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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1334-1346.doi: 10.3724/SP.J.1006.2018.01334

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Identification and Bioinformatics Analysis of the PIN Family Gene in Brassica napus

Kun GAO1,2(),Ying-Peng HUA1,2,Hai-Xing SONG1,2,Chun-Yun GUAN3,Zhen-Hua ZHANG1,2,Ting ZHOU1,2,*()   

  1. 1 College of Resource and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
    2 Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
    3 Hunan Branch, National Oil Crops Improvement Center, Changsha 410128, Hunan, China
  • Received:2018-01-30 Accepted:2018-06-12 Online:2018-09-10 Published:2018-09-12
  • Contact: Ting ZHOU E-mail:gaokun0874@foxmail.com;zhoutingplant@foxmail.com
  • Supported by:
    This study was supported by the National Key R&D Program of China(2017YFD0200103);National Natural Science Foundation of China(31101596);National Natural Science Foundation of China(31372130);Research Starting Foundation for New Teachers of Hunan Agricultural University(30555|550100100021);Youth Foundation of Hunan Agricultural University(17QN40);China Agriculture Research System

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Abstract:

The PIN family is a type of important carrier elements that regulate the polar transportation of auxin. The PIN genes encode auxin efflux carriers with multiple transmembrane domains that mediate auxin transport in plants. However, there is a lack of systematic research in the genome of complexity Brassica napus. In this study, the BnPIN genes were screened from the Brassica Database using bioinformatics, and study on molecular characteristics of BnPIN proteins, such as copy number variations, transmembrane domains, conserved motifs, chromosomal locations, phylogenetic relationships, secondary and three-dimensional structures, and high-throughput transcriptome sequencing was used to analyze the transcriptional level under low nitrate stress. The results showed that most of the BnPIN proteins which is belonged to the stable protein consisting of basic amino acids. The BnPIN family proteins contained secondary structures similar to those of Arabidopsis PINs accompanied by conserved N-terminal domains. The phylogenetic analysis showed that BnPIN genes were similar to the corresponding homologs of Brassica oleracea and Brassica rapa. High-throughput transcriptome analysis showed that the BnPIN1s, BnPIN2s, and BnPIN3s genes were mainly expressed in roots of Brassica napus under long-term (72 h) low nitrate (NO3 -) stress. The BnPIN6s and BnPIN8s genes were mainly expressed in the shoot and limited NO3 - repressed the BnPIN6s expression. This study is valuable for the research that the roles of the BnPIN family in the regulation of auxin transport. Our results also provide reference for the integrated genomic and transcriptomic studies of gene family in plant species with complex genomes.

Key words: Brassica napus, auxin, PIN, gene family, bioinformatics

Fig. 1

Copy number variation of PIN family genes in Brassica napus, Arabidopsis thaliana, Brassica rapa, and Brassica oleraceaThe number at the top of the histogram is the number of genes copied for that species."

Fig. 2

Domains architecture of BnPINsTransmembrane regions are in blue and low complexities are in pink."

Fig. 3

Amino acid sequence alignment and conserved domain analysis of PIN family in Brassica napusThe yellow area is a highly conserved amino acid site."

Fig. 4

Chromosome mapping of the 23 BnPINs"

Fig. 5

Distribution of conserved motifs in the BnPINsThe different colors on the right correspond to the positions of different conserved motifs on the series, respectively."

Fig. 6

Evolutionary relationships of BnPINs taxaDifferent clades are in different colors, I and II above clades indicate the two subgroups of PIN family."

Fig. 7

Secondary structure analysis of BnPIN5b proteinGOR4 and PSIPRED are two tools for the secondary structure analysis."

Fig. 8

Prediction of three-dimensional structure of BnPIN2a proteinThe three-dimensional structure predicts that the crystal is a transporter."

Fig. 9

Transcriptome analysis of PIN family genes in Brassica napus under low nitrate concentration conditionsS: shoot; R: root; 0, 3, and 72 (h) represent the time course of nitrogen deficiency. The results represent the average of three biological replicates."

Fig. 10

Co-expression network analysis and expression of PIN family genes in Brassica napus under low nitrate concentration conditionA: co-expression network analysis; B: expression of PIN family genes; cycle nodes represent genes, and the size of the nodes represents the power of the interrelation among the nodes by degree value, edges between two nodes represent interactions between genes; S: shoot; R: root; 0, 3, and 72 (h) represents the time course of nitrogen deficiency. The results represent the average of three biological replicates."

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