JCR-Genome-wide identification of Gossypium INDETERMINATE DOMAIN genes and their expression profiles in ovule development and abiotic stress responses

ALI Faiza, QANMBER Ghulam, LI Yonghui, MA Shuya, LU Lili, YANG Zuoren, WANG Zhi and LI Fuguang

[背景] INDETERMINATE DOMAIN（IDD）转录因子是植物中一类保守的超家族蛋白，在植物生长发育的很多过程（如开花）都发挥重要作用。棉花作为一种重要的多倍体经济作物，IDD基因在其多倍体化和生长发育当中的作用和机制还未有报道。

[结果] 本研究分别从亚洲棉（Gossypium arboreum）、雷蒙德氏棉（G. raimondi）和陆地棉（G. hisutum）中鉴定了22、23 和65个IDD基因。序列分析表明GhIDDs具有高度保守的外显子-内含子分布模式和蛋白结构域。系统进化分析表明全基因组复制、染色体片段复制和串联复制等多种类型的基因复制事件导致了陆地棉中IDD基因数量的加倍，同时自然选择压力也在GhIDDs基因进化中发挥重要作用。对陆地棉中多个IDD基因的时空表达模式进行分析发现，大部分GhIDDs在开花7天后的胚珠中高表达，暗示它们可能在纤维伸长期和种子发育中发挥重要作用。在不同的非生物胁迫处理下，多个GhIDDs表达上调，表明GhIDDs可能通过不同的途径参与棉花生长发育中的多种非生物胁迫反应，但它们的具体作用和机制还不清楚。

[结论] 综上所述，本研究鉴定和分析了棉花中IDD基因的系统进化机制和转录表达模式，为进一步了解棉花IDD基因家族的功能和棉花生长发育过程转录调控的作用机理提供了理论基础。

Abstract:

[Background] INDETERMINATE DOMAIN (IDD) transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development, such as flower induction in term of flowering control. Till date, systematic and functional analysis of IDD genes remained infancy in cotton.

[Results] In this study, we identified total of 162 IDD genes from eight different plant species including 65 IDD genes in Gossypium hirsutum. Phylogenetic analysis divided IDDs genes into seven well distinct groups. The gene structures and conserved motifs of GhIDD genes depicted highly conserved exon-intron and protein motif distribution patterns. Gene duplication analysis revealed that among 142 orthologous gene pairs, 54 pairs have been derived by segmental duplication events and four pairs by tandem duplication events. Further, Ka/Ks values of most of orthologous/paralogous gene pairs were less than one suggested the purifying selection pressure during evolution. Spatiotemporal expression pattern by qRT-PCR revealed that most of the investigated GhIDD genes showed higher transcript levels in ovule of seven?days post anthesis, and upregulated response under the treatments of multiple abiotic stresses.

[Conclusions] Evolutionary analysis revealed that IDD gene family was highly conserved in plant during the rapid phase of evolution. Whole genome duplication, segmental as well as tandem duplication significantly contributed to the expansion of IDD gene family in upland cotton. Some distinct genes evolved into special subfamily and indicated potential role in the allotetraploidy Gossypium hisutum evolution and development. High transcript levels of GhIDD genes in ovules illustrated their potential roles in seed and fiber development. Further, upregulated responses of GhIDD genes under the treatments of various abiotic stresses suggested them as important genetic regulators to improve stress resistance in cotton breeding.

Keywords:

Upland cotton; IDD transcription factor; Gene duplication; Collinearity; Spatiotemporal; expression; Abiotic stresses

Journal of Cotton Research. 2019; 2:3

https://doi.org/10.1186/s42397-019-0021-6

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0021-6