bicolor L.) is one of the top five cereal crops in the world in terms of production and planting area and is widely grown in areas with severe abiotic stresses such as drought and saline-alkali land due to its excellent stress resistance. Moreover, sorghum is a rare multipurpose crop that can be classified into grain sorghum, energy sorghum, and silage sorghum according to its domestication direction and utilization traits, endowing it with broad breeding and economic value. In this review, we mainly discuss the latest research progress and regulatory genes of agronomic traits of sorghum as a grain, energy, and silage crop, as well as the future improvement direction of multipurpose sorghum. We also emphasize the feasibility of cultivating multipurpose sorghum through genetic engineering methods by exploring potential targets using wild sorghum germplasm and genetic resources, as well as genomic resources.
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Affiliation(s)
- Hongxiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Yingying Dang
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Institute, Shandong Normal University, Dongying, 257000, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
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Alves-Pereira A, Zucchi MI, Clement CR, Viana JPG, Pinheiro JB, Veasey EA, de Souza AP. Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties. Sci Rep 2022; 12:1268. [PMID: 35075210 PMCID: PMC8786832 DOI: 10.1038/s41598-022-05160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia Dos Agronegócios (APTA), Pólo Centro-Sul. Rodovia SP 127, km 30, Piracicaba, SP, 13400-970, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign (UIUC), AW-101 Turner Hall, 1102 South Goodwin Avenue, Urbana, IL, 61801-4798, USA
| | - José Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil. .,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.
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Al-Rowaily SL, Alghamdi AO, Alghamdi SS, Assaeed AM, Hegazy A, Afzal M, Migdadi HM. Assessment of morphological and molecular variability of some Solanum melongena L. cultivars and wild Solanum incanum L. in Saudi Arabia. Biol Futur 2021; 72:187-199. [PMID: 34554472 DOI: 10.1007/s42977-020-00052-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
The genus Solanum exhibits a wide range of variability in morphology, flavor, and tolerance to biotic and abiotic stresses. Phenotypic and genetic variability using ISSR and RAPD markers of Solanum incanum distributed in Al-Baha province of the Kingdom of Saudi Arabia is assessed. Thirty samples are representing three different locations: Baljershy, Aqeeq, and Tohama, besides twenty-five samples representing five different commercial cultivars tested. Growth type, the number of leaves per plant, fruit size (phenotypic traits), crude protein, carbohydrates, digestive organic matter, and Mg, Ca, P were the principal contributors in the PCA. Molecular analysis showed that 114 ISSR and 80 RAPD alleles with a 100% polymorphism were recorded. The polymorphism information content (PIC) values ranged from 0.84 to 0.91 for ISSR and from 0.59 to 0.89 for RAPD data. Similarity values ranged from 0.16 to 1.00, with an average of 0.47 for ISSR and from 0.01 to 0.97, with an average of 0.36 for RAPD. It resulted in a positive and significant correlation between morphological, molecular, nutritional, and chemical analysis of fruits using Mantel analysis. UPGMA and PCA for morphological traits and molecular data discriminated commercial cultivars and wild relatives. Solanum incanum was more diverse than commercial varieties. This study revealed a wide genetic diversity among and within collected eggplant accessions and may use in breeding programs of eggplants. There is a need to increase the present eggplant collection to widen the genetic diversity of cultivated eggplant varieties in Saudi Arabia.
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Affiliation(s)
- Saud L Al-Rowaily
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdullah O Alghamdi
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdulaziz M Assaeed
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Ahmad Hegazy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Muhammad Afzal
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia. .,National Agricultural Research Centre, P. O Box: 639, Baq'a, 19381, Jordan.
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Silva SMM, Martins K, Costa FHS, Campos TDE, Scherwinski-Pereira JE. Genetic structure and diversity of native Guadua species (Poaceae: Bambusoideae) in natural populations of the Brazilian Amazon rainforest. AN ACAD BRAS CIENC 2020; 92:e20190083. [PMID: 33263658 DOI: 10.1590/0001-3765202020190083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/10/2019] [Indexed: 11/22/2022] Open
Abstract
The Southwestern Region of the Brazilian Amazon is formed by forests dominated by bamboos. The genus Guadua is endemic to the Americas, and little is known about the genetic diversity and structure of species of this genus. This study aimed to evaluate the genetic diversity and structure of two native Guadua species in natural populations in the Southwestern region of the Brazilian Amazon. Therefore, the genetic diversity and structure of Guadua aff. chaparensis and Guadua aff. lynnclarkiae were evaluated with the use of microsatellite molecular markers (SSR). It was verified that the average genetic diversity for the populations studied was considered high ( H ^ e =0.5) compared to other species of bamboo. All populations had rare and private alleles, and none of them presented significant values of inbreeding. The populations were divergent ( G ^ ST = 0.46), resulting in a low apparent gene flow. The Bayesian analysis showed that among the 350 individuals analyzed, five groups (K=5) were formed, with little similarity among the groups (Populations), although two of them presented clonal individuals. According to the results obtained, it can be conclude that populations should be treated as having unique characteristics, mainly when accessed for management and for in situ and ex situ conservation studies.
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Affiliation(s)
- Susana M M Silva
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia/Rede Bionorte, Universidade Federal do Acre, Centro de Ciências Biológicas e da Natureza/CCBN, Rodovia BR 364, Km 04, Distrito Industrial, 69920-900 Rio Branco, AC, Brazil
| | - Karina Martins
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Rodovia João Leme dos Santos, Km 110 - SP-264, Itinga, 18052-780 Sorocaba, SP, Brazil
| | - Frederico H S Costa
- Universidade Federal do Acre, Centro de Ciências Biológicas e da Natureza/CCBN, Campus Universitário, Rodovia BR 364, Km 04, Distrito Industrial, 69920-900 Rio Branco, AC, Brazil
| | - Tatiana DE Campos
- Embrapa Acre, Rodovia BR-364, Km 14 (Rio Branco/Porto Velho), 69900-970 Rio Branco, AC, Brazil
| | - Jonny E Scherwinski-Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte (Final), PqEB, 70770-917 Brasília, DF, Brazil.,Centro de Pesquisa e Aplicação de Bambu e Fibras Naturais - CPAB, SCLN 406, Bloco A, Asa Norte, 70884-510 Brasília, DF, Brazil
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Ananda GKS, Myrans H, Norton SL, Gleadow R, Furtado A, Henry RJ. Wild Sorghum as a Promising Resource for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2020; 11:1108. [PMID: 32765575 PMCID: PMC7380247 DOI: 10.3389/fpls.2020.01108] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/06/2020] [Indexed: 05/21/2023]
Abstract
Sorghum bicolor (L.) Moench is a multipurpose food crop which is ranked among the top five cereal crops in the world, and is used as a source of food, fodder, feed, and fuel. The genus Sorghum consists of 24 diverse species. Cultivated sorghum was derived from the wild progenitor S. bicolor subsp. verticilliflorum, which is commonly distributed in Africa. Archeological evidence has identified regions in Sudan, Ethiopia, and West Africa as centers of origin of sorghum, with evidence for more than one domestication event. The taxonomy of the genus is not fully resolved, with alternative classifications that should be resolved by further molecular analysis. Sorghum can withstand severe droughts which makes it suitable to grow in regions where other major crops cannot be grown. Wild relatives of many crops have played significant roles as genetic resources for crop improvement. Although there have been many studies of domesticated sorghum, few studies have reported on its wild relatives. In Sorghum, some species are widely distributed while others are very restricted. Of the 17 native sorghum species found in Australia, none have been cultivated. Isolation of these wild species from domesticated crops makes them a highly valuable system for studying the evolution of adaptive traits such as biotic and abiotic stress tolerance. The diversity of the genus Sorghum has probably arisen as a result of the extensive variability of the habitats over which they are distributed. The wild gene pool of sorghum may, therefore, harbor many useful genes for abiotic and biotic stress tolerance. While there are many examples of successful examples of introgression of novel alleles from the wild relatives of other species from Poaceae, such as rice, wheat, maize, and sugarcane, studies of introgression from wild sorghum are limited. An improved understanding of wild sorghums will better allow us to exploit this previously underutilized gene pool for the production of more resilient crops.
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Affiliation(s)
- Galaihalage K. S. Ananda
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Harry Myrans
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Sally L. Norton
- Australian Grains Genebank, Agriculture Victoria, Horsham, VIC, Australia
| | - Roslyn Gleadow
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- *Correspondence: Robert J. Henry,
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Labeyrie V, Deu M, Dussert Y, Rono B, Lamy F, Marangu C, Kiambi D, Calatayud C, Coppens d'Eeckenbrugge G, Robert T, Leclerc C. Past and present dynamics of sorghum and pearl millet diversity in Mount Kenya region. Evol Appl 2016; 9:1241-1257. [PMID: 27877203 PMCID: PMC5108216 DOI: 10.1111/eva.12405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023] Open
Abstract
Crop populations in smallholder farming systems are shaped by the interaction of biological, ecological, and social processes, occurring on different spatiotemporal scales. Understanding these dynamics is fundamental for the conservation of crop genetic resources. In this study, we investigated the processes involved in sorghum and pearl millet diversity dynamics on Mount Kenya. Surveys were conducted in ten sites distributed along two elevation transects and occupied by six ethnolinguistic groups. Varieties of both species grown in each site were inventoried and characterized using SSR markers. Genetic diversity was analyzed using both individual- and population-based approaches. Surveys of seed lot sources allowed characterizing seed-mediated gene flow. Past sorghum diffusion dynamics were explored by comparing Mount Kenya sorghum diversity with that of the African continent. The absence of structure in pearl millet genetic diversity indicated common ancestry and/or important pollen- and seed-mediated gene flow. On the contrary, sorghum varietal and genetic diversity showed geographic patterns, pointing to different ancestry of varieties, limited pollen-mediated gene flow, and geographic patterns in seed-mediated gene flow. Social and ecological processes involved in shaping seed-mediated gene flow are further discussed.
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Affiliation(s)
- Vanesse Labeyrie
- UMR AGAP CIRAD Montpellier France; Present address: UPR GREEN CIRAD 34398 Montpellier France
| | | | - Yann Dussert
- Ecologie, Systématique et Evolution UMR 8079 CNRS Université Paris-Sud Orsay France; Present address: UMR 1065 Santé et Agroécologie du Vignoble INRA 33140 Villenave d'Ornon France
| | | | - Françoise Lamy
- Ecologie, Systématique et Evolution UMR 8079 CNRS Université Paris-Sud Orsay France; Department of Biologie UVSQ Versailles France
| | - Charles Marangu
- KALRO Embu Kenya; Present address: CIMMYT 00621 Nairobi Kenya
| | - Dan Kiambi
- ICRISAT Nairobi Kenya; Present address: ABCIC P.O. Box 100882-00101 Nairobi Kenya
| | | | | | - Thierry Robert
- Ecologie, Systématique et Evolution UMR 8079 CNRS Université Paris-Sud Orsay France; Sorbonne Universités, UPMC Univ Paris 06, IFD Paris Cedex 05 France
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Pan Y, Wang X, Sun G, Li F, Gong X. Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae). PLoS One 2016; 11:e0166419. [PMID: 27846268 PMCID: PMC5112861 DOI: 10.1371/journal.pone.0166419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/29/2016] [Indexed: 11/19/2022] Open
Abstract
Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis.
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Affiliation(s)
- Yuezhi Pan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xueqin Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Guiling Sun
- Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Mutegi E, Snow AA, Rajkumar M, Pasquet R, Ponniah H, Daunay MC, Davidar P. Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: implications for conservation. AMERICAN JOURNAL OF BOTANY 2015; 102:140-8. [PMID: 25587156 DOI: 10.3732/ajb.1400403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Crop wild relatives represent important genetic resources for crop improvement and the preservation of native biodiversity. Eggplant (Solanum melongena), known as brinjal in India, ranks high among crops whose wild gene pools are underrepresented in ex situ collections and warrant urgent conservation. Knowledge of outcrossing rates and patterns of genetic variation among wild populations can aid in designing strategies for both in situ and ex situ preservation.• METHODS We used 14 microsatellite (simple sequence repeat) markers to examine genetic diversity, population structure, and outcrossing in 10 natural populations of wild/weedy eggplant (S. insanum = S. melongena var. insanum) and three cultivated populations in southern India.• KEY RESULTS Multilocus FST analyses revealed strong differentiation among populations and significant isolation by distance. Bayesian model-based clustering, principal coordinate analysis, and hierarchical cluster analysis grouped the wild/weedy populations into three major clusters, largely according to their geographic origin. The three crop populations were similar to each other and grouped with two wild/weedy populations that occurred nearby. Outcrossing rates among the wild/weedy populations ranged from 5-33%, indicating a variable mixed-mating system.• CONCLUSION Geographic isolation has played a significant role in shaping the contemporary patterns of genetic differentiation among these populations, many of which represent excellent candidates for in situ conservation. In two cases, close genetic affinity between cultivars and nearby wild/weedy populations suggests that gene flow has occurred between them. To our knowledge, this is the first study investigating population-level patterns of genetic diversity in wild relatives of eggplant.
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Affiliation(s)
- Evans Mutegi
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12 St., Columbus, Ohio 43210 USA
| | - Allison A Snow
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12 St., Columbus, Ohio 43210 USA
| | - Muthu Rajkumar
- Department of Ecology and Environmental Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Remy Pasquet
- IRD, UR 072, LEGS 91198 Gif-sur-yvette, France; Université Paris-Sud 11 91400 Orsay, France
| | - Hopeland Ponniah
- Department of Ecology and Environmental Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Marie-Christine Daunay
- INRA, Unité de Génétique & Amélioration des Fruits et Légumes, UR1052, Domaine St Maurice, CS 60094 F-84143 Montfavet cedex, France
| | - Priya Davidar
- Department of Ecology and Environmental Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
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Assessment of genetic diversity among sorghum landraces and their wild/weedy relatives in western Kenya using simple sequence repeat (SSR) markers. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Adugna A. Analysis of in situ diversity and population structure in Ethiopian cultivated Sorghum bicolor (L.) landraces using phenotypic traits and SSR markers. SPRINGERPLUS 2014; 3:212. [PMID: 24877027 PMCID: PMC4033718 DOI: 10.1186/2193-1801-3-212] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/23/2014] [Indexed: 01/16/2023]
Abstract
Genetic diversity is a fundamental input for every plant breeding program, genetic resources conservation, and evolutionary studies. In situ diversity and population genetic structure of eight cultivated sorghum landrace populations were investigated in the center of origin, Ethiopia using seven phenotypic traits and 12 highly polymorphic sorghum SSR markers. In farmers' fields, DNA samples were collected using Whatman® plant saver card and quantitative phenotypic traits were measured from 160 individual plant samples belonging to the eight populations representing three diverse geographical regions. High diversity was observed among the various populations for the measured phenotypic traits. The 12 SSR loci produced a total of 123 alleles of which 78 (63.41%) were rare (frequency ≤0.05) with an average of 10.25 alleles per polymorphic locus. The polymorphism information content (PIC) was in the range 0.39-0.85 showing the good discriminatory power of the SSR loci used. Average observed heterozygosity and gene diversity across all populations and loci ranged 0.04-0.33 and 0.41-0.87, respectively. Neighbor-joining and STRUCTURE analyses grouped the 160 samples from the eight populations differently. AMOVA showed 54.44% of the variation to be within populations, 32.76% among populations within regions, and 12.8% among the regions of origin. There was high divergence in the total populations (FST = 0.40) indicating low level of gene flow (Nm = 0.38), but high gene flow was also observed in some adjacent populations. The populations from Wello displayed close relationship with remote Gibe and Metekel populations indicating that the variation followed human migration patterns. Implications of the results for sorghum improvement and germplasm conservation are discussed.
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Affiliation(s)
- Asfaw Adugna
- Melkassa Agricultural Research Center, P.O. Box 1085, Adama, Ethiopia
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Estimation of in situ mating systems in wild sorghum (Sorghum bicolor (L.) Moench) in Ethiopia using SSR-based progeny array data: implications for the spread of crop genes into the wild. J Genet 2013; 92:3-10. [PMID: 23640403 DOI: 10.1007/s12041-013-0214-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Because transgenic sorghum (Sorghum bicolor L.) is being developed for Africa, we investigated the potential for transgenes to spread to conspecific wild/weedy sorghum populations in Ethiopia, which is considered the centre of origin of cultivated sorghum. In the current study, the extent of outcrossing, and uniparental and biparental inbreeding were investigated in seven wild/weedy sorghum populations collected at elevations ranging from 631 to 1709 m. Based on allele frequency data of 1120 progenies and 140 maternal plants from five polymorphic microsatellite markers, outcrossing rates were estimated using standard procedures. The average multilocus outcrossing rate was 0.51, with a range of 0.31-0.65 among populations, and the family outcrossing rate was in the extreme range of 0 to 100%. The highest outcrossing (t(m) = 0.65) was recorded in a weedy population that was intermixed with an improved crop variety in Abuare (Wello region). It was also observed that the inbreeding coefficient of the progenies (F(p)) tend to be more than the inbreeding coefficient of both their maternal parents (F(m)) and the level of inbreeding expected at equilibrium (F(eq)), which is a characteristic of predominantly outbreeding species. Biparental inbreeding was evident in all populations and averaged 0.24 (range = 0.10-0.33). The high outcrossing rates of wild/weedy sorghum populations in Ethiopia indicate a high potential for crop genes (including transgenes) to spread within the wild pool. Therefore, effective risk management strategies may be needed if the introgression of transgenes or other crop genes from improved cultivars into wild or weedy populations is deemed to be undesirable.
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Billot C, Ramu P, Bouchet S, Chantereau J, Deu M, Gardes L, Noyer JL, Rami JF, Rivallan R, Li Y, Lu P, Wang T, Folkertsma RT, Arnaud E, Upadhyaya HD, Glaszmann JC, Hash CT. Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLoS One 2013; 8:e59714. [PMID: 23565161 PMCID: PMC3614975 DOI: 10.1371/journal.pone.0059714] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/17/2013] [Indexed: 11/19/2022] Open
Abstract
Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.
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Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0353-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sagnard F, Deu M, Dembélé D, Leblois R, Touré L, Diakité M, Calatayud C, Vaksmann M, Bouchet S, Mallé Y, Togola S, Traoré PCS. Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1231-46. [PMID: 21811819 DOI: 10.1007/s00122-011-1662-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/09/2011] [Indexed: 05/08/2023]
Abstract
Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.
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Affiliation(s)
- Fabrice Sagnard
- CIRAD, UMR AGAP, Avenue d'Agropolis, 34398, Montpellier, France
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