番茄FAD基因家族的鉴定与表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-1090

摘要/Abstract

摘要：

【目的】 脂肪酸脱氢酶（fatty acid desaturase，FAD）是一类催化植物不饱和脂肪酸合成的关键酶，在植物生长发育及逆境胁迫响应中起重要作用。鉴定番茄SlFAD基因家族，为番茄SlFAD基因家族功能研究及遗传改良提供理论依据。【方法】 采用生物信息学方法，对其基因家族成员进行鉴定，并对其理化性质、基因结构、系统发育树和表达模式等方面进行研究。【结果】 在番茄基因组中共鉴定出26个SlFAD基因，可分为4个亚族；理化性质分析显示SlFAD蛋白的氨基酸个数在119-912个之间，分子量介于13 288.27-102 522.25 Da，SlFAD蛋白在番茄中主要以碱性蛋白的性质存在，大部分SlFAD家族成员为稳定蛋白和亲水性蛋白；亚细胞定位预测SlFAD基因家族成员主要存在于内质网；基因特征分析显示同一亚族间的成员具有较为相似的基因结构和保守基序；启动子顺式作用元件分析显示数量最多的是光响应与激素响应相关的元件；染色体定位显示26个SlFAD家族成员共分布在10条染色体上，6号和12号染色体上成员最多；二级结构预测显示26个SlFADs家族成员均以α-螺旋和β-转角为主；转录组数据及RT-qPCR分析表明SlFAD1、SlFAD4和SlFAD18基因在成熟花药中高度表达，SlFAD23在根尖中高度表达，说明SlFAD1、SlFAD4和SlFAD18可能参与花药发育，SlFAD23可能参与根尖发育；低温胁迫下，SlFAD6和SlFAD21表达量被抑制，说明SlFAD6和SlFAD21可能与低温响应有关系，SlFAD1和SlFAD14在低温胁迫初期显著上调，随后又被抑制，说明该基因在低温胁迫初期发挥重要作用。【结论】 SlFAD基因家族在番茄根尖、叶片、花药的生长发育过程及低温胁迫中发挥重要作用。

关键词: 番茄, 脂肪酸脱氢酶, FAD基因家族, 生物信息学, 表达分析

Abstract:

【Objective】 Fatty acid desaturase（FAD）is a key enzyme that catalyzes the synthesis of unsaturated fatty acids in plants, and it plays an important role in plant growth and development and response to adversity stress. This work aims to identify the tomato（Solanum lycopersi）SlFAD gene family and provide a theoretical basis for the study of tomato SlFAD gene family function and genetic improvement. 【Method】 Bioinformatics was used to identify the members of its gene family, and to study its physical and chemical properties, gene structure, phylogenetic tree and expression patterns. 【Result】 The total of 26 SlFAD genes were identified in the tomato genome, which can be divided into 4 sub-families. The analysis of physical and chemical properties showed that the number of amino acids of SlFAD protein was 119-912, the molecular weight was 13 288.27-102 522.25 Da. The SlFAD protein mainly existed in the nature of alkaline protein, and most of the members of the SlFAD family were stable proteins and hydrophilic proteins. Subcellular localization predicted that the members of the SlFAD gene family mainly were located in the endoplasmic reticulum. Genetic feature analysis showed that the members of the same subfamily hadsimilar genetic structure and conservative sequence. The analysis of cis-acting elements in the promotor showed that the largest number of components was related to light response and hormone response. Chromosome positioning revealed that 26 members of the SlFAD family were distributed on 10 chromosomes, and the largest number of members on chromosome 6 and 12. Secondary structure prediction demonstrated that 26 members of the SlFADs family were alpha-spiral and β-turning angle were the main ones. Transcriptome data and RT-qPCR analysis showed that the SlFAD1, SlFAD4 and SlFAD18 genes were highly expressed in mature anthers, and SlFAD23 was highly expressed in the root tip, indicating SlFAD1, SlFAD4 and SlFAD18 participated in the anther development, SlFAD23 participated in the root tip development. Under low-temperature stress, the expressions of SlFAD6 and SlFAD21 were inhibited, indicating that SlFAD6 and SlFAD21 might be related to low-temperature response, SlFAD1 and SlFAD14 at the beginning of low-temperature stress. The period significantly increased and then inhibited, indicating that the gene played an important role in the early stage of low-temperature stress. 【Conclusion】 The SlFAD gene family plays an important role in the growth and development of tomato roots, leaves, anthers and low-temperature stress.

Key words: Solanum lycopersicum, fatty acid dehydrogenase, FAD gene family, bioinformatics, expression analysis

张明亚, 庞胜群, 刘玉东, 苏永峰, 牛博文, 韩琼琼. 番茄FAD基因家族的鉴定与表达分析[J]. 生物技术通报, 2024, 40(7): 150-162.

ZHANG Ming-ya, PANG Sheng-qun, LIU Yu-dong, SU Yong-feng, NIU Bo-wen, HAN Qiong-qiong. Identification and Expression Analysis of FAD Gene Family in Solanum lycopersicum[J]. Biotechnology Bulletin, 2024, 40(7): 150-162.

图/表 10

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基因名称Gene name	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
Actin	ATCTTGGCTTCCCTCAGCAC	GCATCTCTGGTCCAGTAGGAAAT
SlFAD1	TCTACGGTGTGCCCCTTCTA	AGTGATGGGTGAGTGTGCTG
SlFAD4	TCAAGAAAGCCATCCCACCC	TGGCAGATCCAGTAAAGCGG
SlFAD6	CTCTTATCACCACCGCCCTC	GCTGCATTCACGATTGGCAT
SlFAD14	CTTCCGTTTCTGTTTCCGCC	TAAGCGGTGCACTTACCCTC
SlFAD18	CACCTGGTCTGTGGGAGTTC	CCAGCCCCAGAAGTAAACCA
SlFAD21	CGAGGTTGAGGTGCTTGACT	TTCCAGGTTGAGTCGGATGC
SlFAD23	CCGTTACTTTTGCATGGCCT	CCCAAGCTAGCCCTTTCATC

基因名称Gene name	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
Actin	ATCTTGGCTTCCCTCAGCAC	GCATCTCTGGTCCAGTAGGAAAT
SlFAD1	TCTACGGTGTGCCCCTTCTA	AGTGATGGGTGAGTGTGCTG
SlFAD4	TCAAGAAAGCCATCCCACCC	TGGCAGATCCAGTAAAGCGG
SlFAD6	CTCTTATCACCACCGCCCTC	GCTGCATTCACGATTGGCAT
SlFAD14	CTTCCGTTTCTGTTTCCGCC	TAAGCGGTGCACTTACCCTC
SlFAD18	CACCTGGTCTGTGGGAGTTC	CCAGCCCCAGAAGTAAACCA
SlFAD21	CGAGGTTGAGGTGCTTGACT	TTCCAGGTTGAGTCGGATGC
SlFAD23	CCGTTACTTTTGCATGGCCT	CCCAAGCTAGCCCTTTCATC

保守基序名称 Conservative motif name	具体序列分布情况 Specific sequence distribution
Motif 1	WVTAHECGHHAFSDYQWJBDTVGFILHSSJLVPYFSWKYSHRRHHSNTGS
Motif 2	NKVFHNITDTHVLHHLFSTIPHYHAVEATKAIKPLLGEYYQFDGTPIYKA
Motif 3	EVKKHNKAKDCWJIISGKVYDVTKFLDDHPGGDEVLLSATG
Motif 4	RVPSSKPPFTJSDIKKAIPPHCFQRSLVRSFSYVVRDJVLVFILYYIAAT
Motif 5	CIYGVPLLIVNGFIVLITYLHHTHASLPHYDSSEWDWLRGA
Motif 6	NVSGRPYDRFASHYBPYSPJYNDRERLQI
Motif 7	KDATDDFEDVGHSSSAREMLDKYYIGEIDSSTIPTKRKYTP
Motif 8	IWRDFKECIYVEKDEESQDKGVFWYKNK
Motif 9	PYNYLAWPIYWIAQGCVFTGI
Motif 10	QPKGNDWFEKQTAGTIDIACSPQMDWFFGGLQFQLEHHLFPRLPRCQLRK

保守基序名称 Conservative motif name	具体序列分布情况 Specific sequence distribution
Motif 1	WVTAHECGHHAFSDYQWJBDTVGFILHSSJLVPYFSWKYSHRRHHSNTGS
Motif 2	NKVFHNITDTHVLHHLFSTIPHYHAVEATKAIKPLLGEYYQFDGTPIYKA
Motif 3	EVKKHNKAKDCWJIISGKVYDVTKFLDDHPGGDEVLLSATG
Motif 4	RVPSSKPPFTJSDIKKAIPPHCFQRSLVRSFSYVVRDJVLVFILYYIAAT
Motif 5	CIYGVPLLIVNGFIVLITYLHHTHASLPHYDSSEWDWLRGA
Motif 6	NVSGRPYDRFASHYBPYSPJYNDRERLQI
Motif 7	KDATDDFEDVGHSSSAREMLDKYYIGEIDSSTIPTKRKYTP
Motif 8	IWRDFKECIYVEKDEESQDKGVFWYKNK
Motif 9	PYNYLAWPIYWIAQGCVFTGI
Motif 10	QPKGNDWFEKQTAGTIDIACSPQMDWFFGGLQFQLEHHLFPRLPRCQLRK

基因名称Gene name	脱落酸响应Abscisic acid response	厌氧诱导响应Anaerobic induction	生长素响应Auxin response	昼夜节律调控Circadian control	防御和应激响应 Defense and stress response	干旱诱导响应Drought- inducibility	低温响应Low-temperature response	赤霉素响应Gibberellin- response	分生组织表达Meristem expression	水杨酸响应Salicylic acid response	茉莉酸响应MeJA- response
SlFAD1	5	4	0	0	1	1	2	0	1	2	8
SlFAD2	0	5	1	0	1	2	1	0	1	0	6
SlFAD3	4	1	0	1	1	1	4	2	0	1	8
SlFAD4	8	3	2	1	2	1	0	0	0	0	6
SlFAD5	13	3	2	0	1	2	0	2	1	1	6
SlFAD6	1	3	2	1	1	4	0	2	1	2	8
SlFAD7	9	5	2	0	1	2	1	3	2	2	10
SlFAD8	8	4	2	0	0	2	3	2	0	2	6
SlFAD9	4	2	0	0	1	1	1	2	1	2	6
SlFAD10	4	1	0	0	1	0	0	1	0	0	4
SlFAD11	3	3	1	0	0	0	0	2	1	3	4
SlFAD12	3	1	0	1	2	0	2	1	1	3	6
SlFAD13	8	2	1	1	0	1	3	3	1	0	0
SlFAD14	5	3	1	0	2	5	2	4	1	0	4
SlFAD15	4	2	3	0	1	1	0	1	0	2	8
SlFAD16	11	2	2	0	0	0	1	2	1	4	16
SlFAD17	3	3	2	0	0	0	0	0	2	1	0
SlFAD18	1	6	1	1	1	2	2	2	1	1	6
SlFAD19	14	1	5	1	1	1	0	1	4	0	24
SlFAD20	10	7	1	1	2	0	3	2	0	0	2
SlFAD21	5	2	0	0	1	0	1	0	0	0	6
SlFAD22	5	1	0	3	1	0	1	3	2	2	6
SlFAD23	4	3	1	1	0	0	2	2	0	2	10
SlFAD24	3	6	0	3	2	2	3	0	0	2	8
SlFAD25	1	4	2	1	2	1	0	2	2	1	4
SlFAD26	0	6	0	0	0	1	0	2	0	2	8