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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (1): 86-98.doi: 10.3724/SP.J.1006.2022.04285

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide identification and characterization of PIF genes and their response to high temperature stress in potato

JIAN Hong-Ju1,2,3(), SHANG Li-Na1,2,3(), JIN Zhong-Hui1,2,3, DING Yi1, LI Yan1,3, WANG Ji-Chun1,2,3, HU Bai-Geng4, Vadim Khassanov5, LYU Dian-Qiu1,2,3,*()   

  1. 1College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
    3Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
    4National Engineering Research Center for Potato, Dezhou 253600, Shandong, China
  • Received:2020-12-29 Accepted:2021-04-14 Online:2022-01-12 Published:2021-05-20
  • Contact: LYU Dian-Qiu E-mail:hjjian518@swu.edu.cn;cxldshanglina@163.com;smallpotatoes@126.com
  • About author:First author contact:** Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(32101659);Science and Technology Partnership Program, Ministry of Science and Technology of China(KY201904016);National Key Research and Development Program of China(2018YFE0127900);Talent Introduction Program of Southwest University Project(SWU019008);Talent Introduction Program of Southwest University Project(SWU020009)

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Abstract:

Phytochrome interacting factors (PIFs) belong to the basic helix-loop-helix (bHLH) transcription factor family, which integrates external environmental signals such as light and temperature with plant endogenous signal pathways, and then form a complex signal transduction network to precisely regulate the growth and development of plants. Up to now, there are few studies of PIF family genes in potato. Identification and analysis of StPIF family members will help to further improve the yield and quality of potatoes. In this study, BlastP analysis was performed in the potato genome database using Arabidopsis PIFs family member protein sequences as source sequences and seven StPIFs family members were identified. Systemic evolution, chromosome distribution, replication events, protein physicochemical properties, gene structure, motif prediction, promoter cis-acting elements, gene expression pattern, and the response to high temperature stress were also conducted. These results showed that all members of the StPIFs gene family contain Motif 1 (bHLH domain) and Motif 2 (APB domain); multiple cis-regulatory elements involved in light response, hormones, drought, low temperature, and circadian rhythm as well as defense and stress response regulatory elements were predicted in the promoter regions of the StPIF genes. Results of gene expression patterns and high temperature stress response at budding stage revealed that StPIFs family members had obvious tissue expression specificity, indicating their functional differentiation, and most StPIFs members had obvious responses to biotic stress and abiotic stresses including high temperature. In conclusion, these foundlings greatly enriched the understanding of the members of the StPIF family, and laid a theoretical foundation for further exploring the functions of StPIFs genes in responses to biotic stress and abiotic stress during potato growth period including high temperature at tuber stage.

Key words: potato (Solanum tuberosum L.), PIF family, bioinformatics, high temperature, the relative expression pattern

Table 1

Primers used in this study"

引物
Primer		 正向序列
Forward sequence (5'-3')		 反向序列
Reverse sequence (5'-3')
ef1α
StPIF1a
StPIF1b
StPIF3
StPIF4
StPIF8		 ATTGGAAACGGATATGCTCCA
GTTTCACACGTACCCGATAATG
GTACTTCGACTGTAGAGATCCG
GAGTTTAGGTATGGGTATGGGG
TGAACTTCCTGTTCCACATCAA
AATCAGTGTGTACCGAGTTG		 TCCTTACCTGAACGCCTGTCA
GAAATGTCACATGTAGTCGTCG
TTTGAATCCACAATCGTCGATG
TACAGCTATTCCTGGATAAGCG
TTCATTAGGATCATAGCCTGGC
CTAACCCATGCATTGCTAAC

Table 2

Sequence characteristics of PIFs family members in potato"

基因
Gene		 基因编号
Gene ID		 氨基酸数目
Number of amino acids (aa)		 分子量Molecular weight (kD) 等电点Isoelectric point (pI) 位置
Location		 功能域
Functional domains
(Start-End, bp)
StPIF1a PGSC0003DMG400018950 578 62.94 6.42 ch09:45450532-45460120 343-406/bHLH
StPIF1b PGSC0003DMG400014705 515 56.41 5.13 ch06:2038519-2047215 309-372/bHLH
StPIF3 PGSC0003DMG400018280 708 75.83 7.26 ch01:79007967-79013234 450-512/bHLH
StPIF4 PGSC0003DMG401015926 517 57.44 7.09 ch07:42074703-42078252 331-394/bHLH
StPIF7a PGSC0003DMG400024554 437 48.17 6.79 ch03:55395567-55398080 237-298/bHLH
StPIF7b PGSC0003DMG400033087 416 46.81 8.71 ch06:51466651-51468759 195-252/bHLH
StPIF8 PGSC0003DMG400025976 464 50.75 7.62 ch01:70077080-70081427 281-344/bHLH

Fig. 1

Alignment of PIFs amino acid sequences from Arabidopsis thaliana, Solanum tubersum, and Solanum lycopersicum A: active phytochrome B-binding (APB) domain; B: active phytochrome A-binding (APA) domain; C: basic helix-loop-helix (bHLH) DNA-binding domain."

Fig. 2

Phylogenic tree of PIFs gene family At: Arabidopsis thaliana; St: Solanum tubersum; Sl: Solanum lycopersicum; Os: Oryza sativa; Zm: Zea mays."

Fig. 3

Structure and conserved motif of PIFs gene in potato Motif: conservative base sequence; UTR: untranslated region; CDS: coding region sequence."

Fig. 4

Conserved motifs of PIFs family members in potato"

Fig. 5

Collinearity analysis of the PIFs gene family in potato"

Fig. 6

Collinearity analysis of PIFs genes among Solanum tubersum, Arabidopsis thaliana, and Solanum lycopersicum"

Fig. 7

Cis-elements in the promoter of StPIFs genes in responses to various stresses and plant development in potato"

Fig. 8

Conserved motif of PIFs promoter sequence in potato"

Fig. 9

Conserved motifs of promoters of PIFs family in potato"

Fig. 10

PIFs promoter sequence binding transcription factor in potato"

Fig. 11

Heat map of PIFs genes in response to environmental stress in potato"

Fig. 12

Relative expression level of StPIFs genes in different tissues under high temperature stress"

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