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

作     者：Jie Chen Hong Zhao Xiujuan Zheng Kangjing Liang Yuchun Guo Xinli Sun 

作者机构：Key Laboratory of Ministry of Education~or Genetics Breeding and Multiple Utilization of Crops Fujian Agriculture & Forestry University Fuzhou 350002China College of Crop Science Fujian Agriculture & Forestry University Fuzhou 350002 China 

出 版 物：《Plant Diversity》 (植物多样性（英文版）)

年 卷 期：2017年第39卷第2期

页      面：73-79页

核心收录：

学科分类：0710[理学-生物学] 0830[工学-环境科学与工程（可授工学、理学、农学学位）] 07[理学] 071007[理学-遗传学] 0901[农学-作物学] 0902[农学-园艺学] 0713[理学-生态学] 

基　　金：supported by National and Fujian Provincial Natural Science Foundation(No.31371557 and K55NI921A) Fujian Provincial Department of Education Project(K58MLV03A) a startup fund from Fujian Agriculture and Forestry University(http://www.fafu.edu.cn/)to X.S 

主　　题：Rice Dwarf Osr4 retrotransposon D1 gene 

摘      要：A novel rice d1 mutant was identified using map-based cloning and comparative analysis of known dl 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 dl-a mutant is different from other dl 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 Osr4LTR-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 1-1,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 1-1 members might have occurred frequently and recently.