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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (9): 2297-2309.doi: 10.3724/SP.J.1006.2024.34193

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

Genome-wide identification and expression analysis of TIFY gene family in potato (Solanum tuberosum L.)

QI Jia-Min1,*(), XU Chun-Miao2, XIAO Bin2   

  1. 1Anding Unit, Administrative Enforcement of Law in Agriculture, Dingxi 743000, Gansu, China
    2Horticulture Workstation of Anding District, Dingxi 743000, Gansu, China
  • Received:2023-11-16 Accepted:2024-04-01 Online:2024-09-12 Published:2024-04-24
  • Contact: *E-mail: 149289262@qq.com
  • Supported by:
    Science and Technology Program of Dingxi City(DX2023BZ81)

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Abstract:

The TIFY family is a gene family of transcription factor unique to plants. It contains conserved TIFY domains (TIF [F/Y]XG), which plays an important role in regulating plant development, responding to abiotic stress, and plant hormones. In this study, a total of 26 members of the StTIFY family at the genome-wide level in potatoes (Solanum tuberosum L.) were identified. Based on phylogenetic characteristics and protein structure, StTIFY was divided into 4 subfamilies, and the JAZ subfamily was divided into 5 subgroups. Tandem duplication and segmental duplication events played a major role in the expansion of the StTIFY gene family. Collinearity analysis showed that there were 21, 5, and 6 orthologous gene pairs between StTIFYs and TIFYs of dicotyledonous plants, which were tomato (Solanum lycopersicum), Arabidopsis, and cabbage (Brassica oleracea). There were only 1 and 2 orthologous gene pairs between StTIFYs and TIFYs of monocotyledonous rice (Oryza sativa) and maize (Zea mays), respectively, which had evolved under purification selection. RNA-seq data analysis showed that TIFY gene and two genes in ZML subfamily were highly expressed in 13 tissues, while the other members exhibited tissue-specificity. Furthermore, we analyzed the response of the StTIFY gene to abiotic stresses and hormone treatments, and found that 19 genes responded to abiotic stress (drought/salt/heat), among which 3 genes and 2 genes simultaneously responded to 3 and 2 abiotic stresses, respectively. Five genes were differentially expressed under BAP, ABA, IAA, and GA3 treatments. The relative expression levels of four candidate genes in drought-tolerant and water-sensitive cultivars under drought stress were further detected using qPCR. The results showed that these four genes were significantly differentially expressed in the two cultivars during flower-falling period. This study provides a theoretical basis for understanding the characteristics of the StTIFY gene family, as well as in-depth analysis of the functions of StTIFY family members response to hormone signals and resistance to abiotic stress.

Key words: potato, TIFY gene family, abiotic stress, hormone treatments, expression analysis

Fig. 1

Phylogenetic tree of AtTIFY and StTIFY family members in Arabidopsis and potato"

Table 1

Physicochemical properties of StTIFY genes family"

基因ID
Gene ID		 染色体定位
Chromosome
localization		 亚族分类
Subgroup		 氨基酸长度
Amino acid
length		 相对分子量
Molecular weight
(Da)		 等电点
Point isoelectric (pI)		 总平均亲水性
GRAVY
Soltu.DM.12G026270 Chr.12 JAZ I 254 28,431.98 9.24 -0.794
Soltu.DM.07G012950 Chr.07 JAZ I 215 23,905.17 8.84 -0.591
Soltu.DM.12G008980 Chr.12 JAZ I 200 22,397.20 9.30 -0.711
Soltu.DM.03G036980 Chr.03 JAZ I 309 33,698.76 8.51 -0.660
Soltu.DM.11G002570 Chr.11 JAZ II 228 26,127.31 6.40 -0.763
Soltu.DM.03G032770 Chr.03 JAZ II 390 41,118.75 9.43 -0.190
Soltu.DM.06G024860 Chr.06 JAZ II 228 24,889.77 10.00 -0.614
Soltu.DM.01G000760 Chr.01 JAZ II 306 32,163.62 8.81 -0.236
Soltu.DM.01G042530 Chr.01 JAZ III 153 17,798.16 8.97 -0.746
Soltu.DM.01G007210 Chr.01 JAZ IV 815 90,598.20 9.41 -0.280
Soltu.DM.05G012690 Chr.05 JAZ IV 176 19,800.60 8.99 -0.489
Soltu.DM.01G007200 Chr.01 JAZ IV 729 80,676.58 9.36 -0.342
Soltu.DM.08G007160 Chr.08 JAZ V 106 12,530.24 9.81 -0.940
Soltu.DM.08G007190 Chr.08 JAZ V 116 13,350.27 9.30 -0.810
Soltu.DM.08G007150 Chr.08 JAZ V 108 12,628.42 10.00 -0.851
Soltu.DM.08G007130 Chr.08 JAZ V 110 12,999.89 9.26 -0.739
Soltu.DM.08G007100 Chr.08 JAZ V 124 14,341.22 9.17 -0.885
Soltu.DM.08G007110 Chr.08 JAZ V 115 13,198.17 9.74 -0.672
Soltu.DM.06G034530 Chr.06 PPD 255 28,312.02 9.03 -0.761
Soltu.DM.09G020260 Chr.09 PPD 339 37,486.27 8.23 -0.665
Soltu.DM.06G019740 Chr.06 TIFY 427 44,702.42 9.32 -0.544
Soltu.DM.04G031220 Chr.04 ZML 354 38,715.17 5.11 -0.604
Soltu.DM.10G013010 Chr.10 ZML 322 34,689.39 6.64 -0.690
Soltu.DM.04G031210 Chr.04 ZML 280 31,238.37 8.84 -0.608
Soltu.DM.01G045340 Chr.01 ZML 375 40,849.43 4.93 -0.557
Soltu.DM.01G045330 Chr.01 ZML 328 34,998.60 6.13 -0.779

Fig. 2

Phylogenetic characteristics, gene structure, and conserved motifs analysis of StTIFY A: phylogenetic tree of StTIFY. B: gene structure (exon/intron) of StTIFY gene. The blue boxes represent exons, the black lines represent the intron, the red boxes represent upstream/downstream sequences. C: the conserved motifs in StTIFY. The 10 different colored boxes represent 10 different motifs."

Fig. 3

Chromosomal localization and duplication of StTIFY genes A: the distribution of StTIFY genes on chromsomes; B: the quantity of StTIFY genes on chromosomes. The pairs of tandemly duplicated genes were marked by purple boxes."

Fig. 4

Segmentally duplication analysis of StTIFY genes members"

Fig. 5

Orthologous relationships of StTIFY with those of AtTIFY, BoTIFY, OsTIFY, and ZmTIFY Different numerical numbers represent the chromosomes of different species, the red lines indicate TIFY orthologous gene pairs between potato and tomato (Solanum lycopersicum), Arabidopsis (Arabidopsis thaliana), cabbage (Brassica oleracea), rice (Oryza sativa) and maize (Zea mays). The violin plot represents the Ka, Ks, and Ka/Ks ratios of TIFY tandem repeats, fragment repeats, and TIFY orthologous genes between potato and different species."

Fig. 6

Relative expression levels of StTIFYs in different tissues of potato The relative expression level of StTIFYs is standardized by log2FPKM, the different color scales (0-8) indicate the relative expression levels of genes in different tissues."

Fig. 7

Relative expression profiles of StTIFYs under different abiotic stresses and different hormone treatments Heatmap represents the log2 (the ratio of gene relative expression level between the treatments and the control)."

Fig. 8

Relative expression analysis of four StTIFY genes in potato cultivars A and Q at three stages (early flowering, full-blooming, and flower-falling stages) A and Q represent “Atlantic” and “Qingshu 9”, respectively. D represents drought stress. Data are means (±SEs) of three independent biological replicates. Different letters above the bars denote significant differences at P < 0.05 (Least Significant Difference, LSD)."

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