title: Identification and characterization of nuclear genes involved in photosynthesis in Populus.
abstract: BACKGROUND
  The gap between the real and potential photosynthetic rate under field conditions suggests that photosynthesis could potentially be improved. Nuclear genes provide possible targets for improving photosynthetic efficiency. Hence, genome-wide identification and characterization of the nuclear genes affecting photosynthetic traits in woody plants would provide key insights on genetic regulation of photosynthesis and identify candidate processes for improvement of photosynthesis.
  
  
  RESULTS
  Using microarray and bulked segregant analysis strategies, we identified differentially expressed nuclear genes for photosynthesis traits in a segregating population of poplar. We identified 515 differentially expressed genes in this population (FC ≥ 2 or FC ≤ 0.5, P < 0.05), 163 up-regulated and 352 down-regulated. Real-time PCR expression analysis confirmed the microarray data. Singular Enrichment Analysis identified 48 significantly enriched GO terms for molecular functions (28), biological processes (18) and cell components (2). Furthermore, we selected six candidate genes for functional examination by a single-marker association approach, which demonstrated that 20 SNPs in five candidate genes significantly associated with photosynthetic traits, and the phenotypic variance explained by each SNP ranged from 2.3% to 12.6%. This revealed that regulation of photosynthesis by the nuclear genome mainly involves transport, metabolism and response to stimulus functions.
  
  
  CONCLUSIONS
  This study provides new genome-scale strategies for the discovery of potential candidate genes affecting photosynthesis in Populus, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.
authors.forename: Bowen
authors.initials: B
authors.lastname: Wang
authors.forename: Qingzhang
authors.initials: Q
authors.lastname: Du
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Yang
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P, R, China. DeqiangZhang@bjfu.edu.cn.
authors.forename: Deqiang
authors.initials: D
authors.lastname: Zhang
mesh_terms: D000704:Analysis of Variance; D002467:Cell Nucleus / Q000235:genetics*; D016000:Cluster Analysis; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056426:Genetic Loci; D006824:Hybridization, Genetic; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D010788:Photosynthesis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032107:Populus / Q000235:genetics* / Q000502:physiology*; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics