Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda)

Yang, Suk-Hwan; Zyl, Leonel van; No, Eun-Gyu; Loopstra, Carol A.

doi:10.1016/j.plantsci.2003.12.030

Cited by 33 publications

(24 citation statements)

References 32 publications

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“…Both of the P. glauca tubulins were expressed preferentially in xylem and shared sequenced homologies with tubulins from P. taeda that are highly abundant among ESTs from xylem cDNA libraries (Yang et al 2004) and SAGE sequencing data (Lorenz and Dean 2002).…”

Section: Resultsmentioning

confidence: 97%

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

et al. 2011

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Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker-trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P # 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q # 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P # 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a b-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.

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Section: Resultsmentioning

confidence: 97%

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

et al. 2011

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“…There is abundant evidence for differential expression of genes involved in wood/xylem development among tissues (Loopstra and Sederoff 1995;Allona et al 1998;Zhang et al 2000;Yang et al 2004;2005). However, very little work has been done to examine differential expression among individuals .…”

Section: Communicated By J Deanmentioning

confidence: 99%

“…The CslA1 gene formed a cluster with MYB8 and PIN1, suggesting that it might be regulated by these two transcription factors, either directly or indirectly. Of the seven no-hit genes (genes with no significant matches in other plants but selected due to preferential expression in loblolly pine xylem; Yang et al 2004) included in our project, five of them clustered together with the following genes: LP-6 (a chitinase homolog), PutAMS (a putative S-adoMet synthetase), translation initiation factor eIF-4A, and transcription factor Hap5A. One of the no-hit genes, NH-9, formed a cluster with 1,4-benzoquinone reductase (BQR), pinoresinollariciresinol reductase (PLR), phenylcoumaran benzylic ether reductase (PCBER), and β-ketoacyl-ACP synthetase I-2 (BKACPS) genes.…”

Section: A C G C W M R W M Rmentioning

confidence: 99%

Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.)

Palle

Seeve

Eckert

et al. 2010

Tree Genetics & Genomes

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Gene expression analyses using native populations can contribute to the understanding of plant development and adaptation in multiple ways. These include the identification of candidate genes and genetic polymorphisms affecting expression and phenotypic traits and characterization of transcriptional networks. We analyzed the expression of 111 genes with probable roles in xylem/wood development in a population of loblolly pine (Pinus taeda L.) covering much of the natural range. Loblolly pine is one of the most commercially important forest tree species in the United States, and the discovery of genes and alleles contributing to desirable wood properties would be valuable. Of the 111 genes analyzed using quantitative reverse transcriptionpolymerase chain reaction, there were significant differences in gene expression between clones for 106 genes.Genes encoding lignin biosynthetic enzymes and arabinogalactan proteins were more variable than those encoding cellulose synthases or those involved in signal transduction. Several groups of genes with related functions form clusters. A network analysis identified transcription factors that may be key regulators of xylem development in pine. Secondary wall-associated NAC domain protein 1 (SND1) in particular appears to be involved in the regulation of many other genes. The cluster analysis using clones did not result in discrete populations but did identify some expression differences between regions. In the future, the gene expression data will be used for association analyses and promoter studies to understand how these gene expression differences are associated with specific genetic polymorphisms in other genes and promoters.

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“…Microarrays based on comprehensive transcriptomic data can be used to advance pine research, however most examples of Pinus microarrays published in the last 10 years are based on very modest collections containing less than 3,500 sequenced genes (Heath et al 2002;Yang et al 2004;Myburg et al 2006;Adomas et al 2007;Balk et al 2007;Perdiguero et al 2012;Li et al 2012). A cDNA microarray based on 26,496 sequences for P. taeda was recently used to assess the effects of drought in P. taeda L. (Lorenz et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Heterologous hybridisation to a Pinus microarray: profiling of gene expression in Pinus radiata saplings exposed to ethephon

Dubouzet¹,

Donaldson²,

Black³

et al. 2014

N.Z. j. of For. Sci.

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Background: The design, construction and application of a Pinus microarray platform are described. The oligonucleotide microarray was developed using publicly available Pinus cDNA sequences mostly derived from Pinus taeda to test whether heterologous hybridisation of microarray probes will generate useful data when hybridised with cRNA constructed from the dominant New Zealand forestry species Pinus radiata.

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Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda)

Cited by 33 publications

References 32 publications

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.)

Heterologous hybridisation to a Pinus microarray: profiling of gene expression in Pinus radiata saplings exposed to ethephon

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