Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice.
BACKGROUND
MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages, including grain development in japonica rice. To identify novel miRNAs in indica rice and to study their expression patterns during the entire grain filling process, small RNAs from all stages of grain development were sequenced and their expression patterns were studied using customized miRNA chips.


RESULTS
A total of 21 conserved and 91 non-conserved miRNA families were found in developing indica grains. We also discovered 11 potential novel miRNAs based on the presence of their miRNA*s. Expression patterns of these identified miRNAs were analyzed using customized miRNA chips. The results showed that during the filling phase about half of the detected miRNAs were up-regulated, whereas the remainder were down-regulated. Predicted targets of differentially expressed miRNAs may participate in carbohydrate metabolism, hormone signaling and pathways associated with seed maturity, suggesting potentially important roles in rice grain development.


CONCLUSIONS
This study is the first genome-wide investigation of miRNAs during the grain-filling phase of an indica variety of rice. The novel miRNAs identified might be involved in new miRNA regulatory pathways for grain development. The complexity of these miRNAs and their targets and interactions require further study to obtain a better understanding of the molecular mechanisms underlying grain development.
National Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.
Ying
Y
Lan
Ning
N
Su
Yi
Y
Shen
Rongzhi
R
Zhang
Fuqing
F
Wu
Zhijun
Z
Cheng
Jiulin
J
Wang
Xin
X
Zhang
Xiupin
X
Guo
Cailin
C
Lei
Jie
J
Wang
Ling
L
Jiang
Long
L
Mao
Jianmin
J
Wan
D016000:Cluster Analysis; D019295:Computational Biology; D002523:Edible Grain / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012275:Oryza / Q000235:genetics* / Q000378:metabolism
D035683:MicroRNAs