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Adhikari L, Raupp J, Wu S, Koo DH, Friebe B, Poland J. Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1268370. [PMID: 37915516 PMCID: PMC10616851 DOI: 10.3389/fpls.2023.1268370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.
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Affiliation(s)
- Laxman Adhikari
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, 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
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4
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El Hanafi S, Jiang Y, Kehel Z, Schulthess AW, Zhao Y, Mascher M, Haupt M, Himmelbach A, Stein N, Amri A, Reif JC. Genomic predictions to leverage phenotypic data across genebanks. FRONTIERS IN PLANT SCIENCE 2023; 14:1227656. [PMID: 37701801 PMCID: PMC10493331 DOI: 10.3389/fpls.2023.1227656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023]
Abstract
Genome-wide prediction is a powerful tool in breeding. Initial results suggest that genome-wide approaches are also promising for enhancing the use of the genebank material: predicting the performance of plant genetic resources can unlock their hidden potential and fill the information gap in genebanks across the world and, hence, underpin prebreeding programs. As a proof of concept, we evaluated the power of across-genebank prediction for extensive germplasm collections relying on historical data on flowering/heading date, plant height, and thousand kernel weight of 9,344 barley (Hordeum vulgare L.) plant genetic resources from the German Federal Ex situ Genebank for Agricultural and Horticultural Crops (IPK) and of 1,089 accessions from the International Center for Agriculture Research in the Dry Areas (ICARDA) genebank. Based on prediction abilities for each trait, three scenarios for predictive characterization were compared: 1) a benchmark scenario, where test and training sets only contain ICARDA accessions, 2) across-genebank predictions using IPK as training and ICARDA as test set, and 3) integrated genebank predictions that include IPK with 30% of ICARDA accessions as a training set to predict the rest of ICARDA accessions. Within the population of ICARDA accessions, prediction abilities were low to moderate, which was presumably caused by a limited number of accessions used to train the model. Interestingly, ICARDA prediction abilities were boosted up to ninefold by using training sets composed of IPK plus 30% of ICARDA accessions. Pervasive genotype × environment interactions (GEIs) can become a potential obstacle to train robust genome-wide prediction models across genebanks. This suggests that the potential adverse effect of GEI on prediction ability was counterbalanced by the augmented training set with certain connectivity to the test set. Therefore, across-genebank predictions hold the promise to improve the curation of the world's genebank collections and contribute significantly to the long-term development of traditional genebanks toward biodigital resource centers.
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Affiliation(s)
- Samira El Hanafi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Zakaria Kehel
- International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Max Haupt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Ahmed Amri
- International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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5
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Barbosa CFC, Asunto JC, Koh RBL, Santos DMC, Zhang D, Cao EP, Galvez LC. Genome-Wide SNP and Indel Discovery in Abaca ( Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management. Curr Issues Mol Biol 2023; 45:5776-5797. [PMID: 37504281 PMCID: PMC10377871 DOI: 10.3390/cimb45070365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023] Open
Abstract
Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, this study aimed to discover genome-wide polymorphisms among abaca cultivars and other Musa species and analyze their potential as genetic marker resources. This was achieved through whole-genome Illumina resequencing of abaca cultivars and variant calling using BCFtools, followed by genetic diversity and phylogenetic analyses. A total of 20,590,381 high-quality single-nucleotide polymorphisms (SNP) and DNA insertions/deletions (InDels) were mined across 16 abaca cultivars. Filtering based on linkage disequilibrium (LD) yielded 130,768 SNPs and 13,620 InDels, accounting for 0.396 ± 0.106 and 0.431 ± 0.111 of gene diversity across these cultivars. LD-pruned polymorphisms across abaca, M. troglodytarum, M. acuminata and M. balbisiana enabled genetic differentiation within abaca and across the four Musa spp. Phylogenetic analysis revealed the registered varieties Abuab and Inosa to accumulate a significant number of mutations, eliciting further studies linking mutations to their advantageous phenotypes. Overall, this study pioneered in producing marker resources in abaca based on genome-wide polymorphisms vital for varietal authentication and comparative genotyping with the more studied Musa spp.
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Affiliation(s)
- Cris Francis C Barbosa
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Jayson C Asunto
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
| | - Rhosener Bhea L Koh
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Daisy May C Santos
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ernelea P Cao
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Leny C Galvez
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
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Morales N, Ogbonna AC, Ellerbrock BJ, Bauchet GJ, Tantikanjana T, Tecle IY, Powell AF, Lyon D, Menda N, Simoes CC, Saha S, Hosmani P, Flores M, Panitz N, Preble RS, Agbona A, Rabbi I, Kulakow P, Peteti P, Kawuki R, Esuma W, Kanaabi M, Chelangat DM, Uba E, Olojede A, Onyeka J, Shah T, Karanja M, Egesi C, Tufan H, Paterne A, Asfaw A, Jannink JL, Wolfe M, Birkett CL, Waring DJ, Hershberger JM, Gore MA, Robbins KR, Rife T, Courtney C, Poland J, Arnaud E, Laporte MA, Kulembeka H, Salum K, Mrema E, Brown A, Bayo S, Uwimana B, Akech V, Yencho C, de Boeck B, Campos H, Swennen R, Edwards JD, Mueller LA. Breedbase: a digital ecosystem for modern plant breeding. G3 GENES|GENOMES|GENETICS 2022; 12:6564228. [PMID: 35385099 PMCID: PMC9258556 DOI: 10.1093/g3journal/jkac078] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/14/2022] [Indexed: 01/17/2023]
Abstract
Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.
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Affiliation(s)
- Nicolas Morales
- Boyce Thompson Institute , Ithaca, NY 14853, USA
- Cornell University , Ithaca, NY 14853, USA
| | - Alex C Ogbonna
- Boyce Thompson Institute , Ithaca, NY 14853, USA
- Cornell University , Ithaca, NY 14853, USA
| | | | | | | | | | | | - David Lyon
- Boyce Thompson Institute , Ithaca, NY 14853, USA
| | - Naama Menda
- Boyce Thompson Institute , Ithaca, NY 14853, USA
| | | | - Surya Saha
- Boyce Thompson Institute , Ithaca, NY 14853, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ezenwanyi Uba
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | - Adeyemi Olojede
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | - Joseph Onyeka
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | | | | | - Chiedozie Egesi
- Boyce Thompson Institute , Ithaca, NY 14853, USA
- IITA Ibadan , 200001 Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | - Hale Tufan
- Cornell University , Ithaca, NY 14853, USA
| | | | | | - Jean-Luc Jannink
- Cornell University , Ithaca, NY 14853, USA
- USDA-ARS , Ithaca, NY 14853, USA
| | | | - Clay L Birkett
- Cornell University , Ithaca, NY 14853, USA
- USDA-ARS , Ithaca, NY 14853, USA
| | - David J Waring
- Cornell University , Ithaca, NY 14853, USA
- USDA-ARS , Ithaca, NY 14853, USA
| | | | | | | | - Trevor Rife
- Kansas State University , Manhattan, KS 66506, USA
| | | | - Jesse Poland
- Kansas State University , Manhattan, KS 66506, USA
| | | | | | | | | | | | | | | | | | | | - Craig Yencho
- North Carolina State University (NCSU) , Raleigh, NC 27695, USA
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