背景:泛素化是植物UPS(泛素-蛋白酶体系统)中选择性蛋白质降解的重要调节步骤,参与真核生物的各种生物过程。泛素结合酶在蛋白质泛素化反应过程中起中间作用,因此在调节植物生长和对不利环境条件的反应中起着至关重要的作用。然而,尚未对小麦(TriticumaestivumL.)中的UBC基因家族进行全基因组分析。
结果:在这项研究中,号码,理化性质,基因结构,共线性,利用生物信息学方法分析了小麦TaUBC家族成员的系统发育关系。TaUBC基因在不同组织/器官和发育期的表达模式,以及非生物胁迫处理下的转录水平,使用RNA-Seq数据和qRT-PCR进行分析。同时,基于小麦联合数据库中681个小麦品种的小麦重测序数据,研究了TaUBC25的有利单倍型。分析确定了小麦基因组中总共93个含有UBC结构域的TaUBC家族成员。这些基因在21条染色体上分布不均,在基因成员之间观察到许多重复事件。根据系统发育分析,TaUBC家族分为13个E2组和一个单独的UEV组.我们通过定量实时PCR(qRT-PCR)分析了TaUBC家族基因在不同组织/器官和胁迫条件下的表达。结果表明,一些TaUBC基因在某些组织/器官中特异性表达,并且大多数TaUBC基因对NaCl具有响应,PEG6000和ABA处置有分歧水平的表达。此外,我们根据千粒重(TKW)等关键农艺性状对两种单倍型进行了关联分析,内核长度(KL),内核重量(KW),和内核厚度(KT),在三个环境站点检查122份小麦种质。结果表明,TaUBC25-HapII具有明显较高的TKW,KL,KW,和KT比TaUBC25-HapI.单倍型的分布分析表明,TaUBC25-HapII在小麦自然群体中是首选。
结论:我们的结果确定了小麦中TaUBC家族的93个成员,和几个基因参与谷物发育和非生物胁迫反应。基于TaUBC序列中检测到的SNP,两种单倍型,TaUBC25-HapI和TaUBC25-HapII,在小麦品种中鉴定,并通过关联分析验证了其在小麦育种中的潜在价值。上述结果为阐明TaUBC基因家族的进化关系提供了理论基础,为今后研究家族成员的功能奠定了基础。
BACKGROUND: Ubiquitination is an important regulatory step of selective protein degradation in the plant UPS (ubiquitin-proteasome system), which is involved in various biological processes in eukaryotes. Ubiquitin-conjugating enzymes play an intermediate role in the process of protein ubiquitination reactions and thus play an essential role in regulating plant growth and response to adverse environmental conditions. However, a genome-wide analysis of the UBC gene family in wheat (Triticum aestivum L.) has not yet been performed.
RESULTS: In this study, the number, physiochemical properties, gene structure, collinearity, and phylogenetic relationships of TaUBC family members in wheat were analyzed using bioinformatics methods. The expression pattern of TaUBC genes in different tissues/organs and developmental periods, as well as the transcript levels under abiotic stress treatment, were analyzed using RNA-Seq data and qRT-PCR. Meanwhile, favorable haplotypes of TaUBC25 were investigated based on wheat resequencing data of 681 wheat cultivars from the Wheat Union Database. The analyses identified a total of 93 TaUBC family members containing a UBC domain in wheat genome. These genes were unevenly distributed across 21 chromosomes, and numerous duplication events were observed between gene members. Based on phylogenetic analysis, the TaUBC family was divided into 13 E2 groups and a separate UEV group. We investigated the expression of TaUBC family genes under different tissue/organ and stress conditions by quantitative real-time PCR (qRT-PCR) analysis. The results showed that some TaUBC genes were specifically expressed in certain tissues/organs and that most TaUBC genes responded to NaCl, PEG6000, and ABA treatment with different levels of expression. In addition, we performed association analysis for the two haplotypes based on key agronomic traits such as thousand-kernel weight (TKW), kernel length (KL), kernel weight (KW), and kernel thickness (KT), examining 122 wheat accessions at three environmental sites. The results showed that TaUBC25-Hap II had significantly higher TKW, KL, KW, and KT than TaUBC25-Hap I. The distribution analysis of haplotypes showed that TaUBC25-Hap II was preferred in the natural population of wheat.
CONCLUSIONS: Our results identified 93 members of the TaUBC family in wheat, and several genes involved in grain development and abiotic stress response. Based on the SNPs detected in the TaUBC sequence, two haplotypes, TaUBC25-Hap I and TaUBC25-Hap II, were identified among wheat cultivars, and their potential value for wheat breeding was validated by association analysis. The above results provide a theoretical basis for elucidating the evolutionary relationships of the TaUBC gene family and lay the foundation for studying the functions of family members in the future.