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Mastrangelo AM, Hartings H, Lanzanova C, Balconi C, Locatelli S, Cassol H, Valoti P, Petruzzino G, Pecchioni N. Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding. Plants (Basel) 2024; 13:336. [PMID: 38337869 PMCID: PMC10857507 DOI: 10.3390/plants13030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to 'Insubria', 'Microsperma', and 'Scagliolino' genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.
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Affiliation(s)
- Anna Maria Mastrangelo
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Hans Hartings
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Chiara Lanzanova
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Carlotta Balconi
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Sabrina Locatelli
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Helga Cassol
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Paolo Valoti
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Giuseppe Petruzzino
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Nicola Pecchioni
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
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Page R, Huang S, Ronen M, Sela H, Sharon A, Shrestha S, Poland J, Steffenson BJ. Genome-wide association mapping of rust resistance in Aegilops longissima. Front Plant Sci 2023; 14:1196486. [PMID: 37575932 PMCID: PMC10413114 DOI: 10.3389/fpls.2023.1196486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023]
Abstract
The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.
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Affiliation(s)
- Rae Page
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Shuyi Huang
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- KAUST Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
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Kulyan R, Samarina L, Shkhalakhova R, Kuleshov A, Ukhatova Y, Antonova O, Koninskaya N, Matskiv A, Malyarovskaya V, Ryndin A. InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus. Int J Mol Sci 2023; 24:ijms24098276. [PMID: 37175981 PMCID: PMC10179493 DOI: 10.3390/ijms24098276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus Citrus. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency.
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Affiliation(s)
- Raisa Kulyan
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
- "Sirius University of Science and Technology", Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Alexandr Kuleshov
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Yulia Ukhatova
- "Sirius University of Science and Technology", Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia
- Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Olga Antonova
- "Sirius University of Science and Technology", Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Valentina Malyarovskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
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Reis JM, Pereira RJ, Coelho PS, Leitão JM. Assessment of Wild Rocket ( Diplotaxis tenuifolia (L.) DC.) Germplasm Accessions by NGS Identified SSR and SNP Markers. Plants (Basel) 2022; 11:plants11243482. [PMID: 36559594 PMCID: PMC9783343 DOI: 10.3390/plants11243482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 05/14/2023]
Abstract
Rocket is the common designation for two baby-leaf salad crops of the Brassicaceae family: Eruca sativa (L.) Cav., usually referred to as annual garden rocket, and Diplotaxis tenuifolia (L.) DC. commonly named to as perennial wild rocket. E. sativa is used for human consumption since antiquity. However, the growing consumer preference for D. tenuifolia is being accompanied by the fast increase in its production area and commercialization of new cultivars. Nevertheless, the worldwide number of wild rocket accessions maintained in germplasm collections is very reduced, the solution for which situation the project “REMIRucula” intends to contribute, establishing a germplasm collection at the INIAV, Oeiras, Portugal. Herein, we report on the establishment via next generation sequencing (NGS) of the first genome assembly of D. tenuifolia and the identification of specific single sequence repeat (SSR) and single nucleotide polymorphisms (SNP) loci for the establishment of specific DNA-markers for this species. A representative set of 87 D. tenuifolia and 3 E. sativa accessions were assessed by 5 SSR and 9 SNP-CAPS markers, allowing a drastic discrimination between both species and the establishment of unequivocal molecular fingerprints for the analyzed accessions. The non-discrimination within six pairs and one trio of D. tenuifolia accessions is discussed.
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Affiliation(s)
- João M. Reis
- MED—Mediterranean Institute for Agriculture, Environment and Development, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal
- CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Ricardo J. Pereira
- MED—Mediterranean Institute for Agriculture, Environment and Development, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal
- CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Paula S. Coelho
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2784-505 Oeiras, Portugal
| | - José M. Leitão
- MED—Mediterranean Institute for Agriculture, Environment and Development, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal
- CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal
- Correspondence:
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Wang Y, Wu X, Li Y, Feng Z, Mu Z, Wang J, Wu X, Wang B, Lu Z, Li G. Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd. Front Plant Sci 2021; 12:747940. [PMID: 34868131 PMCID: PMC8636714 DOI: 10.3389/fpls.2021.747940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.
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Affiliation(s)
- Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zishan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zihan Mu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiang Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Rantala S, Kaseva J, Nukari A, Laamanen J, Veteläinen M, Häggman H, Karhu S. Successful Cryopreservation of Dormant Buds of Blackcurrant ( Ribes nigrum L.) by Using Greenhouse-Grown Plants and In Vitro Recovery. Plants (Basel) 2021; 10:1414. [PMID: 34371617 PMCID: PMC8309241 DOI: 10.3390/plants10071414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
The cryopreservation of dormant buds can be a feasible method for preserving germplasm of cold-tolerant woody plants. In the present study, we evaluated the effects of pre-desiccation, thawing method, and the rehydration of bud sections on the post-cryopreservation recovery of dormant blackcurrant buds in vitro. The estimated recovery of small- and medium-sized buds was 80.1 and 62.7% respectively for desiccated buds and 67.8 and 72.3% respectively for non-desiccated buds. The pre-desiccation of bud sections enhanced the number of the shoots regenerated from vegetative buds (2.3 vs. 4.7). The estimated recovery of fast-thawed buds was better after 14-day than after 7-day rehydration (85 vs. 59%). In slowly thawed buds the difference between 14-day and 7-day rehydration was not significant (73 vs. 62%). The estimated recovery of vegetative and flower buds was 77.7 and 41.1% respectively after 7-day rehydration, and 95.2 and 43.6% respectively after a 14-day rehydration period. The rehydration of bud sections was not necessary for the in vitro recovery of non-desiccated, fast-thawed buds. Of the 23 blackcurrant cultivars cryopreserved using non-desiccated dormant buds collected from a greenhouse, the estimated recovery of 22 cultivars ranged between 42 and 90%.
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Affiliation(s)
- Saija Rantala
- Natural Resources Institute Finland (Luke), Production Systems, Survontie 9 A, FI-40500 Jyväskylä, Finland
- Ecology and Genetics Unit, Faculty of Science, University of Oulu, P.O. Box 3000, FI-90014 Oulu, Finland;
| | - Janne Kaseva
- Natural Resources Institute Finland (Luke), Natural Resources, Tietotie 4, FI-31600 Jokioinen, Finland;
| | - Anna Nukari
- Natural Resources Institute Finland (Luke), Production Systems, Latokartanonkaari 9, FI-00790 Helsinki, Finland;
| | - Jaana Laamanen
- Natural Resources Institute Finland (Luke), Natural Resources, Survontie 9 A, FI-40500 Jyväskylä, Finland;
| | - Merja Veteläinen
- Boreal Plant Breeding Ltd., Myllytie 10, FI-31600 Jokioinen, Finland;
| | - Hely Häggman
- Ecology and Genetics Unit, Faculty of Science, University of Oulu, P.O. Box 3000, FI-90014 Oulu, Finland;
| | - Saila Karhu
- Natural Resources Institute Finland (Luke), Production Systems, Itäinen Pitkäkatu 4 A, FI-20520 Turku, Finland;
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Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
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Tuberosa R, Cattivelli L, Ceriotti A, Gadaleta A, Beres BL, Pozniak CJ. Editorial: Proceedings of FSTP3 Congress-A Sustainable Durum Wheat Chain for Food Security and Healthy Lives. Front Plant Sci 2021; 12:675510. [PMID: 33897752 PMCID: PMC8063101 DOI: 10.3389/fpls.2021.675510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Roberto Tuberosa
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Aldo Ceriotti
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Rome, Italy
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy
| | - Brian L. Beres
- Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Curtis J. Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Borrell JS, Biswas MK, Goodwin M, Blomme G, Schwarzacher T, Heslop-Harrison JS(P, Wendawek AM, Berhanu A, Kallow S, Janssens S, Molla EL, Davis AP, Woldeyes F, Willis K, Demissew S, Wilkin P. Enset in Ethiopia: a poorly characterized but resilient starch staple. Ann Bot 2019; 123:747-766. [PMID: 30715125 PMCID: PMC6526316 DOI: 10.1093/aob/mcy214] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/16/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. SCOPE Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. CONCLUSION Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop.
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Affiliation(s)
| | - Manosh K Biswas
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Mark Goodwin
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Guy Blomme
- Bioversity International, Addis Ababa, Ethiopia
| | | | | | | | - Admas Berhanu
- Department of Biology and Biotechnology, Wolkite University, Hawassa, Ethiopia
| | - Simon Kallow
- Conservation Science Department, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, UK
- Division of Crop Biotechnics, Katholieke Universiteit Leuven, Willem de Croylaan, Leuven, Belgium
| | - Steven Janssens
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Katholieke Universiteit Leuven, Kasteelpark, Arenberg, Leuven, Belgium
| | - Ermias L Molla
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Kathy Willis
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Sebsebe Demissew
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Gullele Botanic Garden, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
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10
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Anderson JE, Kono TJY, Stupar RM, Kantar MB, Morrell PL. Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans. G3 (Bethesda) 2016; 6:835-43. [PMID: 26818076 PMCID: PMC4825654 DOI: 10.1534/g3.116.026914] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/22/2016] [Indexed: 01/04/2023]
Abstract
Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael B Kantar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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11
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Mason AS, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. High-throughput genotyping for species identification and diversity assessment in germplasm collections. Mol Ecol Resour 2015; 15:1091-101. [PMID: 25641370 DOI: 10.1111/1755-0998.12379] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 12/01/2022]
Abstract
Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.
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Affiliation(s)
- Annaliese S Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jing Zhang
- Ministry of Agriculture (MOA) key laboratory of Huazhong Crop Physiology, Ecology and Production, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.,Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Reece Tollenaere
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paula Vasquez Teuber
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jessica Dalton-Morgan
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Liyong Hu
- Ministry of Agriculture (MOA) key laboratory of Huazhong Crop Physiology, Ecology and Production, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guijun Yan
- Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.,The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Robert Redden
- Department of Environment and Primary Industries, Australian Grains Genebank, Horsham, VIC, 3401, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.,Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia
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