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1.  ADP1 Affects Plant Architecture by Regulating Local Auxin Biosynthesis 
PLoS Genetics  2014;10(1):e1003954.
Plant architecture is one of the key factors that affect plant survival and productivity. Plant body structure is established through the iterative initiation and outgrowth of lateral organs, which are derived from the shoot apical meristem and root apical meristem, after embryogenesis. Here we report that ADP1, a putative MATE (multidrug and toxic compound extrusion) transporter, plays an essential role in regulating lateral organ outgrowth, and thus in maintaining normal architecture of Arabidopsis. Elevated expression levels of ADP1 resulted in accelerated plant growth rate, and increased the numbers of axillary branches and flowers. Our molecular and genetic evidence demonstrated that the phenotypes of plants over-expressing ADP1 were caused by reduction of local auxin levels in the meristematic regions. We further discovered that this reduction was probably due to decreased levels of auxin biosynthesis in the local meristematic regions based on the measured reduction in IAA levels and the gene expression data. Simultaneous inactivation of ADP1 and its three closest homologs led to growth retardation, relative reduction of lateral organ number and slightly elevated auxin level. Our results indicated that ADP1-mediated regulation of the local auxin level in meristematic regions is an essential determinant for plant architecture maintenance by restraining the outgrowth of lateral organs.
Author Summary
Plant architecture is one of the key factors that affect plant survival and productivity. It is well established that the plant hormone auxin plays an essential role in organ initiation and pattern formation, thus affecting plant architecture. We found that a putative MATE (multidrug and toxic compound extrusion) transporter, ADP1, which was expressed in the meristematic regions, through regulating the level of auxin biosynthesis, controls lateral organ outgrowth so as to maintain normal architecture in Arabidopsis. The more ADP1 was expressed, the less levels of local auxin were detected in the meristematic regions of the plant, resulting in increased growth rate and a greater number of axillary branches and flowers. The reduction of auxin levels is probably due to decreased level of auxin biosynthesis in the local meristematic regions. Down-regulated expression of ADP1 and its three closely related genes caused plants to grow slower and to produce less lateral organs. Our results indicated that ADP1-mediated regulation of the local auxin levels in meristematic regions is an essential determinant for plant architecture by restraining the outgrowth of lateral organs.
doi:10.1371/journal.pgen.1003954
PMCID: PMC3879159  PMID: 24391508
2.  Targeted mutagenesis in rice using CRISPR-Cas system 
Cell Research  2013;23(10):1233-1236.
doi:10.1038/cr.2013.123
PMCID: PMC3790239  PMID: 23999856
3.  Transcriptional Profiling of Rice Early Response to Magnaporthe oryzae Identified OsWRKYs as Important Regulators in Rice Blast Resistance 
PLoS ONE  2013;8(3):e59720.
Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive. Therefore, we carried out a transcriptome study on rice early defense response to M. oryzae. We found that the transcriptional profiles of rice compatible and incompatible interactions with M. oryzae were mostly similar, with genes regulated more prominently in the incompatible interactions. The functional analysis showed that the genes involved in signaling and secondary metabolism were extensively up-regulated. In particular, WRKY transcription factor genes were significantly enriched among the up-regulated genes. Overexpressing one of these WRKY genes, OsWRKY47, in transgenic rice plants conferred enhanced resistance against rice blast fungus. Our results revealed the sophisticated transcriptional reprogramming of signaling and metabolic pathways during rice early response to M. oryzae and demonstrated the critical roles of WRKY transcription factors in rice blast resistance.
doi:10.1371/journal.pone.0059720
PMCID: PMC3609760  PMID: 23544090
4.  Allelic Analyses of the Arabidopsis YUC1 Locus Reveal Residues and Domains Essential for the Functions of YUC Family of Flavin Monooxygenases 
Flavin monooxygenases (FMOs) play critical roles in plant growth and development by synthesizing auxin and other signaling molecules. However, the structure and function relationship within plant FMOs is not understood. Here we defined the important residues and domains of the Arabidopsis YUC1 FMO, a key enzyme in auxin biosynthesis. We previously showed that simultaneous inactivation of YUC1 and its homologue YUC4 caused severe defects in vascular and floral development. We mutagenized the yuc4 mutant and screened for mutants with phenotypes similar to those of yuc1 yuc4 double mutants. Among the isolated mutants, five of them contained mutations in the YUC1 gene. Interestingly, the mutations identified in the new yuc1 alleles were concentrated in the two GXGXXG motifs that are highly conserved among the plant FMOs. One such motif presumably binds to flavin adenine dinucleotide (FAD) cofactor and the other binds to nicotinamide adenine dinucleotide phosphate (NADPH). We also identified the Ser139 to Phe conversion in yuc1, a mutation that is located between the two nucleotide-binding sites. By analyzing a series of yuc1 mutants, we identified key residues and motifs essential for the functions of YUC1 FMO.
doi:10.1111/j.1744-7909.2010.01007.x
PMCID: PMC3060657  PMID: 21205174
5.  The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences 
BMC Plant Biology  2010;10:22.
Background
In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China.
Results
A data set comprising 77 accessions of A. thaliana, including 19 field-collected Chinese accessions together with three related species (A. arenosa, A. suecica, and Olimarabidopsis cabulica) as the out-group, was compiled. The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). The estimated divergence time of the two MDHCs was about 0.39 mya. Forty-nine haplotypes were detected among the 77 accessions, which exhibited nucleotide diversity (π) of 0.00169. The Chinese populations along the Yangtze River were characterized by five haplotypes, and the two accessions collected from the middle range of the Altai Mountains in China shared six specific variable sites.
Conclusions
The dimorphism in the chloroplast DNA could be due to founder effects during late Pleistocene glaciations and interglacial periods, although introgression cannot be ruled out. The Chinese populations along the Yangtze River may have dispersed eastwards to their present-day locations from the Himalayas. These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. Two accessions collected from the middle range of the Altai Mountains in China may have survived in a local refugium during late Pleistocene glaciations. The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections.
doi:10.1186/1471-2229-10-22
PMCID: PMC2827422  PMID: 20141622

Results 1-5 (5)