Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis

Jianbo Xie; Jiaxing Tian; Qingzhang Du; Jinhui Chen; Ying Li; Xiaohui Yang; Bailian Li; Deqiang Zhang

doi:10.1093/jxb/erw151

Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis

J Exp Bot. 2016 May;67(11):3325-38. doi: 10.1093/jxb/erw151. Epub 2016 Apr 18.

Authors

Jianbo Xie¹, Jiaxing Tian¹, Qingzhang Du¹, Jinhui Chen¹, Ying Li¹, Xiaohui Yang¹, Bailian Li², Deqiang Zhang³

Affiliations

¹ National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China.
² National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China Department of Forestry, North Carolina State University, Raleigh, NC 27695-8203, USA.
³ National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China DeqiangZhang@bjfu.edu.cn.

PMID: 27091876
DOI: 10.1093/jxb/erw151

Abstract

Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits.

Keywords: Association genetics; Populus tomentosa; epistatic interactions; gibberellins; photosynthesis pathway; transcriptome..

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Gene Expression Regulation, Plant*
Gibberellins / metabolism*
Photosynthesis / genetics*
Plant Proteins / genetics
Plant Proteins / metabolism
Polymorphism, Single Nucleotide*
Populus / genetics*
Populus / growth & development
Populus / metabolism

Substances

Gibberellins
Plant Proteins