ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2012
Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 64 citations in OpenAlex.
- Exploring the Role of Single Nucleotide Polymorphisms in Modern Plant Genomic Research.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Genome-wide characterization of genetic diversity and population structure of the Chilean Mapuche fowl using DArTseq SNP markers.Poultry science · 2026Article
- Phenotypic Variability in Resistance to Anthracnose, White, Brown, and Blight Leaf Spot in Cassava Germplasm.Plants (Basel, Switzerland) · 2024Article
- Advances in Genetic Analysis and Breeding of Cassava (Plants (Basel, Switzerland) · 2022Review
- Current status and impending progress for cassava structural genomics.Plant molecular biology · 2022Review
- DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers' field and genebank collections.Plant molecular biology · 2022Article
- Technological Innovations for Improving Cassava Production in Sub-Saharan Africa.Frontiers in genetics · 2020Review
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- A global overview of cassava genetic diversity.PloS one · 2019Article
- A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus.Scientific reports · 2017Article
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- QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived fromFrontiers in plant science · 2017Article
- Proteomics Profiling Reveals Carbohydrate Metabolic Enzymes and 14-3-3 Proteins Play Important Roles for Starch Accumulation during Cassava Root Tuberization.Scientific reports · 2016Article
- Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Review
- A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes.BMC genomics · 2015Article
- Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping.BMC genomics · 2014Article
- A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.Functional & integrative genomics · 2014Article
- Potential of SNP markers for the characterization of Brazilian cassava germplasm.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
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Corrections and comments
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Authors and funding
10 authors at 8 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of genomic resources can facilitate progress in plant breeding through the application of advanced molecular technologies for crop improvement. This is particularly important in the case of less researched crops such as cassava, a staple and food security crop for more than 800 million people. Here, expressed sequence tags (ESTs) were generated from five drought stressed and well-watered cassava varieties. Two cDNA libraries were developed: one from root tissue (CASR), the other from leaf, stem and stem meristem tissue (CASL). Sequencing generated 706 contigs and 3,430 singletons. These sequences were combined with those from two other EST sequencing initiatives and filtered based on the sequence quality. Quality sequences were aligned using CAP3 and embedded in a Windows browser called HarvEST:Cassava which is made available. HarvEST:Cassava consists of a Unigene set of 22,903 quality sequences. A total of 2,954 putative SNPs were identified. Of these 1,536 SNPs from 1,170 contigs and 53 cassava genotypes were selected for SNP validation using Illumina's GoldenGate assay. As a result 1,190 SNPs were validated technically and biologically. The location of validated SNPs on scaffolds of the cassava genome sequence (v.4.1) is provided. A diversity assessment of 53 cassava varieties reveals some sub-structure based on the geographical origin, greater diversity in the Americas as opposed to Africa, and similar levels of diversity in West Africa and southern, eastern and central Africa. The resources presented allow for improved genetic dissection of economically important traits and the application of modern genomics-based approaches to cassava breeding and conservation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.