中国农业科学 ›› 2014, Vol. 47 ›› Issue (23): 4563-4572.doi: 10.3864/j.issn.0578-1752.2014.23.002

• 作物遗传育种·种质资源 • 上一篇    下一篇

玉米Dof转录因子家族的全基因组鉴定与分析

葛敏,吕远大,李坦,张体付,张晓林,赵涵   

  1. 江苏省农业科学院农业生物技术研究所/江苏省农业生物学重点实验室,南京 210014
  • 收稿日期:2014-04-16 修回日期:2014-06-23 出版日期:2014-12-01 发布日期:2014-12-01
  • 通讯作者: 赵涵,Tel:025-84390751;E-mail:zhaohan@jaas.ac.cn
  • 作者简介:葛敏,E-mail:gemin8614@163.com
  • 基金资助:
    国家自然科学基金(31271728)

Genome-Wide Identification and Analysis of Dof Transcription Factor Family in Maize

GE Min, LÜ Yuan-da, LI Tan, ZHANG Ti-fu, ZHANG Xiao-lin, ZHAO Han   

  1. Institute of Agro-Biotechnology, Jiangsu Academy of Agricultural Sciences/Provincial Key Lab of Agro-Biology, Nanjing 210014
  • Received:2014-04-16 Revised:2014-06-23 Online:2014-12-01 Published:2014-12-01

摘要: 【目的】全基因组水平鉴定并解析玉米Dof(DNA binding with one finger)基因家族。【方法】基于玉米V3基因组数据鉴定玉米Dof基因家族,并从基因的结构、系统发育关系、染色体的位置分布、玉米不同组织和不同生理发育阶段基因的表达谱以及在充足氮(sufficient nitrogen,SN)和低氮(limiting nitrogen,LN)条件下V3期叶组织基因的差异表达5个方面分析玉米Dof基因家族。【结果】玉米参考基因组中存在46个Dof结构域基因,命名为ZmV3Dof1ZmV3Dof46。通过系统发育关系和序列相似性将该基因家族分为8个亚类(Subgroup)S1—S8,每个亚类有3—8个Dof基因。通过分析该家族染色体分布,发现玉米10条染色体,除Chr.9外,均有Dof基因的分布,其中,在Chr.1上分布最为密集,有12个ZmV3Dofs;在Chr.5和Chr.3上分布次之,分别为8和7个ZmV3Dofs;在其他染色体上则分布较少,此外,Dofs在Chr.1的底部、Chr.5的顶部和底部分布密度相对较高。表达谱分析结果表明,Dof基因家族成员在不同组织及不同发育阶段均有差异表达,预示不同Dof基因功能的多样性以及在植物发育过程中扮演着不同角色,且同一亚类Dof基因表达模式存在一定程度的相似性。此外,玉米Dof基因家族对氮响应较为敏感,充足氮(SN)和低氮(LN)条件下,V3期叶组织基因的RNAseq表达结果显示35个Dof基因在2种氮处理下表达量存在差异,其中13个基因表达量差异较大。值得注意的是21个Dof基因在低氮处理下表达量上调,其中8个基因只在低氮条件下表达。【结论】基于最新版基因组数据鉴定玉米在自交系B73基因组中存在46个Dof基因,Dof基因家族成员参与玉米不同生理发育过程中,部分基因可能在氮代谢调控中发挥积极作用。

关键词: 玉米, Dof, 转录因子, 基因家族,

Abstract: 【Objective】The study was carried out for genome-wide identification and analysis of the maize Dof (DNA binding with one finger) gene family. 【Method】Based on maize V3 version, a genome-wide overview of Dof gene family in maize, including the gene structures, phylogeny, and chromosome distribution, and mRNA expression atlas at 18 different development stages were made. A survey of the transcriptomes of V3 stage leaf tissues collected under nitrogen sufficient and limiting conditions was conducted using RNAseq. 【Result】The analyses revealed 46 Dof genes harbored in maize genome, named ZmV3Dof1- ZmV3Dof46. According to the phylogenetic relationships and sequence similarity, the gene family was divided into 8 subgroups, which ranged in size from 3 to 8 Dof genes. Genome chromosomal location analyses revealed that maize Dofs were distributed on almost all chromosomes, except for chromosome 9. In total, 12 ZmV3Dofs were presented on chromosome 1, 8 and 7 on chromosomes 5 and 3, 4 on chromosome 8, 3 on each of chromosomes 2, 4, 6, 7 and 10. Relatively high densities of Dofs were observed in some chromosomal regions, including the bottom of chromosomes 1, the top and bottom of chromosomes 5. Dof gene expression profiling analysis showed that some of genes have played diverse roles in the process of plant development, indicating the diversity of their function. DNA phylogenetic relationships showed the partial consistency with RNA profiles. There are 35 Dof genes showed different expressions in these two nitrogen treatments, and thirteen out of them showed greater differences. There are 21 Dof genes exhibited a significant response to low nitrogen supply, and eight out of them were induced by low nitrogen condition, suggesting Dof genes may play an important role in the regulation of nitrogen metabolism. 【Conclusion】In this study, the Dof gene family in maize known to date was identified. These findings indicate that members of this gene family may be involved in different plant biological processes, some of which probably are involved in plant nitrogen assimilation and metabolism. The preliminary genomic analysis will provide a foundation for future functional dissection of Dof family gene.

Key words: maize, Dof, transcription factor, gene family, nitrogen