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Identification of candidate genes affecting juvenile wood stiffness in Pinus radiata

ABSTRACT: Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared.

ORGANISM(S): Pinus radiata

PROVIDER: GSE23020 | GEO | 2011/06/01

SECONDARY ACCESSION(S): PRJNA131721

REPOSITORIES: GEO

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Identification of candidate genes affecting juvenile wood stiffness in Pinus radiata

Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared. Radiata pine trees used for microarray experiment were selected from two progeny trials planted at Flynn and Kromelite, Australia. Based on the IML-based MOE measurement, five families with highest and lowest MOE each were selected from each trial, which represented two segregant populations with contrasting wood stiffness. Two individuals from each selected family were further sampled. Developing xylem tissues of selected trees in Flynn trial were sampled in spring (October) and autumn (April), representing earlywood (EW) and latewood (LW) of juvenile aged trees, respectively. Collection of xylem tissues from Kromelite trial was arranged in summer (late November) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. In Flynn trial EW and LW tissues were collected from the same sampled trees on opposite sides of the trunk. Transcript accumulation was compared in trees with highest (HS) and lowest stiffness (LS) using xylem samples from Flynn collected in spring (EW) and autumn (LW), as well as Kromelite in summer (LW), respectively. Bulked segregant analysis (BSA) was used for the experiment design. Total RNA samples extracted from the five trees with HS were pooled at equal amount, and compared to the bulked five individuals with LS. This pooling strategy can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.

2011-06-01 | E-GEOD-23020 | biostudies-arrayexpress

Identification of candidate genes affecting juvenile wood density in Pinus radiata

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Identification of candidate genes affecting juvenile wood density in Pinus radiata

Project description:Wood density is a foundamental quality trait for structural timber, bioenergy and pulp industries. We investigated genes differentially transcribed in radiate pine juvneile trees with distinct wood density using cDNA microarrays. Radiata pine trees were selected from a progeny trial planted at Flynn, Australia. Based on the gravitical measurement of wood cores, 12 families with highest and lowest density each were selected, representing two groups of trees with contrasting wood density. One individual with higher or lower density were further sampled in each selected family. Developing xylem tissues of selected trees were sampled in autumn (April) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. Wood cores of the sampled trees were further measured using SilviScan 2. Total RNA extracted from ten developing xylem tissues with confirmed distinct density in each tree group were pooled into two bulks (five trees each), and the two bulks of HD were compared with two LD bulks in the microarray experiment (named the bulk experiment). Six developing xylem tissues with the most distinct density from each tree group were further chosen. Six xylem tissues with HD were individually compared with bulked six xylem tissues with LD in the second microarray experiment (named individual experiment). These two different pooling strategies can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.

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Transcriptome reorganization during wood maturation in Pinus radiata

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Transcriptome profiling of Pinus radiata branches reveals new insights into compression wood formation in response to gravity stress

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Transcriptome profiling of Pinus radiata branches reveals new insights into compression wood formation in response to gravity stress

Project description:Compression (CW) and opposite wood (OW) are formed in the uniderside and upperside of conifer branches respectively in response to gravity stress. We investigated genes differentially transcribed between the underside and upside of radiate pine branches using cDNA microarrays with a view to plant gravitropism. Six trees with well-developed branches were selected from a radiata pine commercial plantation (aged 13 years) located at Bondo, NSW, Australia (35Âº 16' 44.04 S, 148Âº 26' 54.66 E). The largest branch from each tree was further selected for sampling, including three branches sampled in April 2007 (autumn in Bondo) and three sampled in October 2007 (spring). Bark was removed from the base part (about 10 cm in length) of each branch. Developing xylem tissues were scraped from the exposed upperside and underside surface respectively with a sharp chisel. Samples were immediately placed into 50 ml BD FalconTM tubes filled with liquid nitrogen. Gene expression in the underside and upperside of branches was compared using radiata pine cDNA microarrays.

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