SNP of 74 cassava accessions sequenced with 36 markers
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ABSTRACT:
ORGANISM(S): Cassava
SUBMITTER:
PROVIDER: S-BSST912 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description: Not available
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Project description:Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.
| S-EPMC4190189 | biostudies-literature
Project description:Genetic diversity is fundamentally important in crop improvement and provides plants with the capacity to meet the demands of changing environments. This work was carried out to assess the diversity and the extent of genetic relatedness among a number of assembled cassava (Manihot esculenta Crantz) accessions. We conducted a microsatellite marker analysis of 89 cassava accessions collected from Ghanaian and exotic sources. These accessions were assayed using 35 simple sequence repeat (SSR) markers. A total of 167 alleles were detected from 35 polymorphic markers with an average of 4.77 alleles per locus. High allelic frequency was detected across the accessions, ranging from 0.32 to 0.99 with an average of 0.62 per marker. Observed heterozygosity ranged from 0.03 - 0.97 across the accessions. Polymorphism information content (PIC) ranged from 0.03 to 0.78 with a mean of 0.45, indicating high level of polymorphism across the accessions. Comparatively, higher number of alleles, gene diversity and observed heterozygosity were detected among the local accessions compared with the exotic accessions indicating rich genetic diversity among them. Population structure analysis based on STRUCTURE identified two subpopulations and a large number of admixtures. Cluster analysis based on the neighbour joining algorithim further separated the collection into seven sub-groupings irrespective of geographical origin. This indicates the possible sharing of common genomic regions occurring across the accessions. High allelic frequency differences and levels of heterozygosity were observed among the germplasm. These findings indicated significant genetic variability in the germplasm to warrant selection.
| S-EPMC7002781 | biostudies-literature
Project description:Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava (Manihot esculenta) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT's cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions.
| S-EPMC10830726 | biostudies-literature
Project description:We deeply sequenced two pairs of widely used infectious clones (4 plasmids) of the bipartite begomoviruses African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV). The ACMV clones were quite divergent from published sequences. Raw reads, consensus plasmid sequences, and the infectious clones themselves are all publicly available.
| S-EPMC7660992 | biostudies-literature
Project description:Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d'Ivoire, it represents, along with other yam species, the largest food crop and significantly contributes to food security. However, studies focusing on better understanding the structure and extent of genetic diversity among D. alata accessions, using molecular and phenotypic traits, are limited. This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. Genetic diversity assessment using molecular-based SNP markers showed a high proportion of polymorphic SNPs (87.81%). The analysis of molecular variance (AMOVA) showed low molecular variability within genetic groups. In addition, the agronomic traits evaluated for two years in field conditions showed a high heritability and high variability among D. alata accessions. This study provides insights into the genetic diversity among accessions in the CNRA genebank and opens an avenue for sustainable resource management and the identification of promising parental clones for water yam breeding programs in Côte d'Ivoire.
| S-EPMC8705775 | biostudies-literature
Project description:This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = - 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.
| S-EPMC8319206 | biostudies-literature
Project description:Cassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5' covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells. To characterize cassava eIF4Es and their potential role in CBSD tolerance and susceptibility, we cloned five eIF4E transcripts from cassava (accession TMS60444). Sequence analysis indicated that the cassava eIF4E family of proteins consisted of one eIF4E, two eIF(iso)4E, and two divergent copies of novel cap-binding proteins (nCBPs). Our data demonstrated experimentally the coding of these five genes as annotated in the published cassava genome and provided additional evidence for refined annotations. Illumina resequencing data of the five eIF4E genes were analyzed from 14 cassava lines tolerant or susceptible to CBSD. Abundant single nucleotide polymorphisms (SNP) and biallelic variations were observed in the eIF4E genes; however, most of the SNPs were located in the introns and non-coding regions of the exons. Association studies of non-synonymous SNPs revealed no significant association between any SNP of the five eIF4E genes and the tolerance or susceptibility to CBSD. However, two SNPs in two genes were weakly associated with the CBSD responses but had no direct causal-effect relationship. SNPs in an intergenic region upstream of eIF4E_me showed a surprising strong association with CBSD responses. Digital expression profile analysis showed differential expression of different eIF4E genes but no significant difference in gene expression was found between susceptible and tolerant cassava accessions despite the association of the intergenic SNPs with CBSD responses.
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Project description:Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea.The Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs was used to genotype 96 cowpea accessions including 43 landraces and cultivars from the Iberian Peninsula, and 53 landraces collected worldwide. Four subpopulations were identified. Most Iberian Peninsula accessions clustered together with those from other southern European and northern African countries. Only one accession belonged to another subpopulation, while two accessions were 'admixed'. A lower genetic diversity level was found in the Iberian Peninsula accessions compared to worldwide cowpeas.The genetic analyses performed in this study brought some insights into worldwide genetic diversity and structure and possible dispersion routes of cultivated cowpea. Also, it provided an in-depth analysis of genetic diversity in Iberian Peninsula cowpeas that will help guide crossing strategies in breeding programs.
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Project description:Pseudogenes (?s), including processed and non-processed ?s, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed ?s utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of ?s within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ?28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these ?s on chromosomes showed a significantly negative correlation between ?s/ORFs and their local gene densities, suggesting a higher proportion of ?s in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-? loci, even the intact coding sequences (CDSs) in the ? loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the ?s mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.
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