ArticleGenome biology2015
Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Genetic Diversity Analysis of Cotton Cultivars Using a 40K Liquid Chip in Northern Xinjiang.International journal of molecular sciences · 2026Article
- Reduced representation sequencing reveals genetic diversity and adaptive genetic divergence in Calamus rhabdocladus.Scientific reports · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Genomic evolution and insights into agronomic trait innovations of Sesamum species.Plant communications · 2024Article
- Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding.Frontiers in plant science · 2024Review
- A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize (Frontiers in plant science · 2024Article
- Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits.Journal of advanced research · 2023Article
- Identification and Expression Analysis ofPlants (Basel, Switzerland) · 2023Article
- The evolution and expansion of RWP-RK gene family improve the heat adaptability of elephant grass (Pennisetum purpureum Schum.).BMC genomics · 2023Article
- Genome-wide association study identifies GhSAL1 affects cold tolerance at the seedling emergence stage in upland cotton (Gossypium hirsutum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton.Plant biotechnology journal · 2022Article
- Genetic diversity and population structure of Caryopteris mongholica revealed by reduced representation sequencing.BMC plant biology · 2022Article
- Article
- Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View.Plants (Basel, Switzerland) · 2022Review
- Dynamic Quantitative Trait Loci Mapping for Plant Height in Recombinant Inbred Line Population of Upland Cotton.Frontiers in plant science · 2022Article
- Identification of elite fiber quality loci in upland cotton based on the genotyping-by-target-sequencing technology.Frontiers in plant science · 2022Article
- Efficient construction of a linkage map and haplotypes for Mentha suaveolens using sequence capture.G3 (Bethesda, Md.) · 2021Article
- High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement.Nature genetics · 2021Article
- Construction of a high-density genetic linkage map and QTL analysis of morphological traits in an F1Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.).BMC plant biology · 2021Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSNPs are the most abundant polymorphism type, and have been explored in many crop genomic studies, including rice and maize. SNP discovery in allotetraploid cotton genomes has lagged behind that of other crops due to their complexity and polyploidy. In this study, genome-wide SNPs are detected systematically using next-generation sequencing and efficient SNP genotyping methods, and used to construct a linkage map and characterize the structural variations in polyploid cotton genomes.
resultsWe construct an ultra-dense inter-specific genetic map comprising 4,999,048 SNP loci distributed unevenly in 26 allotetraploid cotton linkage groups and covering 4,042 cM. The map is used to order tetraploid cotton genome scaffolds for accurate assembly of G. hirsutum acc. TM-1. Recombination rates and hotspots are identified across the cotton genome by comparing the assembled draft sequence and the genetic map. Using this map, genome rearrangements and centromeric regions are identified in tetraploid cotton by combining information from the publicly-available G. raimondii genome with fluorescent in situ hybridization analysis.
conclusionsWe report the genotype-by-sequencing method used to identify millions of SNPs between G. hirsutum and G. barbadense. We construct and use an ultra-dense SNP map to correct sequence mis-assemblies, merge scaffolds into pseudomolecules corresponding to chromosomes, detect genome rearrangements, and identify centromeric regions in allotetraploid cottons. We find that the centromeric retro-element sequence of tetraploid cotton derived from the D subgenome progenitor might have invaded the A subgenome centromeres after allotetrapolyploid formation. This study serves as a valuable genomic resource for genetic research and breeding of cotton.
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