Expression and nucleotide diversity of the poplar <Emphasis Type="Italic">COBL</Emphasis> gene |
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Authors: | Deqiang Zhang Xiaohui Yang Zhiyi Zhang Bailian Li |
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Institution: | (1) National Engineering Laboratory for Tree Breeding, Beijing, 100083, People’s Republic of China;(2) Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing, 100083, People’s Republic of China;(3) Department of Forestry, North Carolina State University, Raleigh, NC 27695-8203, USA |
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Abstract: | The COBRA gene encodes a putative glycosyl-phosphatidylinositol-anchored protein that regulates cellulose deposition and oriented cell
expansion in the plant cell wall. This study reports the identification of PtCOBL4, a first COBRA gene from the tree Populus tomentosa. The full-length cDNA of PtCOBL4 was isolated from a xylem cDNA library. The deduced protein sequence shares 72.7% identity with Arabidopsis AtCOBL4 protein involved in secondary cell wall deposition. Analysis of differential tissue expression by real-time polymerase
chain reaction (PCR) indicated that PtCOBL4 is expressed predominantly in the mature xylem zone. By using the sequenced whole genome and DNA microarray data of Populus, we demonstrated that COBRA is a multigene family of 11 members, each of which exhibit different tissue-specific expression patterns. To evaluate the
functional consequences of nucleotide polymorphisms in the PtCOBL4 locus, the patterns of variation in a 2,002-bp region of the gene were surveyed in 40 unrelated individuals representative
of almost the entire natural range of P. tomentosa. Sixty-one single-nucleotide polymorphisms (SNPs) were identified at a frequency of one SNP per 32.8 bp of sequence, giving
an estimated nucleotide diversity of π
T = 0.00800 and θ
w = 0.00716. Within coding regions, nonsynonymous diversity (π
nonsyn = 0.00285) was markedly lower than synonymous diversity (π
syn = 0.02128); the π
nonsyn/π
syn ratio was 0.13, significantly less than 1, indicating that the synonymous sites were subject to strong purifying selection.
These results provide the necessary foundation for improving the quantity and quality of cellulose via genetic engineering
or by candidate-gene-based association genetics in P. tomentosa. |
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Keywords: | |
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