He Yajun, Mao Shaoshuai, Gao Yulong, Zhu Liying, Wu Daoming, Cui Yixin, Li Jiana, Qian Wei
College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
Yunnan Academy of Tobacco Agricultural Sciences, Yuxi 653100, China.
PLoS One. 2016 Jun 20;11(6):e0157558. doi: 10.1371/journal.pone.0157558. eCollection 2016.
WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions, indicating tandem duplicate WRKYs in the adaptive responses to environmental stimuli during the evolution process. Our results provide a framework for future studies regarding the function of WRKY genes in response to stress in B. napus.
WRKY转录因子在植物对环境胁迫刺激的响应中发挥着重要作用。通过全基因组结构域分析，我们在甘蓝型油菜的测序基因组中鉴定出287个含有343个WRKY结构域的WRKY基因，其中A亚基因组中有139个，C亚基因组中有148个。基于系统发育分析，这些基因被分为八组。在这343个WRKY结构域中，共有26个成员在WRKY结构域上存在差异，其中21个属于第一组。这一发现表明，与其他组的基因相比，第一组中的WRKY基因更具活性和变异性。通过对甘蓝型油菜WRKY基因家族进行全基因组鉴定和分析，我们观察到了基因组加倍、染色体/片段重复和串联重复。所有这些重复都导致了WRKY基因家族的扩张。检测到的重复片段表明，基因组加倍事件发生在两个二倍体祖先白菜和甘蓝结合形成甘蓝型油菜之前。对甘蓝型油菜的公共微阵列数据库和EST数据库分析表明，74个WRKY基因在胁迫条件下被诱导或优先表达。根据公共QTL数据，我们在与各种胁迫耐受性相关的31个QTL区域中鉴定出77个WRKY基因。我们通过qRT-PCR进一步评估了26个BnaWRKY基因在多种胁迫下的表达情况。大多数基因受到低温、盐度和干旱胁迫的诱导，这表明WRKY基因在甘蓝型油菜的胁迫响应中发挥着重要作用。此外, 三个BnaWRKY基因对这三种多重胁迫同时有强烈响应，这表明这3个WRKY基因在胁迫耐受性方面可能具有多功能作用，并有可能用于培育新的油菜品种。我们还发现了六对串联重复序列在各种胁迫条件下表现出相似的表达谱，其中三对位于与胁迫相关的QTL区域，这表明串联重复的WRKY基因在进化过程中对环境刺激的适应性反应中发挥作用。我们的研究结果为今后研究WRKY基因在甘蓝型油菜胁迫响应中的功能提供了一个框架。
