Genome-wide identification and expression analysis of U-box gene family in wild emmer wheat (Triticum turgidum L. ssp. dicoccoides)
Genome-wide identification and expression analysis of U-box gene family in wild emmer wheat (Triticum turgidum L. ssp. dicoccoides)
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野生二粒小麦U-box基因家族的全基因组鉴定和表达分析（Triticum turgidum L. ssp. dicoccoides）
DOI：
10.1016/j.gene.2021.145840
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发表时间：
2021
期刊：
影响因子：
3.5
通讯作者：
Nie Xiaojun
中科院分区：
文献类型：
--
作者：
Yang Guang;Ying Gao;Wang Zhenyu;Pan Wenqiu;Linghu Bin;Pan Yan;Song Weining;Cui Licao;Nie Xiaojun
本研究通过基因组搜索的方法在野生二粒小麦（TdPUBs）中鉴定了82个U-box基因。系统发育分析将它们分为7个类群，同一类群的基因具有相似的外显子-内含子结构、基序组织和顺式元件组成。不同物种间U-box基因的同线性分析表明，片段重复和多倍化是TdPUBs扩增的主要原因。此外，还研究了野生二粒小麦、驯化二粒小麦和硬粒小麦的U盒基因的遗传变异。结果表明，四倍体二粒小麦在驯化过程中出现了明显的遗传瓶颈。其中12个TdPUB与已知的驯化相关QTL共定位。最后，通过RNA-seq分析鉴定了组织特异性和胁迫响应性TdPUB基因。结合对19个盐响应TdPUBs的qPCR验证，获得了与盐响应相关的候选基因。为进一步了解U-box家族在二粒小麦及其他小麦品种中的调控作用奠定了基础。
In this study, 82 U-box genes were identified in wild emmer wheat (TdPUBs) through a genome-search method. Phylogenetic analysis classified them into seven groups and the genes belonging to the same group shared the similar exon–intron structure, motif organization andcis-element compositions. Synteny analysis of the U-box genes between different species revealed that segmental duplication and polyploidization mainly contributed to the expansion of TdPUBs. Furthermore, the genetic variations of U-box were investigated in wild emmer, domesticated emmer and durum wheat. Results showed that significant genetic bottleneck has occurred during domestication process of tetraploid emmer wheat. Meanwhile, 12TdPUBswere co-located with known domestication related QTLs. Finally, the tissue-specific and stress-responsiveTdPUBgenes were identified through RNA-seq analysis. Combined with qPCR validation of 19 salt-responsiveTdPUBs, the candidates involving in salt response were obtained. It lays the foundation to better understand the regulatory roles of U-box family in emmer wheat and beyond.