糜子GRF转录因子全基因组鉴定及在茎分生组织中的表达特征

Genome-wide identification of GRF transcription factors and their expression profile in stem meristem of broomcorn millet(Panicum miliaceum L.)

为了解糜子(Panicum miliaceum L.)GRF(growth-regulating factor)基因家族成员全基因组信息及其在营养生长阶段分生组织中的表达特征,本研究通过生物信息学和转录组测序相结合的方法,分析了糜子GRF基因家族成员的染色体分布、基因结构、系统进化关系、顺式作用元件及其在营养器官茎分生组织中的表达特征。结果表明:糜子GRF基因家族包含21个成员,家族成员含有1~4个内含子和2~5个外显子,编码蛋白长度为224~618个氨基酸,等电点为4.93~9.69;PmGRF基因不均等分布于12条染色体上,除PmGRF13定位于细胞核和叶绿体外,其余均定位于细胞核。系统进化分析显示,糜子21个GRF基因分为4个亚族(A、B、C和D)。顺式作用元件分析表明,在糜子GRF基因上游2000 bp序列中,普遍存在数目不等、种类不同的参与光响应、激素响应、干旱诱导、低温和其他环境胁迫响应的顺式作用元件。对糜子高秆品种陇糜12号和矮秆品种张778拔节期节间和节部分生组织分别取样进行转录组测序及qRT-PCR分析,结果发现:PmGRF3、PmGRF12在矮秆品种张778中表达量显著高于高秆品种陇糜12号,而PmGRF4、PmGRF16和PmGRF21的表达特征与之相反;PmGRF2和PmGRF5在张778节间分生组织中的表达量显著高于陇糜12号,其余GRF基因不表达或差异表达不显著,表明PmGRF2、PmGRF3、PmGRF4、PmGRF5、PmGRF12、PmGRF16和PmGRF21等7个基因与糜子株高的形成相关。

To understand the genome-wide information of the GRF family genes in broomcorn millet and their expression profile in the vegetative meristems,bioinformatic methods and transcriptome sequencing were used to analyze the characteristics,physical and chemical properties,phylogenetic relationship,chromosome distribution,gene structure,cis-acting elements and expression profile in stem meristem for the GRF family members.The results showed that the GRF gene family of millet contains 21 members,and the PmGRF gene is unevenly distributed on 12 chromosomes.The lengths of PmGRF proteins vary from 224 to 618 amino acids,and the isoelectric points are between 4.93-9.69.Each member of the family has 1-4 introns and 2-5 exons.The protein PmGRF13 is localized in both the nucleus and chloroplast,and the rest PmGRF proteins are located in the nucleus.Phylogenetic analysis showed that the 21 GRF genes were divided into 4 subfamilies(A,B,C and D)in broomcorn millet.The analysis of cis-acting elements showed that there were many cis-acting elements involved in light response,hormone response,drought induction,low temperature response and other environmental stress responses in the 2000 bp sequence upstream of the GRF genes.Transcriptome sequencing and qRT-PCR analyses showed that the expression levels of PmGRF3 and PmGRF12 in the dwarf variety Zhang778 were significantly higher than those of the tall variety Longmi12 in the internode and node meristems at the jointing stage,while the expression patterns of PmGRF4,PmGRF16 and PmGRF21 were reverse.In addition,the expression levels of PmGRF2 and PmGRF5 in the internode of Zhang778 were significantly higher than Longmi12.The other GRF genes were not or insignificantly expressed.These results indicated that seven genes,PmGRF2,PmGRF3,PmGRF4,PmGRF5,PmGRF12,PmGRF16 and PmGRF21,were related to the formation of plant height in broomcorn millet.