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Nie H, Park H, Kim S, Kim D, Kim S, Kwon SY, Kim SH. Genetic diversity assessment and genome-wide association study reveal candidate genes associated with component traits in sweet potato (Ipomoea batatas (L.) Lam). Mol Genet Genomics 2023; 298:653-667. [PMID: 36943475 DOI: 10.1007/s00438-023-02007-3] [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: 02/16/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023]
Abstract
The Korean sweet potatoes were bred by various cultivars introduced from Japanese, American, Porto Rico, China, and Burundi. This issue enriched their genetic diversity but also resulted in a mixture of cultivars. For genotyping, we collected and sequenced 66 sweet potato germplasms from different localities around Korea, including 36 modern cultivars, 5 local cultivars, and 25 foreign cultivars. This identified 447.6 million trimmed reads and 324.8 million mapping reads and provided 39,424 single nucleotide polymorphisms (SNPs) markers. Phylogenetic clustering and population structure analysis distinctly classified these germplasms into 5 genetic groups, group 1, group 2, group 3, group 4, and group 5, containing 20, 15, 10, 7, and 14 accessions, respectively. Sixty-three significant SNPs were selected by genome-wide association for sugar composition-related traits (fructose, glucose, and total sugars), total starch, amylose content, and total carotenoid of the storage root. A total of 37 candidate genes encompassing these significant SNPs were identified, among which, 7 genes were annotated to involve in sugar and starch metabolism, including galactose metabolism (itf04g30630), starch and sucrose metabolism (itf03g13270, itf15g09320), carbohydrate metabolism (itf14g10250), carbohydrate and amino acid metabolism (itf12g19270), and amino sugar and nucleotide sugar metabolism (itf03g21950, itf15g04880). This results indicated that sugar and starch are important characteristics to determine the genetic diversity of sweet potatoes. These findings not only illustrate the importance of component traits to genotyping sweet potatoes but also explain an important reason resulting in genetic diversity of sweet potato.
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Affiliation(s)
- Hualin Nie
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hyungjun Park
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Sujung Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, 58545, Republic of Korea
| | - Doyeon Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Sun-Hyung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea.
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Behn A, Lizana C, Zapata F, Gonzalez A, Reyes-Díaz M, Fuentes D. Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile. FRONTIERS IN PLANT SCIENCE 2023; 13:1045894. [PMID: 36704150 PMCID: PMC9872146 DOI: 10.3389/fpls.2022.1045894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
The potato (Solanum tuberosum L) is one of the four most important crops worldwide in production and consumption. It originated from South America along the Andes, where six hotspots of diversity known as subcenters of origin are described from Venezuela to Chiloe Island in Chile, and where the greatest diversity of potatoes in the world is found. Today, the use of ancestral genetic resources has gained significant relevance, recovering and producing foods with a greater nutrient content and beneficial to human health. Therefore, native potatoes possess a set of characteristics with great potential for use in potato breeding guided primarily to produce better feed, especially potatoes of the Chilotanum Group that are easily crossed with conventional varieties. The primary objective of this study was to evaluate 290 accessions of S. tuberosum subsp tuberosum belonging to the Chilotanum Group using a set of molecular markers and correlate them to its phenotypic traits for future use in breeding programs. For this purpose, 290 accessions were analysed through 22 specific microsatellites described previously, correlating them with flesh and skin colour, total phenolic content, and anthocyanin content. A division into groups considering all the 290 accessions resulted in two clusters using STRUCTURE analysis and seven different genetic clusters using UPGMA. The latter exhibited common phenotypic characteristics as well as anthocyanin content, strongly supporting a correlation between phenotypic traits and the genetic fingerprint. These results will enable breeders to focus on the development of potatoes with high polyphenol and anthocyanin content.
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Affiliation(s)
- Anita Behn
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Carolina Lizana
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Felipe Zapata
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alvaro Gonzalez
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Derie Fuentes
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
- Centro de Biotecnología de Sistemas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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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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Selection of Sweetpotato Parental Genotypes Using Simple Sequence Repeat Markers. PLANTS 2022; 11:plants11141802. [PMID: 35890436 PMCID: PMC9315999 DOI: 10.3390/plants11141802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022]
Abstract
Knowledge of the genetic diversity and genetic relationship is important in crop improvement. The objective of this study was to determine the genetic diversity of 31 sweetpotato genotypes and furthermore to select distantly related individuals for breeding of superior parental clones. The genotypes (sourced from the Agricultural Research Council, South Africa) originating from Africa and American continent were genotyped using eight highly polymorphic SSR markers. The SSR markers generated a total of 83 putative alleles. The polymorphic information content (PIC) of the tested simple sequence markers varied from 0.73 to 0.91, with a mean of 0.85. At least 11 different alleles were found in 8 loci within the population, with 7 effective alleles per locus. Although high diversity was found among the genotypes, genetic distances among the genotypes were relatively low. Cluster analysis revealed the existence of three distinct genetic groups, and the clustering patterns follow to some extent the geographic origin and pedigree of the genotypes. High gene flow was observed among different sweetpotato accessions. The selected SSR markers were found to be highly polymorphic with high discriminatory power for genetic characterization studies and are useful genomic tool to complement phenotyping of sweetpotato genotypes. Two heterotic groups were found in the study. The heterotic group A was composed of 14 genotypes mainly of South African origin, while the heterotic group B consisted of 17 genotypes of American origin. The two distinct groups were important for the selection of breeding clones that were distantly related to be used as parental clones in the advancement of traits of interest.
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Scariolo F, Palumbo F, Vannozzi A, Sacilotto GB, Gazzola M, Barcaccia G. Genotyping Analysis by RAD-Seq Reads Is Useful to Assess the Genetic Identity and Relationships of Breeding Lines in Lavender Species Aimed at Managing Plant Variety Protection. Genes (Basel) 2021; 12:genes12111656. [PMID: 34828262 PMCID: PMC8621978 DOI: 10.3390/genes12111656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental plants and important source of essential oils that are destinated to the production of cosmetics, pharmaceuticals and foodstuffs. Because of the increasing number of cases of illegal commercialization of selected varieties, the protection of plant breeders’ rights has become of main relevance for the recognition of breeding companies’ royalties. With this aim, genomic tools based on molecular markers have been demonstrated to be very reliable and transferable among laboratories, and also much more informative than morphological descriptors. With the rising of the next-generation sequencing (NGS) technologies, several genotyping-by-sequencing approaches are now available. This study deals with a deep characterization of 15 varietal clones, belonging to two distinct Lavandula species, by means of restriction-site associated DNA sequencing (RAD-Seq). We demonstrated that this technology screens single nucleotide variants that enable to assess the genetic identity of individual accessions, to reconstruct genetic relationships among related breeding lines, to group them into genetically distinguishable main subclusters, and to assign their molecular lineages to distinct ancestors. Moreover, a number of polymorphic sites were identified within genes putatively involved in biosynthetic pathways related to both tissue pigmentation and terpene production, useful for breeding and/or protecting newly registered varieties. Overall, the results highlighted the presence of pure ancestries and interspecific hybrids for the analyzed Lavandula species, and demonstrated that RAD-Seq analysis is very informative and highly reliable for characterizing Lavandula clones and managing plant variety protection.
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Affiliation(s)
- Francesco Scariolo
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
| | - Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
| | - Alessandro Vannozzi
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
| | - Gio Batta Sacilotto
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Marco Gazzola
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
- Correspondence:
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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Mercati F, Sunseri F. Genetic Diversity Assessment and Marker-Assisted Selection in Crops. Genes (Basel) 2020; 11:genes11121481. [PMID: 33317175 PMCID: PMC7763926 DOI: 10.3390/genes11121481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 01/22/2023] Open
Affiliation(s)
- Francesco Mercati
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e Biorisorse (IBBR), Corso Calatafimi 414, 90129 Palermo, Italy
- Correspondence: (F.M.); (F.S.)
| | - Francesco Sunseri
- Dipartimento di Agraria, Università Mediterranea degli Studi di Reggio Calabria, Loc. Feo di Vito, 89124 Reggio Calabria, Italy
- Correspondence: (F.M.); (F.S.)
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