ArticleBMC genomics2014
Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Genome-Wide Identification of Melon Single-Nucleotide Polymorphisms and Structural Variations Associated with Resistance toPlants (Basel, Switzerland) · 2026Article
- Identification of Genomic Regions Associated with Powdery Mildew Resistance in Watermelon through Genome-Wide Association Study.Plants (Basel, Switzerland) · 2024Article
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- Explainable artificial intelligence for genotype-to-phenotype prediction in plant breeding: a case study with a dataset from an almond germplasm collection.Frontiers in plant science · 2024Article
- Exploring the genetic diversity and population structure of aerial yams (Dioscorea bulbifera L.) DArT-seq and agronomic traits.PloS one · 2024Article
- Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing.Molecular genetics and genomics : MGG · 2022Article
- Article
- The History of Lentil (Frontiers in plant science · 2021Article
- Population structure and genetic diversity of watermelon (3 Biotech · 2020Article
- Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies.Frontiers in genetics · 2020Review
- Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection.Plant biotechnology journal · 2019Article
- Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits.Nature genetics · 2019Article
- Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon.International journal of molecular sciences · 2019Article
- Article
- Article
- Genetic Diversity Analysis of Olive Germplasm (Frontiers in genetics · 2019Article
- Article
- Whole-genome resequencing ofHorticulture research · 2019Article
- GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars.Scientific reports · 2018Article
- Genomic approaches for studying crop evolution.Genome biology · 2018Review
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12 authors.
Funding
Abstract
backgroundA large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise FST distributions among worldwide cultivated watermelons to track signals of domestication.
resultsWe examined 183 Citrullus lanatus var. lanatus accessions representing domesticated watermelon and generated a set of 11,485 SNP markers using genotyping by sequencing. With a diverse panel of worldwide cultivated watermelons, we identified a set of 5,254 SNPs with a minor allele frequency of ≥ 0.05, distributed across the genome. All ancestries were traced to Africa and an admixture of various ancestries constituted secondary gene pools across various continents. A sliding window analysis using pairwise FST values was used to resolve selective sweeps. We identified strong selection on chromosomes 3 and 9 that might have contributed to the domestication process. Pairwise analysis of adjacent SNPs within a chromosome as well as within a haplotype allowed us to estimate genome-wide LD decay. LD was also detected within individual genes on various chromosomes. Principal component and ancestry analyses were used to account for population structure in a genome-wide association study. We further mapped important genes for soluble solid content using a mixed linear model.
conclusionsInformation concerning the SNP resources, population structure, and LD developed in this study will help in identifying agronomically important candidate genes from the genomic regions underlying selection and for mapping quantitative trait loci using a genome-wide association study in sweet watermelon.
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