Crops ›› 2022, Vol. 38 ›› Issue (2): 54-63.doi: 10.16035/j.issn.1001-7283.2022.02.008

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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 E-mail:luping10925@163.com;lixueyin2010@163.com

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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

Table 1

Basic information of sit-miR169 family members"

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

Fig.1

Chromosome location of sit-MIR169 genes"

Fig.2

Phylogenetic analysis of sit-miR169 family"

Fig.3

Phylogenetic analysis of the miR169 family in foxtail millet, rice and Arabidopsis ▲ represent sit-MIR169, ● represent osa-MIR169, ■ represent ath-MIR169"

Fig.4

Base conservativeness of sit-miR169 sequences a: precursor sequence; b: mature sequence; c: star sequence"

Fig.5

Secondary stem-loop structure of sit-MIR169 a-g: sit-MIR169a - sit-MIR169g, h-o: sit-MIR169h - sit-MIR169o. Colors from blue to red indicate the probability of base pairing from 0 to 1"

Fig.6

Expression of sit-miR169 in different tissues “*”represents star sequences"

Table 2

Prediction of miR169 target genes in foxtail millet"

Fig. 7

Expression of sit-miR169 target genes in different tissues and environment conditions L1-2W-HL: leaf 1, 2 weeks, highlight; L2-2W-HL: leaf 2, 2 weeks, highlight; L3-2W-HL: leaf 3, 2 weeks, highlight; L4-2W-HL: Leaf 4, 2 weeks, highlight; L5-2W-HL: leaf 5, 2 weeks, highlight; L6-2W-HL: leaf 6, 2 weeks highlight; TA-BL: total aerial, blue light; TA-RL: total aerial, red light; TA-D: total aerial, dark; TA-FRL: total aerial, far red light; R-10D-L: root, 10 days, light; R-U: root, urea; R-A: root, ammonia; R-N: root, nitrate; R-D: root, drought;S-1W-HL: shoot, 1 week, highlight; P-S1-HL: panicle, stage 1, highlight; P-S2-HL: panicle, stage 2, highlight; ES-5D-D: eiolated seedling, 5 days, dark; GS-6D-D: germ shoot, 6 days, dark"

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