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作物杂志,2022, 第2期: 54–63 doi: 10.16035/j.issn.1001-7283.2022.02.008

• 遗传育种·种质资源·生物技术 • 上一篇    下一篇

谷子miR169家族及其靶基因的鉴定与功能分析

卢平1(), 康庆芳1, 赵孟瑶1, 张凤洁2, 武强强2, 马芳芳2, 王宇珅2, 韩渊怀2, 王兴春1, 李雪垠1,*()   

  1. 1山西农业大学生命科学学院,030801,山西晋中
    2山西农业大学农学院,030801,山西晋中
  • 收稿日期:2021-04-19 修回日期:2022-02-12 出版日期:2022-04-15 发布日期:2022-04-24
  • 通讯作者: 李雪垠
  • 作者简介:卢平,主要从事植物生物信息学研究,E-mail： luping10925@163.com
  • 基金资助:
    国家重点研发计划(2018YFD1000700);国家重点研发计划(2018YFD1000706);国家自然科学基金(31801434);山西农业大学科技创新基金项目(2017YJ28);山西省重点研发计划项目(201803D221019-2);山西省应用基础研究项目(201801D221298);山西农业大学科技创新基金项目(2017YJ01)

Identification and Functional Analysis of miR169 Family and Its Target Genes in Setaria italica

Lu Ping1(), Kang Qingfang1, Zhao Mengyao1, Zhang Fengjie2, Wu Qiangqiang2, Ma Fangfang2, Wang Yushen2, Han Yuanhuai2, Wang Xingchun1, Li Xueyin1,*()   

  1. 1College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
    2College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
  • Received:2021-04-19 Revised:2022-02-12 Online:2022-04-15 Published:2022-04-24
  • Contact: Li Xueyin

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摘要：

microRNA广泛参与植物中多个生长发育过程,miR169家族是最保守的miRNA家族之一。对谷子miR169（sit-miR169）家族进行生物信息学分析,包括染色体分布、系统进化、碱基保守性、二级结构和sit-miR169及其靶基因的表达。鉴定了15个sit-miR169,分布于7条染色体上。系统进化分析显示,sit-miR169家族前体sit-MIR169大致可以分为2簇,部分sit-MIR169成员与水稻osa-MIR169家族成员亲缘关系较近。sit-miR169的前体均可形成稳定的二级茎环结构,成熟体均产生于前体的5′端臂上,且成熟序列的碱基保守性很强。sit-miR169在花、叶和根中均有表达,具有明显组织表达特异性。sit-miR169的靶基因主要是NF-YA转录因子基因,此外还有L型凝集素类受体蛋白激酶、ω-6脂肪酸去饱和酶、转运蛋白Sec1a、SDG40蛋白、环指跨膜蛋白和核糖体大亚基假尿苷合酶SVR1基因等。miR169通过调控靶基因,尤其是NF-YA的表达量来影响植物的生长发育和对环境的应答。谷子NF-YA基因主要在根和穗中表达,表现出明显的组织表达特异性。此外,sit-miR169靶基因的表达受环境诱导,如干旱条件能进一步诱导Seita.9G521100基因在根中的表达。

关键词: 谷子, miRNA, miR169, 靶基因, 生物信息学

Abstract:

MicroRNA are widely involved in various plant growth and development processes, and the miR169 family is one of the most conservative miRNA families. In this study, a series of bioinformatic analyses were conducted on the miR169 family of Setaria italica (sit-miR169), including chromosomal distribution, phylogeny, base conservativeness, secondary structures, and the expression of sit-miR169 and its target genes. We identified 15 sit-miR169 distributed on seven chromosomes. Phylogenetic analysis showed that the sit-MIR169 family could be mainly divided into two clusters, and some members of sit-MIR169 were closely related to the members of the osa-MIR169 family in rice. All the precursors of sit-miR169 formed a stable secondary stem-loop structure, and the mature ones were all generated from the 5'-end arms of the precursors, and the mature sequences had a strong base conservativeness. The sit-miR169 was expressed in flowers, leaves, and roots, with obvious tissue specificity. The target genes of sit-miR169 were mainly NF-YA transcription factor genes, in addition to L-type lectin-domain containing receptor kinase, ω-6 fatty acid desaturase, protein transporter Secla, protein SDG40, ring finger transmembrane domain-containing protein, and ribosomal large pseudouridine synthase SVR1 genes. The miR169 affected plant growth and development and environmental response by regulating the expression of target genes, especially the NF-YA gene. The NF-YA gene in Setaria italica was mainly expressed in roots and spikes, showing obvious specificity tissue expression. In addition, the expression of sit-miR169 target genes was induced by the environmental conditions, for example, drought condition further induced the expression of Seita.9G521100 in roots.

Key words: Setaria italica, miRNA, miR169, Target gene, Bioinformatics

表1

sit-miR169家族成员的基本信息

miRNA miRNA基因座
miRNA locus		 染色体定位
Chromosome location		 成熟序列
Mature sequence		 碱基数
Base
number		 星标序列
Star sequence		 碱基数
Base
number
sit-miR169a sit-MIR169a Chr1: 6337067-6337254 (-) CAGCCAAGGAUGACUUGCCGG 21 GCAAGUUUGUCCAUGGCUACG 21
sit-miR169b sit-MIR169b Chr4: 30531819-30531966 (+) CAGCCAAGGAUGACUUGCCGG 21 GGCAAGUUGUCCUUGGCUACA 21
sit-miR169c sit-MIR169c Chr6: 1523821-1523981 (-) CAGCCAAGGAUGACUUGCCGG 21 GCAAGUCUGUCCUUGGCUACA 21
sit-miR169d sit-MIR169d Chr6: 1522499-1522640 (-) CAGCCAAGGAUGACUUGCCGG 21 GCAAGUCUGUCCUUGGCUACA 21
sit-miIR169e sit-MIR169e Chr7: 29380903-29381033 (-) CAGCCAAGGAUGACUUGCCGG 21 GCAAGUCUGUCCUUGGCUACA 21
sit-miR169f sit-MIR169f Chr1: 37871079-37871206 (-) UAGCCAAGGAUGACUUGCCGG 21 AGGUUUUUCUCGCUGGCUACA 21
sit-miR169g sit-MIR169g Chr2: 36921080-36921208 (+) UAGCCAAGGAUGACUUGCCUG 21 AGGCAGUCUCCUUGGCUAGCC 21
sit-miR169h sit-MIR169h Chr2: 36923990-36924147 (+) UAGCCAAGGAUGACUUGCCUG 21 AGGCAGUCUCCUUGGCUAGUC 21
sit-miR169i sit-MIR169i Chr2: 36926242-36926373 (+) UAGCCAAGGAUGACUUGCCUG 21 AGGCAGUCUCCUUAGGUAGUC 21
sit-miR169j sit-MIR169j Chr2: 30310044-30310172 (-) UAGCCAAGGAUGACUUGCCUG 21 GGCAAGUCAUCUGUGACUACG 21
sit-miR169k sit-MIR169k Chr3: 6158109-6158242 (+) UAGCCAAGAAUGACUUGCCU 20 AUGGUAGGCAUUCUGGUUAAG 21
sit-miR169l sit-MIR169l Chr6: 33994504-33994663 (+) UAGCCAAGGAUGACUUGCCUG 21 CGGCAGUCUCCUUGGCUAGCC 21
sit-miR169m sit-MIR169m Chr6: 33997852-33997981 (+) UAGCCAAGGAUGACUUGCCUG 21 GGGCAGUCUCCUUGGCUAGCC 21
sit-miR169n sit-MIR169n Chr6: 34000992-34001127 (+) UAGCCAAGGAUGACUUGCCUG 21 AGGCAGUCUCCUUGGCUAGCC 21
sit-miR169o sit-MIR169o Chr8: 12119169-12119306 (+) UAGCCAAGAAUGACUUGCCU 20 GGCGAGUCUUCUUGGCUAGCC 21

图1

sit-MIR169基因的染色体定位

图2

sit-miR169家族的系统进化分析

图3

谷子、水稻和拟南芥miR169家族系统进化分析 ▲代表sit-MIR169,●代表osa-MIR169,■代表ath-MIR169

图4

sit-miR169序列碱基保守性 a：前体序列;b：成熟序列;c：星标序列

图5

sit-MIR169的二级茎环结构 a~g：sit-MIR169a - sit-MIR169g,h~o：sit-MIR169h - sit-MIR169o。颜色由蓝到红表示碱基配对概率由0到1

图6

sit-miR169在不同组织中的表达情况 “*”代表星标序列

表2

谷子miR169靶基因预测

图7

sit-miR169靶基因在不同组织和环境诱导条件下的表达情况 L1-2W-HL：叶1,2周,强光处理;L2-2W-HL：叶2,2周,强光处理;L3-2W-HL：叶3,2周,强光处理;L4-2W-HL：叶4,2周,强光处理;L5-2W-HL：叶5,2周,强光处理;L6-2W-HL：叶6,2周,强光处理;TA-BL：地上部分,蓝光处理;TA-RL：地上部分,红光处理;TA-D：地上部分,暗处理;TA-FRL地上部分,远红光处理;R-10D-L：根,10d,光照;R-U：根,尿素处理;R-A：根,氨处理;R-N：根,硝酸盐处理;R-D：根,干旱处理;S-1W-HL;芽,1周,强光处理;P-S1-HL：穗,时期1,强光处理;P-S2-HL：穗,时期2,强光处理;ES-5D-D：白化苗,5d,暗处理;GS-6D-D：胚芽,6d,暗处理

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