小麦 SPL 基因家族的全基因组鉴定、系统发育和表达分析。
Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat.
机构信息
College of Agronomy, Northwest A&F University, Yangling, 712100, China.
College of Life Science, Wuhan University, Wuhan, 430072, China.
出版信息
BMC Plant Biol. 2020 Sep 11;20(1):420. doi: 10.1186/s12870-020-02576-0.
BACKGROUND
Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat.
RESULTS
In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR).
CONCLUSIONS
The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.
背景
植物特有的 SPL 基因家族（SBP 结合蛋白样）成员含有 SBP 保守结构域，参与植物生长发育的调控，包括植物花和植物表皮毛的发育、植物应激反应和次生代谢物的合成。该家族已在各种植物中被鉴定出来。然而，在小麦全基因组水平上，对 SPL 基因家族还没有进行系统的分析。
结果
本研究利用比较基因组学方法鉴定了 56 个小麦 TaSPL 基因，根据它们在染色体上的分布，重新命名为 TaSPL001-TaSPL056。根据无根邻接聚类系统发育树、基因结构和基序分析，将 56 个 TaSPL 基因分为 8 个亚组。共鉴定出 81 个 TaSPL 基因对是由复制事件产生的，64 个相互作用的蛋白质分支被鉴定为参与蛋白质相互作用网络。通过定量实时聚合酶链反应（qRT-PCR）检测了 21 个随机选择的 TaSPL 基因在不同组织（根、茎、叶和花序）和 4 种处理（脱落酸、赤霉素、干旱和盐）下的表达模式。
结论
小麦基因组含有 56 个 TaSPL 基因，同一亚家族的基因具有相似的基因结构和基序。TaSPL 基因的扩张是通过片段复制事件发生的。结合转录和 qRT-PCR 分析的结果，发现这些 TaSPL 基因大多数调节花序和穗发育。此外，我们发现 13 个 TaSPLs 被脱落酸上调，表明 TaSPL 基因在幼苗阶段的脱落酸介导途径中发挥积极作用。本研究为小麦 SPL 基因家族提供了全面的信息，为阐明 TaSPLs 的生物学功能和提高小麦产量奠定了基础。
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