ArticlePlant biotechnology journal2019
Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a 'sweet' crop with 'bitter' genomes.
Article in Plant biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Environmental Association Analyses in Plants and the Influence of Methodological Decisions.Molecular ecology · 2026Review
- Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly.Genome biology · 2026Article
- High-Resolution Chloroplast SNV Profiling of 409 Grapevine (International journal of molecular sciences · 2026Article
- Establishment of an efficientFrontiers in plant science · 2026Article
- The repeatome landscape in the "Frontiers in plant science · 2026Article
- Identification of candidate single-nucleotide polymorphisms (SNPs) and genes associated with sugarcane leaf scald disease.Scientific reports · 2024Article
- A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane.International journal of molecular sciences · 2023Article
- Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers.Frontiers in plant science · 2023Article
- Experimental evaluation of genomic selection prediction for rust resistance in sugarcane.The plant genome · 2021Article
- A linkage disequilibrium-based approach to position unmapped SNPs in crop species.BMC genomics · 2021Article
- Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance.Scientific reports · 2021Article
- Three founding ancestral genomes involved in the origin of sugarcane.Annals of botany · 2021Article
- Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential.Frontiers in plant science · 2021Review
- Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance.Scientific reports · 2020Article
- Genome-wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.).The plant genome · 2020Article
- Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars.Chromosoma · 2020Article
- Article
- Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Article
- A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.).PloS one · 2019Article
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14 authors.
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Abstract
Sugarcane (Saccharum spp.) is a highly energy-efficient crop primarily for sugar and bio-ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high-quality genome-wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in-depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.
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