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Anglin NL, Chavez O, Soto-Torres J, Gomez R, Panta A, Vollmer R, Durand M, Meza C, Azevedo V, Manrique-Carpintero NC, Kauth P, Coombs JJ, Douches DS, Ellis D. Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection. FRONTIERS IN PLANT SCIENCE 2024; 15:1341788. [PMID: 39011311 PMCID: PMC11246962 DOI: 10.3389/fpls.2024.1341788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/29/2024] [Indexed: 07/17/2024]
Abstract
A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.
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Affiliation(s)
- Noelle L Anglin
- International Potato Center (CIP), Lima, Peru
- Seed Savers - Preservation Department, United States Department of Agriculture Agriculture Research Service (USDA ARS) Small Grains and Potato Germplasm Research, Aberdeen, ID, United States
| | | | | | - Rene Gomez
- International Potato Center (CIP), Lima, Peru
| | - Ana Panta
- International Potato Center (CIP), Lima, Peru
| | | | | | - Charo Meza
- International Potato Center (CIP), Lima, Peru
| | | | | | - Philip Kauth
- Seed Savers Exchange, Decorah, IA, United States
- REAP Food Group, Madison, WI, United States
| | - Joesph J Coombs
- Department of Plant Soil and Microbial Sciences, Michigan State University (MSU), East Lansing, MI, United States
| | - David S Douches
- Department of Plant Soil and Microbial Sciences, Michigan State University (MSU), East Lansing, MI, United States
| | - David Ellis
- International Potato Center (CIP), Lima, Peru
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Slonecki TJ, Rutter WB, Olukolu BA, Yencho GC, Jackson DM, Wadl PA. Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato ( Ipomoea batatas) collection. FRONTIERS IN PLANT SCIENCE 2023; 13:1022555. [PMID: 36816486 PMCID: PMC9932972 DOI: 10.3389/fpls.2022.1022555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/28/2022] [Indexed: 06/18/2023]
Abstract
Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.
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Affiliation(s)
- Tyler J. Slonecki
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - William B. Rutter
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - G. Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - D. Michael Jackson
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - Phillip A. Wadl
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
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Vollmer R, Villagaray R, Castro M, Cárdenas J, Pineda S, Espirilla J, Anglin N, Ellis D, Rennó Azevedo VC. The world's largest potato cryobank at the International Potato Center (CIP) - Status quo, protocol improvement through large-scale experiments and long-term viability monitoring. FRONTIERS IN PLANT SCIENCE 2022; 13:1059817. [PMID: 36523628 PMCID: PMC9746984 DOI: 10.3389/fpls.2022.1059817] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Long-term conservation of Plant Genetic Resources (PGR) is a key priority for guaranteeing food security and sustainability of agricultural systems for current and future generations. The need for the secure conservation of genetic resources collections ex situ is critical, due to rapid and extreme climatic changes which are threatening and reducing biodiversity in their natural environments. The International Potato Center (CIP) conserves one of the most complete and diverse genetic resources collections of potato, with more than 7500 accessions composed of 4900 cultivated potato and 2600 potato wild relative accessions. The clonal conservation of cultivated potato, principally landraces, through in vitro or field collections is indispensable to maintain fixed allelic states, yet it is costly and labor-intensive. Cryopreservation, the conservation of biological samples in liquid nitrogen (-196°C), is considered the most reliable and cost-efficient long-term ex-situ conservation method for clonal crops. Over the last decade, CIP has built one of the largest potato cryobanks worldwide, cyopreserving more than 4000 cultivated potato accessions which represents 84% of the total cultivated potato collection currently conserved at CIP. In approximately, four years the entire potato collection will be cryopreserved. The development of an applied, robust cryopreservation protocol for potato, serves as a model for other clonally maintained crop collections. The CIP cryobank designs experiments with a high number of genetically diverse genotypes (70-100 accessions, seven cultivated species), to obtain reliable results that can be extrapolated over the collection as genotypes can often respond variably to the same applied conditions. Unlike most published reports on cryopreservation of plants, these large-scale experiments on potato are unique as they examine the acclimatization process of in vitro plants prior to, as well as during cryopreservation on up to ten times the number of genotypes conventionally reported in the published literature. As a result, an operational cryopreservation protocol for potato has advanced that works well across diverse potato accessions, not only with reduced processing time and costs, but also with an increased average full-plant recovery rate from 58% to 73% (+LN) for routine cryopreservation. The present article describes the composition of CIP's cryobank, the cryopreservation protocol, methodology for the dynamic improvement of the operational protocol, as well as data collected on regeneration from long term cryopreserved potatoes.
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Affiliation(s)
| | | | - Mario Castro
- Genebank, International Potato Center (CIP), Lima, Peru
| | - José Cárdenas
- Genebank, International Potato Center (CIP), Lima, Peru
| | - Sandra Pineda
- Genebank, International Potato Center (CIP), Lima, Peru
| | | | - Noelle Anglin
- Genebank, International Potato Center (CIP), Lima, Peru
- Small Grains and Potato Germplasm Research unit, US Department of Agriculture (USDA), Aberdeen, ID, United States
| | - Dave Ellis
- Genebank, International Potato Center (CIP), Lima, Peru
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Yan M, Nie H, Wang Y, Wang X, Jarret R, Zhao J, Wang H, Yang J. Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives. PLANT COMMUNICATIONS 2022; 3:100332. [PMID: 35643086 PMCID: PMC9482988 DOI: 10.1016/j.xplc.2022.100332] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 05/14/2023]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important root crops cultivated worldwide. Because of its adaptability, high yield potential, and nutritional value, sweetpotato has become an important food crop, particularly in developing countries. To ensure adequate crop yields to meet increasing demand, it is essential to enhance the tolerance of sweetpotato to environmental stresses and other yield-limiting factors. The highly heterozygous hexaploid genome of I. batatas complicates genetic studies and limits improvement of sweetpotato through traditional breeding. However, application of next-generation sequencing and high-throughput genotyping and phenotyping technologies to sweetpotato genetics and genomics research has provided new tools and resources for crop improvement. In this review, we discuss the genomics resources that are available for sweetpotato, including the current reference genome, databases, and available bioinformatics tools. We systematically review the current state of knowledge on the polyploid genetics of sweetpotato, including studies of its origin and germplasm diversity and the associated mapping of important agricultural traits. We then outline the conventional and molecular breeding approaches that have been applied to sweetpotato. Finally, we discuss future goals for genetic studies of sweetpotato and crop improvement via breeding in combination with state-of-the-art multi-omics approaches such as genomic selection and gene editing. These approaches will advance and accelerate genetic improvement of this important root crop and facilitate its sustainable global production.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Haozhen Nie
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yunze Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xinyi Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | | | - Jiamin Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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