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Hassett K, Muria-Gonzalez MJ, Martin A, Karakaya A, Çelik Oğuz A, Bakonyi J, Knight NL, Prins R, Ellwood SR. Global Spread, Genetic Differentiation, and Selection of Barley Spot Form Net Blotch Isolates. PHYTOPATHOLOGY 2024; 114:1542-1553. [PMID: 38619562 DOI: 10.1094/phyto-11-23-0442-r] [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: 04/16/2024]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread worldwide in the twentieth century. Genetic relationships were analyzed to determine the diversity, survival, and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor, and Europe. The results, based on genome-wide DArTseq data, indicated that isolates from Turkey were the most differentiated with regional sub-structuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged, and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent Cyp51A mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of the promoter and counterselection elsewhere. Individuals from Western Australia shared genomic regions and Cyp51A haplotypes with South African isolates, suggesting a recent common origin. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Aziz Karakaya
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Arzu Çelik Oğuz
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Jószef Bakonyi
- Plant Protection Institute, HUN-REN Centre for Agricultural Research, Herman Ottó str. 15, 1022 Budapest, Hungary
| | - Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Renée Prins
- CenGen (Pty) Ltd., Worcester, 6850, South Africa
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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Prohaska A, Rey-Serra P, Petit J, Petit A, Perrotte J, Rothan C, Denoyes B. Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae137. [PMID: 38988619 PMCID: PMC11233882 DOI: 10.1093/hr/uhae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria × ananassa). Taking into account the requirements of both growers and consumers when selecting high-quality cultivars is a real challenge. Here, we used a diversity panel enriched with unique European accessions and the 50 K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by genome-wide association studies (GWAS), and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition, and appearance occurred simultaneously in European and American cultivars. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosomal regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new quantitative trait locus (QTL), demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf life. Moreover, major QTL for firmness, glossiness, skin resistance, and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness, and skin resistance. Overall, our study provides a potential avenue for extending shelf life without compromising flavor and color as well as the genetic markers needed to achieve this goal.
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Affiliation(s)
- Alexandre Prohaska
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | - Pol Rey-Serra
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
| | - Johann Petit
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
| | - Aurélie Petit
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | - Justine Perrotte
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | | | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
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Daduwal HS, Bhardwaj R, Srivastava RK. Pearl millet a promising fodder crop for changing climate: a review. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:169. [PMID: 38913173 DOI: 10.1007/s00122-024-04671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
The agricultural sector faces colossal challenges amid environmental changes and a burgeoning human population. In this context, crops must adapt to evolving climatic conditions while meeting increasing production demands. The dairy industry is anticipated to hold the highest value in the agriculture sector in future. The rise in the livestock population is expected to result in an increased demand for fodder feed. Consequently, it is crucial to seek alternative options, as crops demand fewer resources and are resilient to climate change. Pearl millet offers an apposite key to these bottlenecks, as it is a promising climate resilience crop with significantly low energy, water and carbon footprints compared to other crops. Numerous studies have explored its potential as a fodder crop, revealing promising performance. Despite its capabilities, pearl millet has often been overlooked. To date, few efforts have been made to document molecular aspects of fodder-related traits. However, several QTLs and candidate genes related to forage quality have been identified in other fodder crops, which can be harnessed to enhance the forage quality of pearl millet. Lately, excellent genomic resources have been developed in pearl millet allowing deployment of cutting-edge genomics-assisted breeding for achieving a higher rate of genetic gains. This review would facilitate a deeper understanding of various aspects of fodder pearl millet in retrospect along with the future challenges and their solution. This knowledge may pave the way for designing efficient breeding strategies in pearl millet thereby supporting sustainable agriculture and livestock production in a changing world.
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Affiliation(s)
- Harmanpreet Singh Daduwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Ruchika Bhardwaj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India.
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Omondi DO, Dida MM, Berger DK, Beyene Y, Nsibo DL, Juma C, Mahabaleswara SL, Gowda M. Combination of linkage and association mapping with genomic prediction to infer QTL regions associated with gray leaf spot and northern corn leaf blight resistance in tropical maize. Front Genet 2023; 14:1282673. [PMID: 38028598 PMCID: PMC10661943 DOI: 10.3389/fgene.2023.1282673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Among the diseases threatening maize production in Africa are gray leaf spot (GLS) caused by Cercospora zeina and northern corn leaf blight (NCLB) caused by Exserohilum turcicum. The two pathogens, which have high genetic diversity, reduce the photosynthesizing ability of susceptible genotypes and, hence, reduce the grain yield. To identify population-based quantitative trait loci (QTLs) for GLS and NCLB resistance, a biparental population of 230 lines derived from the tropical maize parents CML511 and CML546 and an association mapping panel of 239 tropical and sub-tropical inbred lines were phenotyped across multi-environments in western Kenya. Based on 1,264 high-quality polymorphic single-nucleotide polymorphisms (SNPs) in the biparental population, we identified 10 and 18 QTLs, which explained 64.2% and 64.9% of the total phenotypic variance for GLS and NCLB resistance, respectively. A major QTL for GLS, qGLS1_186 accounted for 15.2% of the phenotypic variance, while qNCLB3_50 explained the most phenotypic variance at 8.8% for NCLB resistance. Association mapping with 230,743 markers revealed 11 and 16 SNPs significantly associated with GLS and NCLB resistance, respectively. Several of the SNPs detected in the association panel were co-localized with QTLs identified in the biparental population, suggesting some consistent genomic regions across genetic backgrounds. These would be more relevant to use in field breeding to improve resistance to both diseases. Genomic prediction models trained on the biparental population data yielded average prediction accuracies of 0.66-0.75 for the disease traits when validated in the same population. Applying these prediction models to the association panel produced accuracies of 0.49 and 0.75 for GLS and NCLB, respectively. This research conducted in maize fields relevant to farmers in western Kenya has combined linkage and association mapping to identify new QTLs and confirm previous QTLs for GLS and NCLB resistance. Overall, our findings imply that genetic gain can be improved in maize breeding for resistance to multiple diseases including GLS and NCLB by using genomic selection.
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Affiliation(s)
- Dennis O. Omondi
- Department of Crops and Soil Sciences, School of Agriculture, Food Security and Environmental Sciences, Maseno University, Kisumu, Kenya
- Crop Science Division Bayer East Africa Limited, Nairobi, Kenya
| | - Mathews M. Dida
- Department of Crops and Soil Sciences, School of Agriculture, Food Security and Environmental Sciences, Maseno University, Kisumu, Kenya
| | - Dave K. Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yoseph Beyene
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - David L. Nsibo
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Collins Juma
- Crop Science Division Bayer East Africa Limited, Nairobi, Kenya
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Suresh L. Mahabaleswara
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Manje Gowda
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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Dossa EN, Shimelis H, Mrema E, Shayanowako ATI, Laing M. Genetic resources and breeding of maize for Striga resistance: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1163785. [PMID: 37235028 PMCID: PMC10206272 DOI: 10.3389/fpls.2023.1163785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/07/2023] [Indexed: 05/28/2023]
Abstract
The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.
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Affiliation(s)
- Emeline Nanou Dossa
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Emmanuel Mrema
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Tanzania Agricultural Research Institute, Tumbi Center, Tabora, Tanzania
| | | | - Mark Laing
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Muñoz P, Castillejo C, Gómez JA, Miranda L, Lesemann S, Olbricht K, Petit A, Chartier P, Haugeneder A, Trinkl J, Mazzoni L, Masny A, Zurawicz E, Ziegler FMR, Usadel B, Schwab W, Denoyes B, Mezzetti B, Osorio S, Sánchez-Sevilla JF, Amaya I. QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase. HORTICULTURE RESEARCH 2023; 10:uhad006. [PMID: 36938573 PMCID: PMC10022485 DOI: 10.1093/hr/uhad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Strawberry (Fragaria × ananassa) fruits are an excellent source of L-ascorbic acid (AsA), a powerful antioxidant for plants and humans. Identifying the genetic components underlying AsA accumulation is crucial for enhancing strawberry nutritional quality. Here, we unravel the genetic architecture of AsA accumulation using an F1 population derived from parental lines 'Candonga' and 'Senga Sengana', adapted to distinct Southern and Northern European areas. To account for environmental effects, the F1 and parental lines were grown and phenotyped in five locations across Europe (France, Germany, Italy, Poland and Spain). Fruit AsA content displayed normal distribution typical of quantitative traits and ranged five-fold, with significant differences among genotypes and environments. AsA content in each country and the average in all of them was used in combination with 6,974 markers for quantitative trait locus (QTL) analysis. Environmentally stable QTLs for AsA content were detected in linkage group (LG) 3A, LG 5A, LG 5B, LG 6B and LG 7C. Candidate genes were identified within stable QTL intervals and expression analysis in lines with contrasting AsA content suggested that GDP-L-Galactose Phosphorylase FaGGP(3A), and the chloroplast-located AsA transporter gene FaPHT4;4(7C) might be the underlying genetic factors for QTLs on LG 3A and 7C, respectively. We show that recessive alleles of FaGGP(3A) inherited from both parental lines increase fruit AsA content. Furthermore, expression of FaGGP(3A) was two-fold higher in lines with high AsA. Markers here identified represent a useful resource for efficient selection of new strawberry cultivars with increased AsA content.
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Affiliation(s)
- Pilar Muñoz
- Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140, Málaga, Spain
- PhD program in Advanced Biotechnology, Universidad de Málaga, 29071, Málaga, Spain
| | - Cristina Castillejo
- Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140, Málaga, Spain
| | | | - Luis Miranda
- Finca el Cebollar, Centro IFAPA las Torres, 04745, Huelva, Spain
| | | | | | | | | | - Annika Haugeneder
- Biotechnology of Natural Products, Technische Universität München, 85354, Freising, Germany
| | - Johanna Trinkl
- Biotechnology of Natural Products, Technische Universität München, 85354, Freising, Germany
| | - Luca Mazzoni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Agnieszka Masny
- Department of Horticultural Crop Breeding, the National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | | | | | - Björn Usadel
- Institute of Bio- and Geosciences, Bioinformatics (IBG-4), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, 85354, Freising, Germany
| | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
| | - Bruno Mezzetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain
- Unidad Asociada de I+D+i IFAPA-CSIC Biotecnología y Mejora en Fresa, 29010, Málaga, Spain
| | - José F Sánchez-Sevilla
- Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140, Málaga, Spain
- Unidad Asociada de I+D+i IFAPA-CSIC Biotecnología y Mejora en Fresa, 29010, Málaga, Spain
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Guimarães JB, Nunes C, Pereira G, Gomes A, Nhantumbo N, Cabrita P, Matos J, Simões F, Veloso MM. Genetic Diversity and Population Structure of Cowpea ( Vigna unguiculata (L.) Walp.) Landraces from Portugal and Mozambique. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040846. [PMID: 36840194 PMCID: PMC9963184 DOI: 10.3390/plants12040846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 05/14/2023]
Abstract
Cowpea (Vigna unguiculata (L.) Walp.) is currently a legume crop of minor importance in Europe but a highly relevant staple crop in Africa and the second most cultivated legume in Mozambique. In Portugal and Mozambique, cowpea's phenotypic and genetic variation has been maintained locally by farmers in some areas. We used the molecular markers SSR, SilicoDArT and SNP to analyze the genetic diversity and population structure of 97 cowpea accessions, mainly from Portugal (Southern Europe) and Mozambique (Southern Africa). As far as we know, this is the first time that the genetic variation and the relationship between cowpea landraces collected in Portugal with those originated in Mozambique is reported. Despite the shared historical past, the Portuguese landraces did not share a common genetic background with those from Mozambique, and two different gene pools were revealed. Knowledge of the genetic structure of cowpea landraces offers an opportunity for individual selection within landraces adapted to particular eco-physiological conditions and suggests the existence of a valuable gene pool for exploitation in future Portugal-PALOP (Portuguese-speaking African countries) cowpea breeding programs.
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Affiliation(s)
- Joana Bagoin Guimarães
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
| | - Cátia Nunes
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
- Correspondence:
| | - Graça Pereira
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
| | - Ana Gomes
- Divisão de Agricultura, Instituto Superior Politécnico de Manica (DivAG-ISPM), Campus de Matsinho, Vanduzi, Manica CEP 0607-01, Mozambique
| | - Nascimento Nhantumbo
- Divisão de Agricultura, Instituto Superior Politécnico de Manica (DivAG-ISPM), Campus de Matsinho, Vanduzi, Manica CEP 0607-01, Mozambique
| | - Paula Cabrita
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
| | - José Matos
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Fernanda Simões
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
| | - Maria Manuela Veloso
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, Instituto Público, Av. República, 2784-505 Oeiras, Portugal
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8
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Manzoor I, Samantara K, Bhat MS, Farooq I, Bhat KM, Mir MA, Wani SH. Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios. FRONTIERS IN PLANT SCIENCE 2023; 13:1048217. [PMID: 36743560 PMCID: PMC9893892 DOI: 10.3389/fpls.2022.1048217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2023]
Abstract
Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.
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Affiliation(s)
- Ikra Manzoor
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Momin Showkat Bhat
- Division of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Iqra Farooq
- Field Station Bonera, Pulwama, Council of Industrial and Scientific Research (CSIR) Indian Institute of Integrative Medicine, J&K, Jammu, India
| | - Khalid Mushtaq Bhat
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Amin Mir
- Ambri Apple Research Centre, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shopian, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, Anantnag, India
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9
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Ferreira PHN, Souza FHS, de Moraes RL, Perez MF, Sassi FDMC, Viana PF, Feldberg E, Ezaz T, Liehr T, Bertollo LAC, Cioffi MDB. The Genetic Differentiation of Pyrrhulina (Teleostei, Characiformes) Species is Likely Influenced by Both Geographical Distribution and Chromosomal Rearrangements. Front Genet 2022; 13:869073. [PMID: 35601496 PMCID: PMC9114635 DOI: 10.3389/fgene.2022.869073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Allopatry is generally considered to be one of the main contributors to the remarkable Neotropical biodiversity. However, the role of chromosomal rearrangements including neo-sex chromosomes for genetic diversity is still poorly investigated and understood. Here, we assess the genetic divergence in five Pyrrhulina species using population genomics and combined the results with previously obtained cytogenetic data, highlighting that molecular genetic diversity is consistent with their chromosomal features. The results of a principal coordinate analysis (PCoA) indicated a clear difference among all species while showing a closer relationship of the ones located in the same geographical region. This was also observed in genetic structure analyses that only grouped P. australis and P. marilynae, which were also recovered as sister species in a species tree analysis. We observed a contradictory result for the relationships among the three species from the Amazon basin, as the phylogenetic tree suggested P. obermulleri and P. semifasciata as sister species, while the PCoA showed a high genetic difference between P. semifasciata and all other species. These results suggest a potential role of sex-related chromosomal rearrangements as reproductive barriers between these species.
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Affiliation(s)
- Pedro H. N. Ferreira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Fernando H. S. Souza
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Renata L. de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Manolo F. Perez
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Francisco de M. C. Sassi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Patrik F. Viana
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, NSW, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Friedrich Schiller University, University Hospital Jena, Jena, Germany
- *Correspondence: Thomas Liehr,
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo de B. Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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10
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Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula RA, Acharya CB, Lee S, Verma S, Whitaker VM, Bassil N, Zurn J, Cole GS, Bird K, Edger PP, Knapp SJ. Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry. Mol Biol Evol 2021; 38:2285-2305. [PMID: 33507311 PMCID: PMC8136507 DOI: 10.1093/molbev/msab024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.
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Affiliation(s)
- Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Charlotte B Acharya
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Seonghee Lee
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Sujeet Verma
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Vance M Whitaker
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 92182, USA
| | - Jason Zurn
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 92182, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Kevin Bird
- Department of Horticultural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Patrick P Edger
- Department of Horticultural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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11
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Adu BG, Akromah R, Amoah S, Nyadanu D, Yeboah A, Aboagye LM, Amoah RA, Owusu EG. High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz). PLoS One 2021; 16:e0255290. [PMID: 34314448 PMCID: PMC8315537 DOI: 10.1371/journal.pone.0255290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.
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Affiliation(s)
- Bright Gyamfi Adu
- Council for Scientific and Industrial Research-Plant Genetics Resources Research Institute, Bunso, Ghana
| | - Richard Akromah
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Stephen Amoah
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alex Yeboah
- Council for Scientific and Industrial Research -Savanna Agricultural Research Institute, Tamale, Ghana
| | - Lawrence Missah Aboagye
- Council for Scientific and Industrial Research-Plant Genetics Resources Research Institute, Bunso, Ghana
| | - Richard Adu Amoah
- Council for Scientific and Industrial Research-Plant Genetics Resources Research Institute, Bunso, Ghana
| | - Eva Gyamfuaa Owusu
- Department of Statistics and Actuarial Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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12
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Pincot DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TJ, Runcie DE, Heffelfinger C, Dellaporta SL, Cole GS, Knapp SJ. Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3-GENES GENOMES GENETICS 2021; 11:6117203. [PMID: 33772307 PMCID: PMC8022721 DOI: 10.1093/g3journal/jkab015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/12/2020] [Indexed: 01/22/2023]
Abstract
The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent–offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.
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Affiliation(s)
- Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mirko Ledda
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Thomas J Poorten
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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13
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A Large-Scale Dataset of Barley, Maize and Sorghum Variety Identification Using DNA Fingerprinting in Ethiopia. DATA 2021. [DOI: 10.3390/data6060058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The data described in this paper were part of a large-scale nationally representative household survey, the Ethiopian Socioeconomic Survey (ESS 2018/19). Grain samples of barley, maize and sorghum were collected in six regions in Ethiopia. Variety identification was assessed by matching samples to a reference library composed of released improved materials, using approximately 50,000 markers from DArTseq platforms. This data were part of a study documenting the reach of CGIAR-related germplasms in Ethiopia. These objective measures of crop varietal adoption, unique in the public domain, can be analyzed along with a large set of variables related to agro-ecologies, household characteristics and plot management practices, available in the Ethiopian Socioeconomic Survey 2018/19.
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14
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Niedziela A, Brukwiński W, Bednarek PT. Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa. J Appl Genet 2021; 62:185-198. [PMID: 33409933 PMCID: PMC8032618 DOI: 10.1007/s13353-020-00599-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022]
Abstract
Cytoplasmic male sterility (CMS) is a widely applied plant breeding tool for hybrid seed production. The phenomenon is often caused by chimeric genes with altered open reading frames (ORFs) located in the mitochondrial genomes and expressed as novel genotoxic products that induce pollen abortion. The fertility of CMS plants can be restored by nuclear-encoded genes that inhibit the action of ORFs responsible for pollen sterility. A recombinant inbred line (RIL) mapping population S64/04/01, encompassing 175 individuals, was used for genetic map construction and identification of quantitative trait loci (QTLs) responsible for fertility restoration in rye (Secale cereale L.) with CMS Pampa. The genetic map of all seven rye chromosomes included 15,516 SNP and silicoDArT markers and covered 1070.5 cm. Individual QTLs explaining 60% and 5.5% of the fertility trait’s phenotypic variance were mapped to chromosomes 4R (QRft-4R) and 5R (QRft-5R), respectively. Association mapping identified markers with the highest R2 value of 0.58 (p value = 2.21E-28). Markers showing the highest associations with the trait were also mapped to the 4R chromosome within the QRft-4R region. Based on marker sequence homology, putative genes involved in pollen fertility restoration were suggested. Five silicoDArTs were converted into PCR-based markers for further breeding purposes.
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Affiliation(s)
- Agnieszka Niedziela
- Plant Breeding and Acclimatization Institute, NRI, Radzików, 05-870, Błonie, Poland
| | | | - Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute, NRI, Radzików, 05-870, Błonie, Poland.
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15
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Lee HE, Manivannan A, Lee SY, Han K, Yeum JG, Jo J, Kim J, Rho IR, Lee YR, Lee ES, Kang BC, Kim DS. Chromosome Level Assembly of Homozygous Inbred Line 'Wongyo 3115' Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:696229. [PMID: 34335662 PMCID: PMC8317996 DOI: 10.3389/fpls.2021.696229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/08/2021] [Indexed: 05/02/2023]
Abstract
Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line 'Wongyo 3115', using long- and short-read sequencing technologies. The assembly of 'Wongyo 3115' produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the 'Wongyo 3115' reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the 'BS F2' populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the 'Wongyo 3115' genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of 'BS F2' obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.
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Affiliation(s)
- Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Sun Yi Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Jun-Geol Yeum
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Il Rae Rho
- Department of Agronomy, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
- Do-Sun Kim
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16
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Castillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Muñoz P, Triviño JC, Caruana J, Liu Z, Cobo N, Hardigan MA, Knapp SJ, Vallarino JG, Osorio S, Martín-Pizarro C, Posé D, Toivainen T, Hytönen T, Oh Y, Barbey CR, Whitaker VM, Lee S, Olbricht K, Sánchez-Sevilla JF, Amaya I. Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry ( Fragaria spp.) Fruit. THE PLANT CELL 2020; 32:3723-3749. [PMID: 33004617 PMCID: PMC7721342 DOI: 10.1105/tpc.20.00474] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 05/02/2023]
Abstract
The fruits of diploid and octoploid strawberry (Fragaria spp) show substantial natural variation in color due to distinct anthocyanin accumulation and distribution patterns. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 is the main activator in strawberry fruit. Here, we show that mutations in MYB10 cause most of the variation in anthocyanin accumulation and distribution observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F ×ananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function mutations in MYB10 were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses of octoploid Fragaria spp revealed that FaMYB10-2, one of three MYB10 homoeologs identified, regulates anthocyanin biosynthesis in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in FaEnSpm-2 are responsible for enhanced MYB10-2 expression and anthocyanin biosynthesis in strawberry fruit flesh.
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Affiliation(s)
- Cristina Castillejo
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Veronika Waurich
- Hansabred GmbH & Co. KG, 01108 Dresden, Germany
- Institut für Botanik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Henning Wagner
- Hansabred GmbH & Co. KG, 01108 Dresden, Germany
- Institut für Botanik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Rubén Ramos
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Nicolás Oiza
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Pilar Muñoz
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | | | - Julie Caruana
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Nicolás Cobo
- Department of Plant Sciences, University of California, Davis, California 95616
- Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 01145, Chile
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, California 95616
| | - José G Vallarino
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Sonia Osorio
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Carmen Martín-Pizarro
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - David Posé
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
- National Institute of Agricultural Botany East Malling Research (NIAB EMR), Kent ME19 6BJ, United Kingdom
| | - Youngjae Oh
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Christopher R Barbey
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Seonghee Lee
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | | | - José F Sánchez-Sevilla
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Iraida Amaya
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
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17
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Genetic mapping of male sterility and pollen fertility QTLs in triticale with sterilizing Triticum timopheevii cytoplasm. J Appl Genet 2020; 62:59-71. [PMID: 33230679 PMCID: PMC7822802 DOI: 10.1007/s13353-020-00595-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/27/2020] [Accepted: 11/05/2020] [Indexed: 01/15/2023]
Abstract
Cytoplasmic male sterility (CMS) phenomenon is widely exploited in commercial hybrid seed production in economically important crop species, including rye, wheat, maize, rice, sorghum, cotton, sugar beets, and many vegetables. Although some commercial successes, little is known about QTLs responsible for the trait in case of triticale with sterilizing Triticum timopheevii (Tt) cytoplasm. Recombinant inbred line (RIL) F6 mapping population encompassing 182 individuals derived from the cross of individual plants representing the HT352 line and cv Borwo was employed for genetic map construction using SNP markers and identification of QTLs conferring pollen sterility in triticale with CMS Tt. The phenotypes of the F1 lines resulting from crossing of the HT352 (Tt) with HT352 (maintainer) × Borwo were determined by assessing the number of the F2 seeds per spike. A genetic map with 21 linkage groups encompasses 29,737 markers and spanned over the distance of 2549 cM. Composite (CIM) and multiple (MIM) interval mappings delivered comparable results. Single QTLs mapped to the 1A, 1B, 2A, 2R, 3B, 3R, 4B, and 5B chromosomes, whereas the 5R and 6B chromosomes shared 3 and 2 QTLs, respectively. The QTLs with the highest LOD score mapped to the 5R, 3R, 1B, and 4B chromosomes; however, the QRft-5R.3 has the highest explained variance of the trait.
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18
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Pott DM, Vallarino JG, Cruz-Rus E, Willmitzer L, Sánchez-Sevilla JF, Amaya I, Osorio S. Genetic analysis of phenylpropanoids and antioxidant capacity in strawberry fruit reveals mQTL hotspots and candidate genes. Sci Rep 2020; 10:20197. [PMID: 33214566 PMCID: PMC7677386 DOI: 10.1038/s41598-020-76946-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
Phenylpropanoids are a large class of plant secondary metabolites, which play essential roles in human health mainly associated with their antioxidant activity. Strawberry (Fragaria × ananassa) is a rich source of phytonutrients, including phenylpropanoids, which have been shown to have beneficial effects on human health. In this study, using the F. × ananassa '232' × '1392' F1 segregating population, we analyzed the genetic control of individual phenylpropanoid metabolites, total polyphenol content (TPC) and antioxidant capacity (TEAC) in strawberry fruit over two seasons. We have identified a total of 7, 9, and 309 quantitative trait loci (QTL) for TPC, TEAC and for 77 polar secondary metabolites, respectively. Hotspots of stable QTL for health-related antioxidant compounds were detected on linkage groups LG IV-3, LG V-2 and V-4, and LG VI-1 and VI-2, where associated markers represent useful targets for marker-assisted selection of new varieties with increased levels of antioxidant secondary compounds. Moreover, differential expression of candidate genes for major and stable mQTLs was studied in fruits of contrasting lines in important flavonoids. Our results indicate that higher expression of FaF3'H, which encodes the flavonoid 3'-hydroxylase, is associated with increased content of these important flavonoids.
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Affiliation(s)
- Delphine M Pott
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain.,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
| | - José G Vallarino
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain.,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
| | - Eduardo Cruz-Rus
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain
| | - Lothar Willmitzer
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - José F Sánchez-Sevilla
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain
| | - Iraida Amaya
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain. .,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain.
| | - Sonia Osorio
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain. .,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.
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19
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Valdisser PAMR, Müller BSF, de Almeida Filho JE, Morais Júnior OP, Guimarães CM, Borba TCO, de Souza IP, Zucchi MI, Neves LG, Coelho ASG, Brondani C, Vianello RP. Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:574674. [PMID: 33343591 PMCID: PMC7738703 DOI: 10.3389/fpls.2020.574674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/22/2020] [Indexed: 05/26/2023]
Abstract
Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans' yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r 2 sv ), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r 2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.
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Affiliation(s)
- Paula Arielle Mendes Ribeiro Valdisser
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bárbara S. F. Müller
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | | | | | | | - Tereza C. O. Borba
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
| | - Isabela Pavanelli de Souza
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Postgraduate Program in Biological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Maria Imaculada Zucchi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
- Agribusiness Technology Agency of São Paulo State, Agriculture and Food Supply Secretary of São Paulo, Piracicaba, Brazil
| | | | | | - Claudio Brondani
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
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20
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Pujar M, Gangaprasad S, Govindaraj M, Gangurde SS, Kanatti A, Kudapa H. Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet. Sci Rep 2020; 10:19473. [PMID: 33173120 PMCID: PMC7655845 DOI: 10.1038/s41598-020-76230-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.
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Affiliation(s)
- Mahesh Pujar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India.,University of Agricultural Sciences, Shivamogga, Karnataka, 577 225, India
| | - S Gangaprasad
- University of Agricultural Sciences, Shivamogga, Karnataka, 577 225, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India
| | - A Kanatti
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India
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21
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Emeriewen OF, Richter K, Berner T, Keilwagen J, Schnable PS, Malnoy M, Peil A. Construction of a dense genetic map of the Malus fusca fire blight resistant accession MAL0045 using tunable genotyping-by-sequencing SNPs and microsatellites. Sci Rep 2020; 10:16358. [PMID: 33005026 PMCID: PMC7529804 DOI: 10.1038/s41598-020-73393-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Although, the Pacific crabapple, Malus fusca, is a hardy and disease resistant species, studies relating to the genetics of its unique traits are very limited partly due to the lack of a genetic map of this interesting wild apple. An accession of M. fusca (MAL0045) of Julius Kühn-Institut collection in Germany is highly resistant to fire blight disease, incited by different strains of the causative pathogen—Erwinia amylovora. This is the most destructive bacterial disease of Malus of which most of the domesticated apples (Malus domestica) are susceptible. Using a scarcely dense genetic map derived from a population of 134 individuals of MAL0045 × ‘Idared’, the locus (Mfu10) controlling fire blight resistance mapped on linkage group 10 (LG10) and explained up to 66% of the phenotypic variance with different strains. Although the development of robust and tightly linked molecular markers on LG10 through chromosome walking approach led to the identification of a major candidate gene, any minor effect locus remained elusive possibly due to the lack of marker density of the entire genetic map. Therefore, we have developed a dense genetic map of M. fusca using tunable genotyping-by-sequencing (tGBS) approach. Of thousands of de novo SNPs identified, 2677 were informative in M. fusca and 90.5% of these successfully mapped. In addition, integration of SNP data and microsatellite (SSR) data resulted in a final map comprising 17 LGs with 613 loci spanning 1081.35 centi Morgan (cM). This map will serve as a template for mapping using different strains of the pathogen.
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Affiliation(s)
- Ofere Francis Emeriewen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany.
| | - Klaus Richter
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Thomas Berner
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA.,Plant Sciences Institute, Iowa State University, 2035B Carver, Ames, IA, 50011-3650, USA
| | - Mickael Malnoy
- Research and Innovation Centre, Genomics and Biology of Fruit Crops Department, Fondazione Edmund Mach, Via E. Mach, 1, 38010, San Michele all 'Adige (Trentino), Italy
| | - Andreas Peil
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany.
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22
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ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry ( Fragaria x ananassa). 3 Biotech 2020; 10:353. [PMID: 32760641 PMCID: PMC7385052 DOI: 10.1007/s13205-020-02291-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/07/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F1 population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1723G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F1 plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.
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23
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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform. Genomics 2020; 112:3455-3464. [PMID: 32574831 DOI: 10.1016/j.ygeno.2020.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 04/17/2020] [Indexed: 12/30/2022]
Abstract
Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.
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Affiliation(s)
- Riana van Deventer
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa; Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
| | - Munro Marx
- Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
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24
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Whitaker VM, Knapp SJ, Hardigan MA, Edger PP, Slovin JP, Bassil NV, Hytönen T, Mackenzie KK, Lee S, Jung S, Main D, Barbey CR, Verma S. A roadmap for research in octoploid strawberry. HORTICULTURE RESEARCH 2020; 7:33. [PMID: 32194969 PMCID: PMC7072068 DOI: 10.1038/s41438-020-0252-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/26/2020] [Indexed: 05/02/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
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Affiliation(s)
- Vance M Whitaker
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Steven J Knapp
- 2Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Michael A Hardigan
- 2Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Patrick P Edger
- 3Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Janet P Slovin
- USDA-ARS Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MA 20705 USA
| | - Nahla V Bassil
- 5USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333 USA
| | - Timo Hytönen
- 6Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
- 7Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
- NIAB EMR, Kent, ME19 6BJ UK
| | - Kathryn K Mackenzie
- 6Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
| | - Seonghee Lee
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Sook Jung
- 9Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Dorrie Main
- 9Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Christopher R Barbey
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Sujeet Verma
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
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25
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Lebedev VG, Subbotina NM, Maluchenko OP, Lebedeva TN, Krutovsky KV, Shestibratov KA. Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species. Genes (Basel) 2019; 11:E11. [PMID: 31877734 PMCID: PMC7017068 DOI: 10.3390/genes11010011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/14/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022] Open
Abstract
Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat-SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits.
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Affiliation(s)
- Vadim G. Lebedev
- Pushchino State Institute of Natural Sciences, Prospekt Nauki 3, 142290 Pushchino, Russia; (V.G.L.); (N.M.S.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Russia;
| | - Natalya M. Subbotina
- Pushchino State Institute of Natural Sciences, Prospekt Nauki 3, 142290 Pushchino, Russia; (V.G.L.); (N.M.S.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Russia;
| | - Oleg P. Maluchenko
- All-Russian Research Institute of Agricultural Biotechnology, Timiriazevskaya Str. 42, 127550 Moscow, Russia;
| | - Tatyana N. Lebedeva
- Institute of Physicochemical and Biological Problems of Soil Science, Russian Academy of Sciences, Institutskaya Str. 2, 142290 Pushchino, Russia;
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Str. 3, 119333 Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA
| | - Konstantin A. Shestibratov
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Russia;
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Makombu JG, Stomeo F, Oben PM, Tilly E, Stephen OO, Oben BO, Cheruiyot EK, Tarekegn GM, Zango P, Egbe AE, Ndagyong A, Mialhe E, Ngueguim JR, Mujibi FDN. Morphological and molecular characterization of freshwater prawn of genus Macrobrachium in the coastal area of Cameroon. Ecol Evol 2019; 9:14217-14233. [PMID: 31938513 PMCID: PMC6953584 DOI: 10.1002/ece3.5854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Macrobrachium (Bate, 1868) is a large and cosmopolitan crustacean genus of high economic importance worldwide. We investigated the morphological and molecular identification of freshwater prawns of the genus Macrobrachium in South, South West, and Littoral regions of Cameroon. A total of 1,566 specimens were examined morphologically using a key described by Konan (Diversité morphologique et génétique des crevettes des genres Atya Leach, 1816 et Macrobrachium Bate, 1868 de Côte d'Ivoire, 2009, Université d'Abobo Adjamé, Côte d'Ivoire), leading to the identification of seven species of Macrobrachium: M. vollenhovenii (Herklots, 1857); M. macrobrachion (Herklots, 1851); M. sollaudii (De Man, 1912); M. dux (Lenz, 1910); M. chevalieri (Roux, 1935); M. felicinum (Holthuis, 1949); and an undescribed Macrobrachium species M. sp. To validate the genetic basis of the identified species, 94 individuals representing the species were selected and subjected to genetic characterization using 1,814 DArT markers. The admixture analysis revealed four groups: M. vollenhovenii and M. macrobrachion; M. chevalieri; M. felicinum and M. sp; and M. dux and M. sollaudii. But, the principal component analysis (PCA) separated M. sp and M. felicinum to create additional group (i.e., five groups). Based on these findings, M. vollenhovenii and M. macrobrachion may be conspecific, as well as M. dux and M. sollaudii, while M. felicinum and M. sp seems to be different species, suggesting a potential conflict between the morphological identification key and the genetic basis underlying speciation and species allocation for Macrobrachium. These results are valuable in informing breeding design and genetic resource conservation programs for Macrobrachium in Africa.
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Affiliation(s)
- Judith G. Makombu
- Department of Fisheries and Aquatic Resources ManagementFaculty of Agriculture and Veterinary MedicineUniversity of BueaBueaCameroon
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa – International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
- Present address:
European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Pius M. Oben
- Department of Fisheries and Aquatic Resources ManagementFaculty of Agriculture and Veterinary MedicineUniversity of BueaBueaCameroon
| | - Eldridge Tilly
- Biosciences Eastern and Central Africa – International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Opiyo O. Stephen
- Molecular and Cellular Imaging Center–ColumbusThe Ohio State UniversityColumbusOHUSA
- University of the Sacred Heart GuluGuluUganda
| | - Benedicta O. Oben
- Department of Fisheries and Aquatic Resources ManagementFaculty of Agriculture and Veterinary MedicineUniversity of BueaBueaCameroon
| | - Evans K. Cheruiyot
- USOMI LimitedNairobiKenya
- School of Applied Systems BiologyLa Trobe UniversityBundooraAustralia
| | - Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Department of Animal Production and TechnologyBahir Dar UniversityBahir DarEthiopia
| | - Paul Zango
- Institute of Fisheries and Aquatic SciencesYabassiCameroon
| | - Atem E. Egbe
- Institute of Fisheries and Aquatic SciencesYabassiCameroon
| | | | - Eric Mialhe
- Concepto AzulCdlavernaza NorteGuayaquilEcuador
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Cummins D, Kennington WJ, Rudin-Bitterli T, Mitchell NJ. A genome-wide search for local adaptation in a terrestrial-breeding frog reveals vulnerability to climate change. GLOBAL CHANGE BIOLOGY 2019; 25:3151-3162. [PMID: 31273907 DOI: 10.1111/gcb.14703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
Terrestrial-breeding amphibians are likely to be vulnerable to warming and drying climates, as their embryos require consistent moisture for successful development. Adaptation to environmental change will depend on sufficient genetic variation existing within or between connected populations. Here, we use Single Nucleotide Polymorphism (SNP) data to investigate genome-wide patterns in genetic diversity, gene flow and local adaptation in a terrestrial-breeding frog (Pseudophryne guentheri) subject to a rapidly drying climate and recent habitat fragmentation. The species was sampled across 12 central and range-edge populations (192 samples), and strong genetic structure was apparent, as were high inbreeding coefficients. Populations showed differences in genetic diversity, and one population lost significant genetic diversity in a decade. More than 500 SNP loci were putatively under directional selection, and 413 of these loci were correlated with environmental variables such as temperature, rainfall, evaporation and soil moisture. One locus showed homology to a gene involved in the activation of maturation in Xenopus oocytes, which may facilitate rapid development of embryos in drier climates. The low genetic diversity, strong population structuring and presence of local adaptation revealed in this study shows why management strategies such as targeted gene flow may be necessary to assist isolated populations to adapt to future climates.
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Affiliation(s)
- Deanne Cummins
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - W Jason Kennington
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Tabitha Rudin-Bitterli
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Nicola J Mitchell
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
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High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs. Sci Rep 2019; 9:3275. [PMID: 30824841 PMCID: PMC6397268 DOI: 10.1038/s41598-019-39808-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/29/2019] [Indexed: 11/08/2022] Open
Abstract
Recent advances in high-throughput genome sequencing technologies are now making the genetic dissection of the complex genome of cultivated strawberry easier. We sequenced Maehyang (short-day cultivar) × Albion (day-neutral cultivar) crossing populations using double digest restriction-associated DNA (ddRAD) sequencing technique that yielded 978,968 reads, 80.2% of which were aligned to strawberry genome allowing the identification of 13,181 high quality single nucleotide polymorphisms (SNPs). Total 3051 SNPs showed Mendelian segregation in F1, of which 1268 were successfully mapped to 46 linkage groups (LG) spanning a total of 2581.57 cM with an average interval genetic distance of 2.22 cM. The LGs were assigned to the 28 chromosomes of Fragaria × ananassa as determined by positioning the sequence tags on F. vesca genome. In addition, seven QTLs namely, qRU-5D, qRU-3D1, qRU-1D2, qRU-4D, qRU-4C, qRU-5C and qRU-2D2 were identified for runner production with LOD value ranging from 3.5–7.24 that explained 22–38% of phenotypic variation. The key candidate genes having putative roles in meristem differentiation for runnering and flowering within these QTL regions were identified. These will enhance our understanding of the vegetative vs sexual reproductive behavior in strawberry and will aid in setting breeding targets for developing perpetual flowering and profuse runnering cultivar.
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Vallarino JG, Pott DM, Cruz-Rus E, Miranda L, Medina-Minguez JJ, Valpuesta V, Fernie AR, Sánchez-Sevilla JF, Osorio S, Amaya I. Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit. HORTICULTURE RESEARCH 2019; 6:4. [PMID: 30603090 PMCID: PMC6312544 DOI: 10.1038/s41438-018-0077-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 05/09/2023]
Abstract
Improvement of nutritional and organoleptic quality of fruits is a key goal in current strawberry breeding programs. The ratio of sugars to acids is a determinant factor contributing to fruit liking, although different sugars and acids contribute in varying degrees to this complex trait. A segregating F1 population of 95 individuals, previously characterized for several fruit quality characters, was used to map during 2 years quantitative trait loci (QTL) for 50 primary metabolites, l-ascorbic acid (L-AA) and other related traits such as soluble solid content (SSC), titratable acidity (TA), and pH. A total of 133 mQTL were detected above the established thresholds for 44 traits. Only 12.9% of QTL were detected in the 2 years, suggesting a large environmental influence on primary metabolite content. An objective of this study was the identification of key metabolites that were associated to the overall variation in SSC and acidity. As it was observed in previous studies, a number of QTL controlling several metabolites and traits were co-located in homoeology group V (HG V). mQTL controlling a large variance in raffinose, sucrose, succinic acid, and L-AA were detected in approximate the same chromosomal regions of different homoeologous linkage groups belonging to HG V. Candidate genes for selected mQTL are proposed based on their co-localization, on the predicted function, and their differential gene expression among contrasting F1 progeny lines. RNA-seq analysis from progeny lines contrasting in L-AA content detected 826 differentially expressed genes and identified Mannose-6-phosphate isomerase, FaM6PI1, as a candidate gene contributing to natural variation in ascorbic acid in strawberry fruit.
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Affiliation(s)
- José G. Vallarino
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Delphine M. Pott
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Eduardo Cruz-Rus
- Genómica y Biotecnología, Centro de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140 Málaga, Spain
| | - Luis Miranda
- Ingeniería y Tecnología Agroalimentaria, Centro Las Torres-Tomejil, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Alcalá del Río, Sevilla, Spain
| | - Juan J. Medina-Minguez
- Ingeniería y Tecnología Agroalimentaria, Centro de Huelva, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Huelva, Spain
| | - Victoriano Valpuesta
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - José F. Sánchez-Sevilla
- Genómica y Biotecnología, Centro de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140 Málaga, Spain
| | - Sonia Osorio
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Iraida Amaya
- Genómica y Biotecnología, Centro de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140 Málaga, Spain
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Abu Zaitoun SY, Jamous RM, Shtaya MJ, Mallah OB, Eid IS, Ali-Shtayeh MS. Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers. BMC PLANT BIOLOGY 2018; 18:246. [PMID: 30340523 PMCID: PMC6194588 DOI: 10.1186/s12870-018-1475-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Crop landraces embody a source of beneficial genes potentially providing endurance to environmental stress and other agronomic qualities including yield. Our study included 88 snake melon accessions (Cucumis melo var. flexuosus) collected from 9 districts in the Palestinian West-Bank. These accessions represent four landraces of Palestinian snake melon: Green, and White Baladi, and Green, and White Sahouri. RESULTS This is the first report on successful application of genotyping by sequencing in snake melon. Nine thousand seven hundred fifty single-nucleotide polymorphism (SNP) and 7400 DArTseq genetic markers were employed to evaluate genetic biodiversity and population structure of Palestinian snake melon germplasm collection. Clustering based on neighbor-joining-analysis, principle coordinate and Bayesian model implemented in Structure showed that patterns of genetic diversity of snake melon landraces depends on their geographical source and unraveled the presence of two major local landraces (Sahouri, and Baladi) with accessions from each group clustering together. A significant correlation was observed between both types of markers in Mantel correlation test. A significant association between genetic and geographic matrices (P < 0.0001) was also detected. AMOVA indicated that majority of variation (90%) was due to the difference within accessions. CONCLUSION The Palestinian landraces seem to have unique genes that may allow the enhancement of the global snake melon gene pool and developments of the plant production worldwide. Our subsequent objective is to detect genotypes with promising qualities and to conduct association mapping studies concentrating on Fusarium-wilt resistance, yield, and environmental stresses.
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Affiliation(s)
| | - Rana M. Jamous
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
| | - Munqez J. Shtaya
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
- Department of Plant Production and Protection, Faculty of Agriculture, An-Najah University, Tulkarm, Palestine
| | - Omar B. Mallah
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
| | - Imad S. Eid
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
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Genetic diversity of strawberry germplasm using metabolomic biomarkers. Sci Rep 2018; 8:14386. [PMID: 30258188 PMCID: PMC6158285 DOI: 10.1038/s41598-018-32212-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
High-throughput metabolomics technologies can provide the quantification of metabolites levels across various biological processes in different tissues, organs and species, allowing the identification of genes underpinning these complex traits. Information about changes of metabolites during strawberry development and ripening processes is key to aiding the development of new approaches to improve fruit attributes. We used network-based methods and multivariate statistical approaches to characterize and investigate variation in the primary and secondary metabolism of seven domesticated and seven wild strawberry fruit accessions at three different fruit development and ripening stages. Our results demonstrated that Fragaria sub-species can be identified solely based on the gathered metabolic profiles. We also showed that domesticated accessions displayed highly similar metabolic changes due to shared domestication history. Differences between domesticated and wild accessions were detected at the level of metabolite associations which served to rank metabolites whose regulation was mostly altered in the process of domestication. The discovery of comprehensive metabolic variation among strawberry accessions offers opportunities to probe into the genetic basis of variation, providing insights into the pathways to relate metabolic variation with important traits.
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Alam M, Neal J, O’Connor K, Kilian A, Topp B. Ultra-high-throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia. PLoS One 2018; 13:e0203465. [PMID: 30169500 PMCID: PMC6118395 DOI: 10.1371/journal.pone.0203465] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
Macadamia (Macadamia integrifolia, M. tetraphylla and hybrids) is an Australian native nut crop and has a significant economic value in the food industries worldwide. Long juvenility along with traditional breeding strategies impede quick genetic improvement of this crop. The existing cultivars constitute only second to fourth generation of the wild germplasm in the rainforest. The utilisation of molecular markers for genomic selection and genome-wide association studies may accelerate genetic gains. Identification of a robust, reproducible, and cost-effective marker system is instrumental in increasing the efficiency of genomic studies. This study is the first to report the potential of two ultra-high-throughput diversity array technology (DArT) markers (silicoDArT and SNP) in macadamia. Both markers were used to identify the genetic diversity and population structure in 80 macadamia cultivars. Parentage analysis of 25 scions in a rootstock trial was conducted to confirm plant identity where recorded identities did not corroborate with phenotypic field observations. A total of 22,280 silicoDArT and 7,332 SNP markers were reported, of which 11,526 silicoDArT and 3,956 SNP markers were used for analyses after screening with quality control parameters including >95% call rate, >95% reproducibility, and >0.05 one ratio. The average polymorphic information content (PIC) values of silicoDArT and SNP markers were 0.29 and 0.21, respectively. Genetic variance among the cultivars ranged from 0.003 to 0.738 in silicoDArT and 0.004 to 0.412 in SNP markers. Four distinct population groups were identified from SNP data analysis. Most of the accessions used in this study were descended from two or more populations. Cluster analysis clearly separated genotypes of distinct origins, such as the Hawaii Agricultural Experiment Station and Hidden Valley Plantation accessions. Two wild accessions of Macadamia jansenii and M. ternifolia were found to be distantly related to the cultivars. Wild germplasm individuals and their hybrids with cv. ‘660’ formed separate clusters, suggesting that crossing between wild and cultivated genepools can extend genetic diversity. DArTseq-based SNP markers were successfully utilized to confirm the genetic identity of 25 scions in a rootstock trial. Our study suggests that DArT platforms are a robust system for the facilitation of genomic studies with regard to macadamia.
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Affiliation(s)
- Mobashwer Alam
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, the University of Queensland, Nambour, Queensland, Australia
- * E-mail:
| | - Jodi Neal
- Department of Agriculture and Forestry, Maroochy Research Facility, Nambour, Queensland, Australia
| | - Katie O’Connor
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, the University of Queensland, Nambour, Queensland, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Monana St., Canberra ACT, Australia
| | - Bruce Topp
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, the University of Queensland, Nambour, Queensland, Australia
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Resende RT, de Resende MDV, Azevedo CF, Fonseca E Silva F, Melo LC, Pereira HS, Souza TLPO, Valdisser PAMR, Brondani C, Vianello RP. Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris. G3 (BETHESDA, MD.) 2018; 8:2841-2854. [PMID: 29967054 PMCID: PMC6071601 DOI: 10.1534/g3.118.200493] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G × E interaction (c2int ) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging) and 0.43 (productivity), and total genomic heritability accounted for large proportions (72% to ≈100%) of trait heritability. At the same probability threshold, three marker-trait associations were detected using GWAS, while RHM detected eight QTL encompassing 145 markers along five chromosomes. The proportion of genomic heritability explained by RHM was considerably higher (35.48 to 58.02) than that explained by GWAS (28.39 to 30.37). In general, RHM accounted for larger fractions of the additive genetic variance being captured by markers effects inside the defined regions. Nevertheless, a considerable proportion of the heritability is still missing (∼42% to ∼64%), probably due to LD between markers and genes and/or rare allele variants not sampled. RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.
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Affiliation(s)
| | - Marcos Deon V de Resende
- Department of Forestry
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
- EMBRAPA Florestas, Colombo, PR 83411-000, Brazil
| | - Camila F Azevedo
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | | | | | | | | | | | - Claudio Brondani
- Laboratory of Biotechnology, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, GO 75375-000, Brazil
| | - Rosana Pereira Vianello
- Laboratory of Biotechnology, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, GO 75375-000, Brazil
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Barby FF, Ráb P, Lavoué S, Ezaz T, Bertollo LAC, Kilian A, Maruyama SR, Aguiar de Oliveira E, Artoni RF, Santos MH, Ilesanmi Jegede O, Hatanaka T, Tanomtong A, Liehr T, Cioffi MDB. From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes). Genes (Basel) 2018; 9:E306. [PMID: 29921830 PMCID: PMC6027293 DOI: 10.3390/genes9060306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 01/13/2023] Open
Abstract
In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan.
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Canberra, ACT 2617, Australia.
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Mateus Henrique Santos
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25 Mubi. Adamawa State, Nigeria.
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen 40002, Thailand.
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany.
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
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Mogga M, Sibiya J, Shimelis H, Lamo J, Yao N. Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers. PLoS One 2018; 13:e0198012. [PMID: 29856872 PMCID: PMC5983461 DOI: 10.1371/journal.pone.0198012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
Microarray-based markers such as Diversity Arrays Technology (DArT) have become the genetic markers of choice for construction of high-density maps, quantitative trait loci (QTL) mapping and genetic diversity analysis based on their efficiency and low cost. More recently, the DArT technology was further developed in combination with high-throughput next-generation sequencing (NGS) technologies to generate the DArTseq platform representing a new sequencing tool of complexity-reduced representations. In this study, we used DArTseq markers to investigate genetic diversity and genome-wide association studies (GWAS) of grain quality traits in rice (Oryza sativa L.). The study was performed using 59 rice genotypes with 525 SNPs derived from DArTseq platform. Population structure analysis revealed only two distinct genetic clusters where genotypes were grouped based on environmental adaptation and pedigree information. Analysis of molecular variance indicated a low degree of differentiation among populations suggesting the need for broadening the genetic base of the current germplasm collection. GWAS revealed 22 significant associations between DArTseq-derived SNP markers and rice grain quality traits in the test genotypes. In general, 2 of the 22 significant associations were in chromosomal regions where the QTLs associated with the given traits had previously been reported, the other 20 significant SNP marker loci were indicative of the likelihood discovery of novel alleles associated with rice grain quality traits. DArTseq-derived SNP markers that include SNP12_100006178, SNP13_3052560 and SNP14_3057360 individually co-localised with two functional gene groups that were associated with QTLs for grain width and grain length to width ratio on chromosome 3, indicating trait dependency or pleiotropic-effect loci. This study demonstrated that DArTseq markers were useful genomic resources for genome-wide association studies of rice grain quality traits to accelerate varietal development and release.
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Affiliation(s)
- Maurice Mogga
- Ministry of Agriculture and Food Security, Juba, South Sudan
| | - Julia Sibiya
- African Centre for Crop Improvement, School of Agricultural Sciences and Agribusiness, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural Sciences and Agribusiness, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Jimmy Lamo
- Cereals Program, National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Nasser Yao
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Borzęcka E, Hawliczek-Strulak A, Bolibok L, Gawroński P, Tofil K, Milczarski P, Stojałowski S, Myśków B, Targońska-Karasek M, Grądzielewska A, Smolik M, Kilian A, Bolibok-Brągoszewska H. Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye. Sci Rep 2018; 8:8428. [PMID: 29849048 PMCID: PMC5976670 DOI: 10.1038/s41598-018-26541-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.
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Affiliation(s)
- Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Anna Hawliczek-Strulak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Małgorzata Targońska-Karasek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Agnieszka Grądzielewska
- Institute of Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Miłosz Smolik
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari st, ACT 2617, Bruce, Australia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
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Omari S, Kamenir Y, Benichou JIC, Pariente S, Sela H, Perl-Treves R. Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement. BMC Genet 2018; 19:34. [PMID: 29792158 PMCID: PMC5966880 DOI: 10.1186/s12863-018-0619-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/30/2018] [Indexed: 12/05/2022] Open
Abstract
Background Snake melon (Cucumis melo var. flexuosus, “Faqqous”) is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a “Common Garden” rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. Results The different landraces (“populations”) showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties. Yield was assessed by five harvests along the season, with middle harvests producing the highest yields. Yield correlated with early vigor, and with femaleness, but not with late vigor. At the molecular level, 2784 SNP were produced and > 90% were mapped to the melon genome. Populations were very polymorphic (46–72% of the markers biallelic in a 4 individuals sample), and observed heterozygosity was higher than the expected, suggesting gene flow among populations and extensive cross pollination among individuals in the field. Genetic distances between landraces were significantly correlated with the geographical distance between collecting sites, and with long term March precipitation average; variation in yield correlated with April temperature maxima. Conclusions The extensive variation suggests that selection of local snake melon could result in yield improvement. Correlations between traits and climatic variables could suggest local adaptation of landraces to the diverse environment in which they evolved. This study stresses the importance of preserving this germplasm, and its potential for breeding better snake melons as an heirloom crop in our region. Electronic supplementary material The online version of this article (10.1186/s12863-018-0619-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samer Omari
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Yuri Kamenir
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Jennifer I C Benichou
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Sarah Pariente
- Department of Geography and Environment, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Hanan Sela
- Cereal Crop Improvement Institute, Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel Aviv, Israel
| | - Rafael Perl-Treves
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel.
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KOSMOWSKI FRÉDÉRIC, ARAGAW ABIYOT, KILIAN ANDRZEJ, AMBEL ALEMAYEHU, ILUKOR JOHN, YIGEZU BIRATU, STEVENSON JAMES. VARIETAL IDENTIFICATION IN HOUSEHOLD SURVEYS: RESULTS FROM THREE HOUSEHOLD-BASED METHODS AGAINST THE BENCHMARK OF DNA FINGERPRINTING IN SOUTHERN ETHIOPIA. EXPERIMENTAL AGRICULTURE 2018; 55:371-385. [PMID: 33311720 PMCID: PMC7680950 DOI: 10.1017/s0014479718000030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2018] [Indexed: 05/30/2023]
Abstract
Accurate crop varietal identification is the backbone of any high-quality assessment of outcomes and impacts. Sweetpotato (Ipomoea batatas) varieties have important nutritional differences, and there is a strong interest to identify nutritionally superior varieties for dissemination. In agricultural household surveys, such information is often collected based on the farmer's self-report. In this article, we present the results of a data capture experiment on sweet potato varietal identification in southern Ethiopia. Three household-based methods of identifying varietal adoption are tested against the benchmark of DNA fingerprinting: (A) Elicitation from farmers with basic questions for the most widely planted variety; (B) Farmer elicitation on five sweet potato phenotypic attributes by showing a visual-aid protocol; and (C) Enumerator recording observations on five sweet potato phenotypic attributes using a visual-aid protocol and visiting the field. In total, 20% of farmers identified a variety as improved when in fact it was local and 19% identified a variety as local when it was in fact improved. The variety names given by farmers delivered inconsistent and inaccurate varietal identities. Visual-aid protocols employed in methods B and C were better than those in method A, but greatly underestimated the adoption estimates given by the DNA fingerprinting method. Our results suggest that estimating the adoption of improved varieties with methods based on farmer self-reports is questionable and point towards a wider use of DNA fingerprinting in adoption and impact assessments.
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Affiliation(s)
- FRÉDÉRIC KOSMOWSKI
- CGIAR Standing Panel on Impact Assessment, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Roma RM, Italie
| | - ABIYOT ARAGAW
- International Potato Center (CIP), PO Box 10059, Addis Ababa, Ethiopia
| | - ANDRZEJ KILIAN
- Diversity Arrays Technology Pty. Ltd., Building 3, Level D, University of Canberra, Kirinari St. Bruce, ACT2617 (LPO Box 5067), Australia
| | | | - JOHN ILUKOR
- CGIAR Standing Panel on Impact Assessment, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Roma RM, Italie
| | - BIRATU YIGEZU
- Central Statistical Agency of Ethiopia, Piassa, Addis Ababa, Ethiopia
| | - JAMES STEVENSON
- CGIAR Standing Panel on Impact Assessment, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Roma RM, Italie
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High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations. J Appl Genet 2017; 59:23-34. [PMID: 29214520 DOI: 10.1007/s13353-017-0420-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait "shell-thickness" (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.
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Cruz-Rus E, Sesmero R, Ángel-Pérez JA, Sánchez-Sevilla JF, Ulrich D, Amaya I. Validation of a PCR test to predict the presence of flavor volatiles mesifurane and γ-decalactone in fruits of cultivated strawberry ( Fragaria × ananassa). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:131. [PMID: 29070959 PMCID: PMC5624981 DOI: 10.1007/s11032-017-0732-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/22/2017] [Indexed: 05/31/2023]
Abstract
Flavor improvement is currently one of the most important goals for strawberry breeders. At the same time, it is one of the most complex traits to improve, involving the balanced combination of several desired characteristics such as high sweetness, moderate acidity, and the appropriate combination of aroma compounds that are beginning to be delineated in consumer tests. DNA-informed breeding will expedite the selection of complex traits, such as flavor, over traditional phenotypic evaluation, particularly when markers linked to several traits of interests are combined during the breeding process. Natural variation in mesifurane and γ-decalactone, two key volatile compounds providing sweet Sherry and fresh peach-like notes to strawberry fruits, is controlled by the FaOMT and FaFAD1 genes, respectively. In this study, we have optimized a simple PCR test for combined analysis of these genes and determined a prediction accuracy above 91% using a set of 71 diverse strawberry accessions. This high accuracy in predicting the presence of these important volatiles combined with the simplicity of the analytical methodology makes this DNA test an efficient tool for its implementation in current strawberry-breeding programs for the selection of new strawberry cultivars with superior flavor.
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Affiliation(s)
- Eduardo Cruz-Rus
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140 Málaga, Spain
| | - Rafael Sesmero
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140 Málaga, Spain
- Present Address: Departamento de Biología Vegetal, Universidad de Málaga, 29071 Málaga, Spain
| | - José A. Ángel-Pérez
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140 Málaga, Spain
| | - José F. Sánchez-Sevilla
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140 Málaga, Spain
| | - Detlef Ulrich
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 26, 06484 Quedlinburg, Germany
| | - Iraida Amaya
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140 Málaga, Spain
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Vining KJ, Salinas N, Tennessen JA, Zurn JD, Sargent DJ, Hancock J, Bassil NV. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families. PeerJ 2017; 5:e3731. [PMID: 28875078 PMCID: PMC5581533 DOI: 10.7717/peerj.3731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America
| | - Natalia Salinas
- Department of Horticulture, University of Florida, Wimauma, FL, United States of America
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States of America
| | - Jason D Zurn
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
| | - Daniel James Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,East Malling Enterprise Centre, Driscoll's Genetics Limited, East Malling, United Kingdom
| | - James Hancock
- Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
| | - Nahla V Bassil
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America.,National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
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Valdisser PAMR, Pereira WJ, Almeida Filho JE, Müller BSF, Coelho GRC, de Menezes IPP, Vianna JPG, Zucchi MI, Lanna AC, Coelho ASG, de Oliveira JP, Moraes ADC, Brondani C, Vianello RP. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 2017; 18:423. [PMID: 28558696 PMCID: PMC5450071 DOI: 10.1186/s12864-017-3805-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. RESULTS Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. CONCLUSIONS For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
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Affiliation(s)
- Paula A. M. R. Valdisser
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Wendell J. Pereira
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | - Jâneo E. Almeida Filho
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, RJ Brazil
| | - Bárbara S. F. Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | | | - Ivandilson P. P. de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO Brazil
| | - João P. G. Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria I. Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Anna C. Lanna
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | | | | | | | - Claudio Brondani
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | - Rosana P. Vianello
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
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Nagano S, Shirasawa K, Hirakawa H, Maeda F, Ishikawa M, Isobe SN. Discrimination of candidate subgenome-specific loci by linkage map construction with an S 1 population of octoploid strawberry (Fragaria × ananassa). BMC Genomics 2017; 18:374. [PMID: 28499415 PMCID: PMC5429521 DOI: 10.1186/s12864-017-3762-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/03/2017] [Indexed: 01/15/2023] Open
Abstract
Background The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S1 mapping population of the cultivar ‘Reikou’ with an IStraw90 Axiom® SNP array and previously published SSR markers. Results The ‘Reikou’ linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Conclusions Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3762-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Soichiro Nagano
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan
| | - Fumi Maeda
- Chiba Prefectural Agriculture and Forestry Research Center, Chousei, Daizenno-Cyou 808, Midori, Chiba, 299-4335, Japan
| | - Masami Ishikawa
- Chiba Prefectural Agriculture and Forestry Research Center, Chousei, Daizenno-Cyou 808, Midori, Chiba, 299-4335, Japan.,Institute for Horticultural Plant Breeding, Kamishiki 2-5-1, Matsudo, Chiba, 270-2221, Japan
| | - Sachiko N Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan.
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Perrotte J, Gaston A, Potier A, Petit A, Rothan C, Denoyes B. Narrowing down the single homoeologous FaPFRU locus controlling flowering in cultivated octoploid strawberry using a selective mapping strategy. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2176-2189. [PMID: 27168086 PMCID: PMC5095798 DOI: 10.1111/pbi.12574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/23/2016] [Accepted: 05/02/2016] [Indexed: 05/04/2023]
Abstract
Extending the period of fruit production is a way to substantially increase crop yield in many fruit or ornamental species. In the cultivated octoploid strawberry (Fragaria × ananassa), the most consumed small fruit worldwide, fruit production season can be extended by selecting the perpetual flowering (PF) cultivars. This trait is of considerable interest to growers and to the food industry. Four homoeologous loci controlling a single trait can be expected in such a complex octoploid species. However, we recently showed that the PF trait is under the control of the single dominant FaPFRU locus (J. Exp. Bot., 2013, 64, 1837), making it potentially amenable to marker-assisted selection (MAS). Here, we report the successful use of a strategy, based on a selective mapping using a reduced sample of individuals, to identify nine markers in close linkage to the FaPFRU allelic variant. Thus, this strategy can be used to fine map the target homoeologous loci in other complex polyploid crop species. Recombinant analysis further enabled us to reduce the locus to a region flanked by two markers, Bx083_206 and Bx215_131, corresponding to a 1.1 Mb region in the diploid F. vesca reference genome. This region comprises 234 genes, including 15 flowering associated genes. Among these, the FLOWERING LOCUS T (FT) is known to be a key activator of flowering. The close association between the PF trait and the FaPFRU flanking markers was validated using an additional segregating population and genetic resources. This study lays the foundation for effective and rapid breeding of PF strawberry cultivars by MAS.
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Affiliation(s)
- Justine Perrotte
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
- Ciref Création Variétale Fraises Fruits Rouges, Douville, France
| | - Amèlia Gaston
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
| | - Aline Potier
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
| | - Aurélie Petit
- Ciref Création Variétale Fraises Fruits Rouges, Douville, France
| | - Christophe Rothan
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
| | - Béatrice Denoyes
- INRA, UMR 1332 BFP, Villenave d'Ornon, France.
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France.
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Naithani S, Partipilo CM, Raja R, Elser JL, Jaiswal P. FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. FRONTIERS IN PLANT SCIENCE 2016; 7:242. [PMID: 26973684 PMCID: PMC4777718 DOI: 10.3389/fpls.2016.00242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/13/2016] [Indexed: 05/06/2023]
Abstract
FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition of new pathways, enzymes, reactions, compounds, and small molecules in the database. To date, FragariaCyc comprises 66 super-pathways, 488 unique pathways, 2348 metabolic reactions, 3507 enzymes, and 2134 compounds. In addition to searching and browsing FragariaCyc, researchers can compare pathways across various plant metabolic networks and analyze their data using Omics Viewer tool. We view FragariaCyc as a resource for the community of researchers working with strawberry and related fruit crops. It can help understanding the regulation of overall metabolism of strawberry plant during development and in response to diseases and abiotic stresses. FragariaCyc is available online at http://pathways.cgrb.oregonstate.edu.
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