Identification and Expression Analysis of SAT Gene Family in Potato（Solanum tuberosum L.）

doi:10.13560/j.cnki.biotech.bull.1985.2024-0133

Abstract

Abstract:

【Objective】 Serine acetyltransferase（SAT）is a critical enzyme in assimilating sulfur into cysteine（Cys）, participating in various biological processes in plants, especially in plant response to abiotic stress. However, analyses on the potato SAT gene family（StSAT）has not yet be reported. This study systematically and comprehensively identified the potato SAT gene family, providing a theoretical basis for further understanding the characteristics of the StSAT gene family and further analysis of their functions in potato resistance to abiotic stress. 【Method】HMM was used to identify the StSAT gene family in potatoes and analyze their chromosomal distribution, gene structure, protein-conserved motifs, and collinearity across species. Additionally, RNA-seq data downloaded from PGSC were used to analyze the expression patterns of StSATs in different tissue parts of doubled-monoploid（DM）potatoes under abiotic stress and exogenous hormone treatments. qPCR（quantitative real-time PCR）was to analyze the relative expressions of StSATs in tetraploid potatoes under NaCl and PEG treatment（0, 1, 3, and 24 h）【Result】Four StSATs were identified in potatoes, and they were distributed across four chromosomes. Based on phylogenetic characteristics, these four StSATs were classified into three subfamilies. According to synteny analysis, there were 4 orthologous SAT genes to Arabidopsis, 4 to tomato（Solanum lycopersicum）, 2 to cabbage（Brassica oleracea）, 1 to rice（Oryza sativa）, and 1 to corn（Zea mays）. Expression analysis showed that the expressions of all four StSATs significantly increased over time under NaCl and PEG treatments compared to 0 h, indicating their likely involvement in the potato's response to salt and osmotic stress.【Conclusion】 StSAT gene family members play an essential role in potato responses to salt and osmotic stress.

Key words: potato, SAT genes family, cis-acting element, abiotic stress, expression analysis

SHEN Peng, GAO Ya-Bin, DING Hong. Identification and Expression Analysis of SAT Gene Family in Potato（Solanum tuberosum L.）[J]. Biotechnology Bulletin, 2024, 40(9): 64-73.

Figures/Tables 9

Table 1 Primer information for qPCR

基因ID Gene ID	正向引物Forward primer（5'-3'）	反向引物Reverse primer（5'-3'）
Soltu06G005680	GGTCGTGTTGAGACTGGTGTGATC	GCTTCGTGGTGCATCTCTACAGAC
Soltu02G022850	CTGTCGCTAACACCGCTTCTACTC	GCTCAATGCCCGTTCCAAACAATC
Soltu12G025770	GACACGGCGGAAGAAGCTATCTG	AGTGAGCGTTCAAGCGAAGAGTG
Soltu07G027060	CCAAACAAGCCCCAAATCGACAAC	GCAGGAAGCAAGGTCAGGGAAAG
Soltu10G001180	TGGTGCTGGTACTTGTGTTCTTGG	AGCAGTAGTTCTTGCAGGCACTTC

Table 2 Chromosomal localization and physicochemical properties of StSATs

基因ID Gene ID	染色体定位 Chromosome localization		氨基酸长度 Amino acid length	相对分子量 Molecular weight/ kD	等电点 Point isoelectric（pI）
Soltu.DM.02G022850	chr02	36 554 173-36 560 967	349	37.43	6.41
Soltu.DM.07G027060	chr07	56 287 590-56 289 231	359	39.04	8.80
Soltu.DM.10G001180	chr10	978 595-980 158	365	40.23	6.50
Soltu.DM.12G025770	chr12	55 741 243-55 744 365	293	31.27	6.38

Fig. 1 Phylogenetic tree of SAT proteins in multiple species and analysis in evolutionary relationship, gene structure and protein conserved motifs of StSAT gene family members A: Phylogenetic tree of SAT proteins in multiple species. The different colored lines represent the three subfamilies（blue for C1, red for C2, and green for C3）. The blue pentagrams indicate the potato SAT gene family member（StSATs）, orange pentagrams indicate the tomato SAT gene family member（SlSATs）, yellow circles indicate the corn SAT gene family member（ZmSATs）, purple circles indicate the rice SAT gene family member（OsSATs）, red squares indicate the Arabidopsis SAT gene family members（AtSTAs）, and green squares indicate the cabbage SAT gene family member（BoSATs）. B: Evolutionary tree of the StSAT gene family. The blue squares indicate the C1 subfamily, the red squares indicate the C2 subfamily, and the green squares indicate the C3 subfamily. C: Gene structure of StSATs. Blue boxes indicate exons, black lines indicate introns and red boxes indicate upstream/downstream regions. D: Protein conserved motif of StSATs

Fig. 2 Collinearity analysis of SAT genes in multiple species Different numerical numbers indicate the chromosomes of different species, and the red lines indicate orthologous gene pairs between different species

Table 3 Ka/Ks ratios of orthologous genes between potato and other species

Gene ID1	Gene ID2	Ka	Ks	Ka/Ks
Soltu02G022850	Solyc02g082850	0.040 2	0.110 7	0.363 2
Soltu12G025770	Solyc12g008780	0.003 1	0.074 1	0.041 4
Soltu07G027060	Solyc07g065340	0.010 6	0.072 8	0.145 3
Soltu10G001180	Solyc10g006040	0.009 5	0.050 7	0.187 0
Soltu02G022850	AT2G17640	0.192 7	1.660 3	0.116 1
Soltu12G025770	AT5G56760	0.118 8	2.718 1	0.043 7
Soltu07G027060	AT3G13110	0.238 7	2.356 3	0.101 3
Soltu10G001180	AT1G55920	0.234 9	3.864 2	0.060 8
Soltu12G025770	Bo3g019690	0.122 7	3.050 0	0.040 2
Soltu07G027060	Bo6g035890	0.202 6	3.867 2	0.052 4
Soltu02G022850	Zm00001d027536	0.178 5	2.483 9	0.071 8
Soltu02G022850	Os03g04140	0.267 1	3.167 0	0.084 3

Fig. 3 Prediction of cis-acting elements in the promoter region of StSATs

Fig. 4 StSAT gene expressions in different tissues of DM potato The expressions of four StSATs in 13 tissue sites are logarithms base 2, and heat maps are plotted using log2FPKM

Fig. 5 StSAT gene expressions in DM potato under abiotic stress and hormone treatment The ratios of treatment to control are used for abiotic stresses（salt, mannitol, and heat stress）, taken as base 2 logarithms and heat maps are plotted using log2FC

Fig. 6 Relative expressions of StSAT genes under NaCl and PEG treatment in tetraploid potato The relative expressions of four StSAT genes under NaCl and PEG treatment was analyzed by qPCR. Data are means（±SEs）from three independent biological replicates. Different letters above the bar chart indicate significant differences at P<0.05

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