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Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.
PLoS One. 2015; 10(12):e0145144.Plos

Abstract

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Authors+Show Affiliations

State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China. Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China. Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.

Pub Type(s)

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

Language

eng

PubMed ID

26695430

Citation

Li, Fagen, et al. "Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus." PloS One, vol. 10, no. 12, 2015, pp. e0145144.
Li F, Zhou C, Weng Q, et al. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus. PLoS ONE. 2015;10(12):e0145144.
Li, F., Zhou, C., Weng, Q., Li, M., Yu, X., Guo, Y., Wang, Y., Zhang, X., & Gan, S. (2015). Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus. PloS One, 10(12), e0145144. https://doi.org/10.1371/journal.pone.0145144
Li F, et al. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus. PLoS ONE. 2015;10(12):e0145144. PubMed PMID: 26695430.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus. AU - Li,Fagen, AU - Zhou,Changpin, AU - Weng,Qijie, AU - Li,Mei, AU - Yu,Xiaoli, AU - Guo,Yong, AU - Wang,Yu, AU - Zhang,Xiaohong, AU - Gan,Siming, Y1 - 2015/12/22/ PY - 2015/09/08/received PY - 2015/12/01/accepted PY - 2015/12/24/entrez PY - 2015/12/24/pubmed PY - 2016/6/25/medline SP - e0145144 EP - e0145144 JF - PloS one JO - PLoS ONE VL - 10 IS - 12 N2 - Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/26695430/Comparative_Genomics_Analyses_Reveal_Extensive_Chromosome_Colinearity_and_Novel_Quantitative_Trait_Loci_in_Eucalyptus_ L2 - http://dx.plos.org/10.1371/journal.pone.0145144 DB - PRIME DP - Unbound Medicine ER -