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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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Jansky SH, Dawson J, Spooner DM. How do we address the disconnect between genetic and morphological diversity in germplasm collections? AMERICAN JOURNAL OF BOTANY 2015; 102:1213-1215. [PMID: 26290545 DOI: 10.3732/ajb.1500203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Shelley H Jansky
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA
| | - Julie Dawson
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA
| | - David M Spooner
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA
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Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S, Tabata S. Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 31:101-110. [PMID: 23316112 PMCID: PMC3538017 DOI: 10.1007/s11032-012-9774-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/01/2012] [Indexed: 05/04/2023]
Abstract
Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-012-9774-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
| | - Kohei Ishii
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | - Cholgwang Kim
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | | | - Takashi Ito
- Osaka University, Suita, Osaka, 565-0871 Japan
| | | | | | - Noriko Nagata
- Japan Women’s University, Bunkyo, Tokyo, 112-8681 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
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