Genetic diversity and population structure of Uganda cassava germplasm.
Genetic variation
Hierarchical clustering
Polymorphic information content
Single nucleotide polymorphism
Journal
Journal of applied genetics
ISSN: 2190-3883
Titre abrégé: J Appl Genet
Pays: England
ID NLM: 9514582
Informations de publication
Date de publication:
16 Jul 2024
16 Jul 2024
Historique:
received:
08
02
2024
accepted:
07
07
2024
revised:
12
06
2024
medline:
16
7
2024
pubmed:
16
7
2024
entrez:
16
7
2024
Statut:
aheadofprint
Résumé
Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.
Identifiants
pubmed: 39012576
doi: 10.1007/s13353-024-00892-x
pii: 10.1007/s13353-024-00892-x
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Cornell University
ID : 84941-11056
Informations de copyright
© 2024. The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences.
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