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

doi:10.16288/j.yczz.23-210

遗传 ›› 2024, Vol. 46 ›› Issue (3): 242-255.doi: 10.16288/j.yczz.23-210

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

韦恒¹(), 刘天鹏², 何继红², 董孔军², 任瑞玉², 张磊², 李亚伟², 郝子义¹, 杨天育¹^,²()

1.甘肃农业大学生命科学技术学院，兰州 730070
2.甘肃省农业科学院作物研究所，兰州 730070

收稿日期:2023-08-01 修回日期:2024-01-10 出版日期:2024-03-20 发布日期:2024-01-26
通讯作者: 杨天育 E-mail:1715414764@qq.com;13519638111@163.com
作者简介:韦恒，硕士研究生，专业方向：小杂粮遗传育种。E-mail: 1715414764@qq.com
基金资助:
第二次青藏高原综合科学考察研究项目(2019QZKK0303);甘肃省科技计划项目(22CX8NA028);国家现代农业产业技术体系项目(CARS-06-14.5-A8)

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

Heng Wei¹(), Tianpeng Liu², Jihong He², Kongjun Dong², Ruiyu Ren², Lei Zhang², Yawei Li², Ziyi Hao¹, Tianyu Yang¹^,²()

1. College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
2. Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China

Received:2023-08-01 Revised:2024-01-10 Published:2024-03-20 Online:2024-01-26
Contact: Tianyu Yang E-mail:1715414764@qq.com;13519638111@163.com
Supported by:
Second Tibetan Plateau Scientific Expedition and Research Program(2019QZKK0303);Science and Technology Planning Project of Gansu Province(22CX8NA028);China Modern Agricultural Industrial Technology System Project(CARS-06-14.5-A8)

摘要/Abstract

摘要：

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。

关键词: 糜子, GRF基因, 转录组, 株高

Abstract:

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.

Key words: Panicum miliaceum L., GRF genes, transcriptome, plant height

韦恒, 刘天鹏, 何继红, 董孔军, 任瑞玉, 张磊, 李亚伟, 郝子义, 杨天育. 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[J]. 遗传, 2024, 46(3): 242-255.

Heng Wei, Tianpeng Liu, Jihong He, Kongjun Dong, Ruiyu Ren, Lei Zhang, Yawei Li, Ziyi Hao, Tianyu Yang. Genome-wide identification of GRF transcription factors and their expression profile in stem meristem of broomcorn millet (Panicum miliaceum L.)[J]. Hereditas(Beijing), 2024, 46(3): 242-255.

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基因名称	引物序列（5'→3'）
PmGRF2	F：GACACAGCACATGGCAACGA R：GTGAGCGGCACATCAACAGA
PmGRF3	F：GCAGCAACAGCAGCACTTCA R：GACGAGATGAGTAGGCACAGGT
PmGRF4	F：CGGTGCTGCTGGAGACTGAT R：GGCAACGATGTTCCGTGATTCT
PmGRF5	F：TTGAGTCGTCACTGTTCTTGGA R：CGGACAACCTGCCTTACATCTA
PmGRF12	F：GCAGCAACAGCAGCACTTCA R：GACGAGATGAGTAGGCACAGGT
PmGRF16	F：GGTCGCAGTCCATTGGTCAGT R：CGGAGTAGGCAGTTCAGCAGAA
PmGRF21	F：TGCCGTCCAGCTTGCTCCTT R：CACCGCCACTTCTTGCCATCAG
Pmactin	F：GGCATCACACCTTCTACAAC R：TCTCGAACATGATCTGGGTC

基因名称	基因ID	氨基酸数	分子质量 (Da)	等电点	不稳定指数	脂肪族氨基酸指数	亲水性平均系数	亚细胞定位	基因染色体定位
PmGRF1	LM01CHG000904	591	61,524.63	6.57	49.17	70.34	-0.270	细胞核	Chr.1
PmGRF2	LM01CHG001244	505	55,604.61	9.29	53.48	63.25	-0.763	细胞核	Chr.1
PmGRF3	LM02CHG001176	259	27,206.29	5.05	53.67	59.31	-0.669	细胞核	Chr.2
PmGRF4	LM04CHG000872	587	61,483.46	6.57	50.54	68.14	-0.325	细胞核	Chr.4
PmGRF5	LM04CHG001174	421	46,386.86	9.33	55.54	59.45	-0.805	细胞核	Chr.4
PmGRF6	LM04CHG002106	375	40,549.16	9.03	64.84	51.23	-0.866	细胞核	Chr.4
PmGRF7	LM06CHG000359	456	64,962.13	7.20	62.26	54.42	-0.548	细胞核	Chr.6
PmGRF8	LM06CHG000847	591	41,514.19	6.57	60.45	64.39	-0.430	细胞核	Chr.6
PmGRF9	LM06CHG000971	618	23,148.19	9.43	49.83	68.17	-0.266	细胞核	Chr.6
PmGRF10	LM07CHG000108	392	38,520.84	7.05	52.44	55.20	-0.646	细胞核	Chr.7
PmGRF11	LM07CHG000642	224	35,200.07	9.64	59.85	56.34	-0.673	细胞核	Chr.7
PmGRF12	LM11CHG001144	356	27,888.04	8.92	55.18	60.79	-0.626	细胞核	Chr.11
PmGRF13	LM12CHG002278	331	23,779.94	9.11	43.53	69.21	-0.228	叶绿体、细胞核	Chr.12
PmGRF14	LM12CHG002388	267	41,572.33	4.93	60.41	64.87	-0.444	细胞核	Chr.12
PmGRF15	LM12CHG002856	229	41,699.42	9.69	56.70	47.23	-0.733	细胞核	Chr.12
PmGRF16	LM13CHG000540	392	40,124.76	7.05	53.80	66.04	-0.481	细胞核	Chr.13
PmGRF17	LM14CHG000674	371	40,471.29	7.68	54.41	59.10	-0.482	细胞核	Chr.14
PmGRF18	LM15CHG002021	254	40,606.53	9.72	55.03	61.14	-0.478	细胞核	Chr.15
PmGRF19	LM16CHG000105	376	38,631.90	8.74	54.94	54.61	-0.635	细胞核	Chr.16
PmGRF20	LM16CHG000628	376	39,074.77	8.81	66.46	61.72	-0.493	细胞核	Chr.16
PmGRF21	LM17CHG001185	358	40,177.86	8.93	53.50	66.46	-0.466	细胞核	Chr.17

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.)

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