ArticleBMC genomics2017
Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 68 citations in OpenAlex.
- Phenotypic Differentiation Between Highland and Coastal Quinoa Under Cold Stress Conditions.Plant, cell & environment · 2026Article
- Population-resourced species-specific InDel markers for identifying putative interspecific hybrids between Populus euphratica and Populus pruinosa.BMC genomic data · 2026Article
- Quinoa as a naturally stress-resistant crop: current status and future promises.Stress biology · 2026Review
- Assessment of Genetic Diversity in Quinoa Landraces Cultivated in the Ecuadorian Highlands Since the Early 1980s.Plants (Basel, Switzerland) · 2025Article
- Article
- Early Flowering and Maturity Promote the Successful Adaptation and High Yield of Quinoa (Plants (Basel, Switzerland) · 2024Article
- Empirical phenotyping and genome-wide association study reveal the association of panicle architecture with yield inFrontiers in microbiology · 2024Article
- Agro-morphological and nutritional assessment of chenopod and quinoa germplasm-Highly adaptable potential crops.Food science & nutrition · 2023Article
- Genomic Sequence of CanadianPlants (Basel, Switzerland) · 2023Article
- Genetic resources and breeding approaches for improvement of amaranth (Frontiers in nutrition · 2023Review
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Article
- High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Frontiers in plant science · 2022Article
- Genetic diversity analysis and development of molecular markers for the identification of largemouth bass (Frontiers in genetics · 2022Article
- Quinoa (Plants (Basel, Switzerland) · 2021Article
- Quinoa Phenotyping Methodologies: An International Consensus.Plants (Basel, Switzerland) · 2021Review
- The genotype-dependent phenotypic landscape of quinoa in salt tolerance and key growth traits.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties ofFrontiers in plant science · 2020Article
- Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability.Frontiers in genetics · 2020Review
- A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers.Plant methods · 2020Article
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundQuinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and to develop novel Insertion/Deletion (InDel) markers for quinoa by whole-genome re-sequencing.
resultsWe re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7× to 23× the quinoa genome. Based on the 1453-megabase (Mb) assembly from the reference accession Riobamba, 8,441,022 filtered bi-allelic single nucleotide polymorphisms (SNPs) and 842,783 filtered InDels were identified, with an estimated SNP and InDel density of 5.81 and 0.58 per kilobase (kb). From the genomic InDel variations, 85 dimorphic InDel markers were newly developed and validated. Together with the 62 simple sequence repeat (SSR) markers reported, a total of 147 markers were used for genotyping the 129 quinoa accessions. Molecular grouping analysis showed classification into two major groups, the Andean highland (composed of the northern and southern highland subgroups) and Chilean coastal, based on combined STRUCTURE, phylogenetic tree and PCA (Principle Component Analysis) analyses. Further analysis of the genetic diversity exhibited a decreasing tendency from the Chilean coast group to the Andean highland group, and the gene flow between subgroups was more frequent than that between the two subgroups and the Chilean coastal group. The majority of the variations (approximately 70%) were found through an analysis of molecular variation (AMOVA) due to the diversity between the groups. This was congruent with the observation of a highly significant F
conclusionsThe large number of SNPs and InDels identified in this study demonstrated that the quinoa genome is enriched with genomic variations. Genetic population structure, genetic core germplasms and dimorphic InDel markers are useful resources for genetic analysis and quinoa breeding.
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