Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon.
MADS-box genes are important transcription factors for plant development, especially floral organogenesis. Brachypodium distachyon is a model for biofuel plants and temperate grasses such as wheat and barley, but a comprehensive analysis of MADS-box family proteins in Brachypodium is still missing. We report here a genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. We identified 57 MADS-box genes and classified them into 32 MIKC(c)-type, 7 MIKC*-type, 9 Mα, 7 Mβ and 2 Mγ MADS-box genes according to their phylogenetic relationships to the Arabidopsis and rice MADS-box genes. Detailed gene structure and motif distribution were then studied. Investigation of their chromosomal localizations revealed that Brachypodium MADS-box genes distributed evenly across five chromosomes. In addition, five pairs of type II MADS-box genes were found on synteny blocks derived from whole genome duplication blocks. We then performed a systematic expression analysis of Brachypodium MADS-box genes in various tissues, particular floral organs. Further detection under salt, drought, and low-temperature conditions showed that some MADS-box genes may also be involved in abiotic stress responses, including type I genes. Comparative studies of MADS-box genes among Brachypodium, rice and Arabidopsis showed that Brachypodium had fewer gene duplication events. Taken together, this work provides useful data for further functional studies of MADS-box genes in Brachypodium distachyon.
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China.
Bo
B
Wei
National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China.
Rong-Zhi
RZ
Zhang
National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China.
Juan-Juan
JJ
Guo
National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China.
Dan-Mei
DM
Liu
National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China.
Ai-Li
AL
Li
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China.
Ren-Chun
RC
Fan
National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China.
Long
L
Mao
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China.
Xiang-Qi
XQ
Zhang
D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics; D058431:Brachypodium / Q000187:drug effects / Q000235:genetics*; D003080:Cold Temperature; D017124:Conserved Sequence / Q000235:genetics; D055864:Droughts; D020440:Gene Duplication / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D020131:Genes, Duplicate; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D026161:MADS Domain Proteins / Q000235:genetics*; D005810:Multigene Family; D059372:Nucleotide Motifs / Q000235:genetics; D012275:Oryza / Q000187:drug effects / Q000235:genetics; D010802:Phylogeny; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics
D026161:MADS Domain Proteins; D012965:Sodium Chloride