title: Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice.
abstract: BACKGROUND
  The inferior spikelets are defined to be those at portions where the grains receive less photosynthetic products during the seed development. The typical inferior spikelets are physically located on the proximal secondary branches in a rice panicle and traditionally characterized by a later flowering time and a slower grain-filling rate, compared to those so-called superior spikelets. Grains produced on the inferior spikelets are consequently under-developed and lighter in weight than those formed on the superior spikelets. MicroRNAs (miRNAs) are recognized as key players in regulating plant development through post-transcriptional gene regulations. We previously presented the evidence that miRNAs may influence grain-filling rate and played a role in determining the grain weight and yield in rice.
  
  
  RESULTS
  In this study, further analyses of the expressed small RNAs in superior and inferior spikelets were conducted at five distinct developmental stages of grain development. Totally, 457 known miRNAs and 13 novel miRNAs were analyzed, showing a differential expression of 141 known miRNAs between superior and inferior spikelets with higher expression levels of most miRNAs associated with the superior than the inferior spikelets during the early stage of grain filling. Genes targeted by those differentially expressed miRNAs (i.e. miR156, miR164, miR167, miR397, miR1861, and miR1867) were recognized to play roles in multiple developmental and signaling pathways related to plant hormone homeostasis and starch accumulation.
  
  
  CONCLUSIONS
  Our data established a complicated link between miRNA dynamics and the traditional role of hormones in grain filling and development, providing new insights into the widely accepted concepts of the so-called superior and inferior spikelets in rice production.
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. lypengting@163.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. lypengting@163.com.
authors: Ting
authors: T
authors: Peng
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. sunhongzheng@foxmail.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. sunhongzheng@foxmail.com.
authors: Hongzheng
authors: H
authors: Sun
authors: Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA. mqiao@mtu.edu.
authors: Mengmeng
authors: M
authors: Qiao
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. zhaoyafan3701@163.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. zhaoyafan3701@163.com.
authors: Yafan
authors: Y
authors: Zhao
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. duyanxiu@gmail.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. duyanxiu@gmail.com.
authors: Yanxiu
authors: Y
authors: Du
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. zhjing98@126.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. zhjing98@126.com.
authors: Jing
authors: J
authors: Zhang
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. lijunzhou199899@126.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. lijunzhou199899@126.com.
authors: Junzhou
authors: J
authors: Li
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. gtang1@mtu.edu.|Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA. gtang1@mtu.edu.
authors: Guiliang
authors: G
authors: Tang
authors: Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. qzzhaoh@126.com.|Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China. qzzhaoh@126.com.
authors: Quanzhi
authors: Q
authors: Zhao
mesh_terms: D015870:Gene Expression; D035683:MicroRNAs / Q000378:metabolism*; D012275:Oryza / Q000254:growth & development / Q000378:metabolism*; D010641:Phenotype; D012639:Seeds / Q000254:growth & development*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs