Genotyping by Sequencing Reveals Genetic Relatedness and Duplicates amongst Local Cassava (Manihot esculenta Crantz) Landraces and Improved Genotypes in Kenya
Charles Orek, Martina Kyallo, Shorinola Oluwaseyi, Nasser Yao, Oluwaseyi , Shorinola, Oluwaseyi, Shorinola; id_orcid
Biotechnology Journal International · pp. 29–46 · Published 31 Aug 2023
10.9734/bji/2023/v27i5694Abstract
Future demand for cassava is expected to increase in order to mitigate climatic changes, sustain food security and provide raw materials for industry. To meet these demands, adoption of modern omics methods ensures reliability, precision and timely delivery of more productive and resilient varieties. A total of 112 mix of duplicate clones, diverse local cassava landraces (LARs) and improved genotypes (IMGs) were genotyped using single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing (GBS) approach. About 17% (5808) of the 33672 SNPs were used for hierarchical clustering and ADMIXTURE analysis for ancestries. Approximately 48 and 52% of the germplasms respectively formed 17 independent clusters (identical clones or duplicates) and admixtures (unique or non-duplicated clones). Of the duplicates, 10 clusters were formed from LARs, four from IMGs and three from a mix of both LARs and IMGs, revealing their genetic relatedness. Approximately 71 and 29% of clusters comprised cassava accessions from the same and different geographical regions, respectively, with the geographical restriction of clusters attributed to the limited movement of planting materials across the country, possibly due to a weak seed distribution system or disease-driven quarantine measures. The historical sharing or exchange of stakes or stem cuttings by farmers was linked to the duplication of LARs, whereas IMGs duplication may be associated with convergent evolution, selection, or sharing of common parentage. The high number of admixtures or unique clones implied minimal loss of genetic diversity. These findings can aid designing efficient and effective cassava improvement programs through development of a core set of diagnostic markers.
References (48)
- 1 PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses [DOI]
- 2 APE: Analyses of Phylogenetics and Evolution in R language [DOI]
- 3 Fast and Efficient Estimation of Individual Ancestry Coefficients [DOI]
- 4 Diversity Arrays Technology: A Generic Genome Profiling Technology on Open Platforms [DOI]
- 5 Tropical root and tuber crops: cassava, sweet potato, yams and aroids [DOI]
- 6 Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz) [DOI]
- 7 Adoption and Promotion of Resilient Crops for Climate Risk Mitigation and Import Substitution: A Case Analysis of Cassava for South African Agriculture [DOI]
- 8 Cassava traits and end-user preference: Relating traits to consumer liking, sensory perception, and genetics [DOI]
- 9 Excellence in Cassava Breeding: Perspectives for the Future [DOI]
- 10 From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers [DOI]
- 11 A global overview of cassava genetic diversity [DOI]
- 12 Technological Innovations for Improving Cassava Production in Sub-Saharan Africa [DOI]
- 13 Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava [DOI]
- 14 SNPs, SSRs and inferences on cassava’s origin [DOI]
- 15 Phylogeography and the origin of cassava: New insights from the northern rim of the Amazonian basin [DOI]
- 16 Physical, Hematological, and Histopathological Signs of Toxicity Induced by African Medicinal Plants [DOI]
- 17 Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava [DOI]
- 18 Local varieties of cassava: conservation, cultivation and use in Uganda [DOI]
- 19 Efficiency of cassava brown streak virus transmission by two whitefly species in coastal Kenya [DOI]
- 20 Genetic diversity among farmer-preferred cassava landraces in Uganda.
- 21 Farmers’ participatory selection for early bulking cassava genotypes in semi-arid Eastern Kenya [DOI]
- 22 Genetic diversity, SNP-trait associations and genomic selection accuracy in a west African collection of Kersting’s groundnut [Macrotyloma geocarpum(Harms) Maréchal & Baudet] [DOI]
- 23 Cassava cultivation in sub-Saharan Africa [DOI]
- 24 New cassava germplasm for food and nutritional security in Central Africa [DOI]
- 25 DNA fingerprinting at farm level maps rice biodiversity across Bangladesh and reveals regional varietal preferences [DOI]
- 26 The cassava monitoring survey in Nigeria: final report.
- 27 Identification of duplicates in cassava germplasm banks based on single-nucleotide polymorphisms (SNPs) [DOI]
- 28 Participatory appraisal of preferred traits, production constraints and postharvest challenges for cassava farmers in Rwanda [DOI]
- 29 Cassava farmers' preferences for varieties and seed dissemination system in Nigeria: gender and regional perspectives
- 30 DArTSeq SNP-based genetic diversity and population structure studies among taro [(Colocasia esculenta (L.) Schott] accessions sourced from Nigeria and Vanuatu [DOI]
- 31 Collection, genotyping and virus elimination of cassava landraces from Tanzania and documentation of farmer knowledge [DOI]
- 32 Viruses Infecting Cassava in Kenya [DOI]
- 33 Genotypic variation of traits related to quality of cassava roots using affinity propagation algorithm [DOI]
- 34 Assessment of genetic diversity among cassava landraces using single nucleotide polymorphic markers [DOI]
- 35 Farmer’s Knowledge on Selection and Conservation of Cassava (Manihot esculenta) Genetic Resources in Tanzania.
- 36 Genetic diversity study of Kenyan cassava germplasm using simple sequence repeats [DOI]
- 37 Farmers’ Perceptions of Production Constraints and Preferences in Cassava Grown in Semi-Arid Areas of Kenya [DOI]
- 38 Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer’s Fields: An Update from 1990 to 2020 [DOI]
- 39 Analysis of local cassava landraces and improved genotypes in response to infections by cassava mosaic begomoviruses under field conditions in Kenya [DOI]
- 40 Response to Cassava Brown Streak Disease Infections in Local and Improved Cassava Genotypes under Field and Greenhouse Assays in Lower Eastern Kenya [DOI]
- 41 Cassava (Manihot esculenta) [DOI]
- 42 Farmer-Cultivated Landraces and Improved Cassava Genotypes Exhibit Varied Response to Cassava Brown Streak Disease Under Natural Infections in Kenya [DOI]
- 43 The cassava transformation: Africa's best-kept secret [DOI]
- 44 Root and Tuber Crops [DOI]
- 45 Cassava: The Nature and Uses [DOI]
- 46 Enhancing food security through improved seed systems of appropriate varieties of cassava, potato and sweetpotato resilient to climate change in Eastern Africa
- 47 Cassava breeding through complementary conventional and participatory approaches in western Kenya.
- 48 An Assessment Of The Effect Of Varietal Attributes On The Adoption Of Improved Cassava In Homa-Bay County, Kenya
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