ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2006
Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- MegaSSR: a web server for large scale microsatellite identification, classification, and marker development.Frontiers in plant science · 2023Article
- Review
- Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential.Frontiers in plant science · 2021Review
- Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.).PloS one · 2019Article
- A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids.BMC bioinformatics · 2018Article
- The Challenge of Analyzing the Sugarcane Genome.Frontiers in plant science · 2018Review
- SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane.BMC genomics · 2017Article
- Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping.Molecular genetics and genomics : MGG · 2016Article
- Natural Allelic Variations in Highly Polyploidy Saccharum Complex.Frontiers in plant science · 2016Article
- Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.PloS one · 2016Article
- DNA Marker Transmission and Linkage Analysis in Populations Derived from a Sugarcane (Saccharum spp.) x Erianthus arundinaceus Hybrid.PloS one · 2015Article
- Genetic control of juvenile growth and botanical architecture in an ornamental woody plant, Prunus mume Sieb. et Zucc. as revealed by a high-density linkage map.BMC genetics · 2014Article
- SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids.Scientific reports · 2013Article
- Article
- QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate.PloS one · 2013Article
- A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers.BMC genetics · 2012Article
- A mixed model QTL analysis for sugarcane multiple-harvest-location trial data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids.PloS one · 2012Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars ('SP80-180' x 'SP80-4966') using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane.
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