Genome-wide identification and transcriptional profiling analysis of auxin response-related gene families in cucumber.
BACKGROUND
Auxin signaling has a vital function in the regulation of plant growth and development, both which are known to be mediated by auxin-responsive genes. So far, significant progress has been made toward the identification and characterization of auxin-response genes in several model plants, while no systematic analysis for these families was reported in cucumber (Cucumis sativus L.), a reference species for Cucurbitaceae crops. The comprehensive analyses will help design experiments for functional validation of their precise roles in plant development and stress responses.


RESULTS
A genome-wide search for auxin-response gene homologues identified 16 auxin-response factors (ARFs), 27 auxin/indole acetic acids (Aux/IAAs), 10 Gretchen Hagen 3 (GH3s), 61 small auxin-up mRNAs (SAURs), and 39 lateral organ boundaries (LBDs) in cucumber. Sequence analysis together with the organization of putative motifs indicated the potential diverse functions of these five auxin-related family members. The distribution and density of auxin response-related genes on chromosomes were not uniform. Evolutionary analysis showed that the chromosomal segment duplications mainly contributed to the expansion of the CsARF, CsIAA, CsGH3, and CsLBD gene families. Quantitative real-time RT-PCR analysis demonstrated that many ARFs, AUX/IAAs, GH3s, SAURs, and LBD genes were expressed in diverse patterns within different organs/tissues and during different development stages. They were also implicated in IAA, methyl jasmonic acid, or salicylic acid response, which is consistent with the finding that a great number of diverse cis-elements are present in their promoter regions involving a variety of signaling transduction pathways.


CONCLUSIONS
Genome-wide comparative analysis of auxin response-related family genes and their expression analysis provide new evidence for the potential role of auxin in development and hormone response of plants. Our data imply that the auxin response genes may be involved in various vegetative and reproductive developmental processes. Furthermore, they will be involved in different signal pathways and may mediate the crosstalk between various hormone responses.
Jian
J
Wu
Songyu
S
Liu
Xiaoyan
X
Guan
Lifei
L
Chen
Yanjun
Y
He
Jie
J
Wang
Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Zijingang Campus, A535 Agriculture building, Hangzhou 310058, Zhejiang, China. glu@zju.edu.cn.
Gang
G
Lu
D032461:Chromosomes, Plant / Q000235:genetics; D018553:Cucumis sativus / Q000187:drug effects / Q000235:genetics*; D019143:Evolution, Molecular; D005638:Fruit / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D020440:Gene Duplication / Q000187:drug effects; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D007210:Indoleacetic Acids / Q000494:pharmacology*; D005810:Multigene Family; D009928:Organ Specificity / Q000187:drug effects / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D020156:Salicylic Acid / Q000494:pharmacology; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
D007210:Indoleacetic Acids; D010940:Plant Proteins; D020156:Salicylic Acid