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A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus.
BMC Genomics. 2011 Apr 14; 12:189.BG

Abstract

BACKGROUND

Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers.

RESULTS

SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome.

CONCLUSIONS

The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species.

Authors+Show Affiliations

Plant Genetics Laboratory, Embrapa-Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília 70770-970, DF, Brazil.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21492453

Citation

Neves, Leandro G., et al. "A High-density Transcript Linkage Map With 1,845 Expressed Genes Positioned By Microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus." BMC Genomics, vol. 12, 2011, p. 189.
Neves LG, Mc Mamani E, Alfenas AC, et al. A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. BMC Genomics. 2011;12:189.
Neves, L. G., Mc Mamani, E., Alfenas, A. C., Kirst, M., & Grattapaglia, D. (2011). A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. BMC Genomics, 12, 189. https://doi.org/10.1186/1471-2164-12-189
Neves LG, et al. A High-density Transcript Linkage Map With 1,845 Expressed Genes Positioned By Microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. BMC Genomics. 2011 Apr 14;12:189. PubMed PMID: 21492453.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. AU - Neves,Leandro G, AU - Mc Mamani,Eva, AU - Alfenas,Acelino C, AU - Kirst,Matias, AU - Grattapaglia,Dario, Y1 - 2011/04/14/ PY - 2010/11/04/received PY - 2011/04/14/accepted PY - 2011/4/16/entrez PY - 2011/4/16/pubmed PY - 2011/8/24/medline SP - 189 EP - 189 JF - BMC genomics JO - BMC Genomics VL - 12 N2 - BACKGROUND: Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. RESULTS: SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. CONCLUSIONS: The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/21492453/A_high_density_transcript_linkage_map_with_1845_expressed_genes_positioned_by_microarray_based_Single_Feature_Polymorphisms__SFP__in_Eucalyptus_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-189 DB - PRIME DP - Unbound Medicine ER -