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草业学报 ›› 2023, Vol. 32 ›› Issue (3): 91-106.DOI: 10.11686/cyxb2022094

• 研究论文 • 上一篇    下一篇

亚麻DMP基因家族的全基因组鉴定与分析

李雯1,2(), 赵丽蓉1,2, 张建平1,2(), 刘自刚1(), 齐燕妮2, 李闻娟2, 谢亚萍2   

  1. 1.甘肃农业大学农学院,甘肃省干旱生境作物重点实验室,甘肃省作物遗传改良与种质资源创新重点实验室,甘肃 兰州 730070
    2.甘肃省农业科学院作物研究所,甘肃 兰州 730070
  • 收稿日期:2022-02-23 修回日期:2022-04-06 出版日期:2023-03-20 发布日期:2022-12-30
  • 通讯作者: 张建平,刘自刚
  • 作者简介:E-mail: 739015868@qq.com
    E-mail: 401101917@qq.com
    李雯(1997-),女,甘肃会宁人,在读硕士。E-mail: 3028149845@qq.com
  • 基金资助:
    国家特色油料产业技术体系;甘肃省农业科学院现代生物育种项目(2020GAAS08);国家自然基金项目(31760426)

Genome-wide identification and analysis of the DMP gene family in flax (Linum usitatissimum

Wen LI1,2(), Li-rong ZHAO1,2, Jian-ping ZHANG1,2(), Zi-gang LIU1(), Yan-ni QI2, Wen-juan LI2, Ya-ping XIE2   

  1. 1.College of Agriculture,Gansu Agricultural University,Key Laboratory of Arid Land Crop of Gansu Province,Key Laboratory of Crop Genetic Improvement and Germplasm Resources Innovation of Gansu Province,Lanzhou 730070,China
    2.Institute of Crop Research,Gansu Academy of Agricultural Sciences,Lanzhou 730070,China
  • Received:2022-02-23 Revised:2022-04-06 Online:2023-03-20 Published:2022-12-30
  • Contact: Jian-ping ZHANG,Zi-gang LIU

摘要:

DMP家族成员是植物特有的膜蛋白,在植物生殖发育及衰老过程中发挥重要作用。亚麻是我国重要的油料及经济作物,目前关于DMP基因家族在亚麻中的分布及功能研究尚未有报道。本研究利用生物信息学方法对亚麻DMP基因家族进行鉴定,对其序列特征、系统进化、复制事件进行了分析,并利用转录组数据和qRT-PCR分析其在不同组织器官及胁迫处理下的表达模式。本研究以陇亚10号基因组为参照,利用同源性分析共鉴定到17个LuDMP成员,命名为LuDMP-1~LuDMP-17,不均匀分布在9条染色体上。序列特征分析结果表明,除LuDMP-9LuDMP-16LuDMP-17 外,其余成员均不含内含子;基因启动子区含有大量激素与逆境胁迫相关响应元件;编码的蛋白氨基酸长度为195~240 aa,分子量为20946~25830 Da,等电点为4.76~9.71;所有蛋白均为疏水性蛋白,含有2~5个跨膜结构域及4~8个motif,其中有4个motif存在于所有LuDMP蛋白;绝大多数蛋白定位于细胞膜。LuDMP家族共有3对串联复制事件和8对片段复制事件,进化过程中经历了强烈的纯化选择。转录组分析结果表明,大多数LuDMP成员在果实和茎中呈现特异性表达模式。系统进化分析将 DMP蛋白分为5个亚族,第III亚族DMP数量最多,含有11个LuDMP成员,各亚族中DMP蛋白具有单子叶或双子叶特异性聚类模式。第IV亚族中的LuDMP-1和LuDMP-7与拟南芥及玉米单倍体诱导基因具有很近的亲缘关系,位于同一进化分支,序列同源性达到67%以上,而且该基因在成熟花药中的表达量明显高于其他组织,推测其为亚麻单倍体诱导的候选基因。本研究在陇亚10号中克隆到了LuDMP-1,全长为699 bp。LuDMP-1/7启动子区域含有激素响应及逆境胁迫相关作用元件,吲哚乙酸、赤霉素、萘乙酸、聚乙二醇、高温及低温处理下, LuDMP-1/7基因表达量均有不同程度的提高,其中对低温和高温的响应最明显,分别较对照提高了约260和600倍。本研究为阐明亚麻DMP蛋白的功能奠定了基础,并为亚麻单倍体育种提供了基因资源。

关键词: 亚麻, DMP基因家族, 单倍体诱导, 表达分析

Abstract:

Members of the DMP genefamily are plant-specific membrane proteins that play an important role in plant reproductive development and senescence. Flax (Linum usitatissimum) is an important oil and cash crop in China. However, there are no reports on the distribution and functions of the DMP gene family in this flax species. We identified the members of the DMP gene family in flax using bioinformatics analyses, and determined their sequence characteristics, phylogeny, and duplication events. Transcriptome data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analyses were used to analyze the transcriptional profiles of LuDMP genes in different tissues and organs and under stress treatments. Seventeen LuDMP genes, designated as LuDMP-1 to LuDMP-17, were identified from the Longya-10 cultivar by homology analysis, and were found to be unevenly distributed on nine chromosomes. Sequence characteristics analysis showed that only LuDMP-9LuDMP-16, and LuDMP-17 had an intron and the other members had none. All members of the LuDMP family contained many cis-acting elements related to hormone and stress responses in their promoter regions. The coding sequences encoded polypeptides with lengths ranging from 195 to 240 amino acids, molecular weights ranging from 20946 to 25830 Da, and theoretical isoelectric points ranging from 4.76 to 9.71. All LuDMP proteins were predicted to be hydrophobic with two to five transmembrane domains and four to eight motifs. Four motifs were present in all LuDMP proteins. Most LuDMP proteins were predicted to localize in the cell membrane. Three tandem duplication and eight segmental duplication gene pairs were identified in the LuDMP gene family, which has been under strong purification selection during the evolution of flax. Transcriptome analyses showed that most LuDMP members are specifically expressed in the fruit and stem. In a phylogenetic analysis, the 17 DMP proteins were divided into five subgroups. Subgroup III was the largest, with 11 members. The DMP proteins in each subfamily exhibited monocotyledon-specific or dicotyledon-specific clustering patterns. LuDMP-1 and LuDMP-7 in subgroup IV showed the highest homology with haploid induction genes in Arabidopsis and maize (Zea mays) and were located in the same evolutionary branch, with sequence homology higher than 67%. Moreover, these two genes showed the highest transcript levels in the mature anther, suggesting that they are candidate genes for inducing flax haploids. We cloned LuDMP-1 from Longya-10 (full-length coding sequence, 699 bp). The promoter regions of LuDMP-1/7 contained hormone- and stress-responsive elements, and both genes showed increased transcript levels under auxin (indole acetic acid, naphthalene acetic acid), gibberellin, polyethylene glycol, and high temperature and low temperature treatments. Their responses to low temperature and high temperature were the most obvious, with transcript levels increased to 260 times and 600 times that in the control, respectively. The results of this study lay a foundation for elucidating the functions of LuDMPs and identify genetic resources for haploid breeding of flax.

Key words: flax, DMP gene family, haploid induction, expression analysis