? Abstract
Plant Diversity 2017, 39(2) 73-79 DOI:   http://dx.doi.org/10.1016/j.pld.2017.01.003  ISSN: 2096-2703 CN: 53-1233

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Keywords
Rice

Dwarf

Osr4 retrotransposon

D1 gene
Authors
Jie Chen a,b
Hong Zhao b
Xiujuan Zheng a,b
Kangjing Liang a,b
Yuchun Guo a,b
Xinli Sun a,b*
PubMed
Article by Jie Chen a,b
Article by
Article by Hong Zhao b
Article by Xiujuan Zheng a,b
Article by
Article by Kangjing Liang a,b
Article by
Article by Yuchun Guo a,b
Article by
Article by Xinli Sun a,b*
Article by
Article by

Recent amplification of Osr4 LTR-retrotransposon caused rice D1 gene mutation and dwarf phenotype

 Jie Chen a,b,  Hong Zhao b, Xiujuan Zheng a,b, Kangjing Liang  a,b, Yuchun Guo  a,b, Xinli Sun  a,b*

a
Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
b
College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, 350002, China

Abstract

A novel rice d1 mutant was identified using map-based cloning and comparative analysis of known d1
mutants. The mutant (d1-a) shows a mild dwarf trait, which differs only slightly from the wildtype in
plant height at the tillering stage. The d1-a mutant is different from other d1 mutants. We found that it
was interrupted by an Osr4 long terminal repeat (LTR)-retrotransposon, which resulted in the loss of
exon 7 in the mutant D1 mRNA. A paralog of the D1 gene, D1-like, was revealed. D1-like is a truncated
gene that might have resulted from recombination between retrotransposons. We identified 65 Osr4
LTR-retrotransposons in Nipponbare, and found more LTR variants in contrast to coding DNA sequence
(CDS) in the retrotransposons. We also identified five possible regulatory motifs in LTRs which may
control the expression of the retrotransposons. In addition, we predicted six putative functional Osr4
retrotransposons that contain complete CDSs and all important elements. Osr4 retrotransposons were
classified into 4 groups, and this type of retrotransposon only appears to be present in monocots.
Members of group I-1, which included all putative functional retrotransposons, showed a high similarity
with each other. The retrotransposons were expressed in all tissues, at especially higher levels in some
leaves and seeds. These findings imply that transpositions of group I-1 members might have occurred
frequently and recently.

Keywords Rice  
Dwarf
  
Osr4 retrotransposon
  
D1 gene
  
Received 2016-09-18 Revised 2017-01-19 Online:  
DOI: http://dx.doi.org/10.1016/j.pld.2017.01.003
Fund:
Corresponding Authors: * Corresponding author. Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University,xinlisun@hotmail.com (X. Sun). Fuzhou, 350002, China.
Email: xinlisun@hotmail.com (X. Sun).
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