Welcome to Acta Agronomica Sinica，

Acta Agronomica Sinica ›› 2026, Vol. 52 ›› Issue (10): 2875-2885.doi: 10.3724/SP.J.1006.2026.64047

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

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

Cui Yi-Fan(), Sun Xiao-Tong, Shi Ying()   

  1. College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
  • Received:2026-04-10 Accepted:2026-07-15 Online:2026-10-12 Published:2026-07-22
  • Contact: Shi Ying, E-mail: yshi@neau.edu.cn
  • Supported by:
    China Agriculture Research System of MOF and MARA(CARS-09)

RichHTML454

3

PDF

98

Abstract:

Malate dehydrogenase (MDH; EC1.1.1.37) is widely distributed in plants and catalyzes the interconversion of malate and oxaloacetate using NADH or NADPH as cofactors. MDH plays a crucial role in the tricarboxylic acid (TCA) cycle and is involved in regulating various physiological processes, including plant growth, development, and stress responses. In this study, eight MDH family members were identified in the potato genome using bioinformatics approaches. These genes were named StMDH1 to StMDH8 according to their chromosomal locations and were further classified into five subfamilies. Analysis of physicochemical properties showed that the predicted StMDH proteins ranged from 30.11 to 43.85 kD in molecular weight, with isoelectric points ranging from 5.91 to 9.00. Subcellular localization prediction indicated that these proteins are mainly localized in chloroplasts and mitochondria. Gene structure analysis showed that members within the same subfamily had similar exon numbers and conserved motif compositions. Expression profiling based on publicly available transcriptome data revealed that most StMDH genes responded to abiotic stresses and hormone treatments, with StMDH2 showing the strongest salt stress-induced expression pattern. Furthermore, heterologous expression in Saccharomyces cerevisiae confirmed that overexpression of StMDH2 significantly enhanced salt tolerance in yeast cells. This study expands our understanding of the potato MDH gene family and provides potential genetic resources and candidate targets for the molecular breeding of stress-resistant potato varieties.

Key words: Solanum tuberosum L., MDH, genome-wide identification, abiotic stress, salt stress

Table S1

Basic information of 58 MDH genes"

基因名称
Gene name		 基因ID
Gene ID		 ORF长度
ORF length (bp)		 蛋白质长度
Protein length (aa)		 等电点
Isoelectric point		 分子量
Molecular weight (kD)		 亚细胞定位
Subcellular localization
StMDH1 Soltu.DM.01G031350 999 332 7.62 35.69 叶绿体Chloroplast
StMDH2 Soltu.DM.01G045790 1074 357 8.10 37.63 叶绿体, 线粒体
Chloroplast, mitochondrion
StMDH3 Soltu.DM.02G007400 873 290 6.42 30.11 线粒体Mitochondrion
StMDH4 Soltu.DM.03G030110 1239 412 8.04 43.28 叶绿体, 线粒体
Chloroplast, mitochondrion
StMDH5 Soltu.DM.07G023810 1041 346 9.00 36.12 叶绿体, 线粒体
Chloroplast, mitochondrion
StMDH6 Soltu.DM.09G026740 999 332 5.91 35.43 叶绿体Chloroplast
StMDH7 Soltu.DM.09G027890 1239 412 8.69 43.85 叶绿体, 线粒体
Chloroplast, mitochondrion
StMDH8 Soltu.DM.12G030010 1026 341 8.90 35.67 叶绿体, 线粒体
Chloroplast, mitochondrion
AtMDH1 AT1G04410 999 332 6.11 35.57 叶绿体Chloroplast
AtMDH2 AT1G53240 1026 341 8.54 35.80 线粒体Mitochondrion
AtMDH3 AT2G22780 1065 354 8.11 37.47 叶绿体, 线粒体
Chloroplast, mitochondrion
AtMDH4 AT3G15020 1026 341 8.30 35.88 叶绿体, 线粒体
Chloroplast, mitochondrion
AtMDH5 AT3G47520 1212 403 8.66 42.40 叶绿体, 线粒体
Chloroplast, mitochondrion
AtMDH6 AT5G09660 1091 363 9.16 38.74 叶绿体, 线粒体
Chloroplast, mitochondrion
AtMDH7 AT5G43330 999 332 6.33 35.68 叶绿体Chloroplast
AtMDH8 AT5G58330 1332 443 5.81 48.32 叶绿体Chloroplast
AtMDH9 AT5G56720 1020 339 5.75 36.87 叶绿体Chloroplast
GmMDH1 Glyma.01G197700 873 290 6.21 30.90 过氧化物酶体Peroxisome
GmMDH2 Glyma.01G210400 1062 353 6.25 38.20 叶绿体Chloroplast
GmMDH3 Glyma.02G005500 1002 333 5.91 35.50 细胞质Cytoplasm
GmMDH4 Glyma.05G026300 1245 414 6.47 43.60 叶绿体Chloroplast
GmMDH5 Glyma.05G058100 1053 350 6.51 37.80 叶绿体Chloroplast
GmMDH6 Glyma.06G231500 1041 346 8.22 36.00 线粒体Mitochondrion
GmMDH7 Glyma.07G185400 1074 357 8.52 37.50 过氧化物酶体Peroxisome
GmMDH8 Glyma.08G063800 1074 357 8.52 37.40 细胞质Cytoplasm
GmMDH9 Glyma.10G006500 990 329 5.91 35.20 细胞质Cytoplasm
GmMDH10 Glyma.10G197700 1314 437 6.18 47.70 叶绿体Chloroplast
GmMDH11 Glyma.11G031600 690 229 8.79 24.50 叶绿体Chloroplast
GmMDH12 Glyma.11G043900 1065 354 7.55 37.40 过氧化物酶体Peroxisome
GmMDH13 Glyma.12G159300 1041 346 8.23 36.10 线粒体Mitochondrion
GmMDH14 Glyma.13G104800 1125 374 6.13 41.00 细胞质Cytoplasm
GmMDH15 Glyma.17G100600 1233 410 8.11 43.10 叶绿体Chloroplast
GmMDH16 Glyma.17G140600 1053 350 6.55 37.70 叶绿体Chloroplast
GmMDH17 Glyma.20G192200 1278 425 6.34 46.60 叶绿体Chloroplast
OsMDH1 LOC_Os01g46070 1023 640 8.74 35.46 叶绿体, 线粒体Chloroplast, mitochondrion
OsMDH2 LOC_Os01g61380 1191 396 7.63 41.79 叶绿体, 线粒体
Chloroplast, mitochondrion
OsMDH3 LOC_Os02g01510 1179 392 6.74 42.72 细胞质Cytoplasm
OsMDH4 LOC_Os03g56280 1065 654 8.13 37.02 叶绿体, 线粒体
Chloroplast, mitochondrion
OsMDH5 LOC_Os04g46560 1059 352 6.72 38.30 叶绿体Chloroplast
OsMDH6 LOC_Os05g49880 1023 340 8.22 35.44 叶绿体, 线粒体
Chloroplast, mitochondrion
OsMDH7 LOC_Os06g01590 1083 360 7.90 38.72 细胞质Cytoplasm
OsMDH8 LOC_Os07g43700 1215 404 9.00 42.22 叶绿体, 线粒体
Chloroplast, mitochondrion
OsMDH9 LOC_Os08g33720 1194 397 7.02 41.54 叶绿体, 线粒体
Chloroplast, mitochondrion
OsMDH10 LOC_Os08g44810 1302 433 6.96 47.01 叶绿体Chloroplast
OsMDH11 LOC_Os10g33800 999 332 5.75 35.57 叶绿体Chloroplast
OsMDH12 LOC_Os12g43630 1071 356 8.09 37.39 叶绿体, 线粒体
Chloroplast, mitochondrion
SlMDH1 Solyc01g090710 1005 334 6.46 35.88 细胞质Cytoplasm
SlMDH2 Solyc01g106480 1074 357 8.10 37.63 过氧化物酶体Peroxisome
SlMDH3 Solyc02g063490 1059 352 8.13 36.85 叶绿体Chloroplast
SlMDH4 Solyc03g071590 1404 467 7.89 51.66 叶绿体Chloroplast
SlMDH5 Solyc03g115990 1239 412 8.34 43.19 叶绿体Chloroplast
SlMDH6 Solyc07g062650 1041 346 8.73 36.08 线粒体Mitochondrion
SlMDH7 Solyc08g007420 1044 347 5.36 37.64 细胞质Cytoplasm
SlMDH8 Solyc08g078850 1053 350 6.31 37.70 叶绿体Chloroplast
SlMDH9 Solyc09g090140 999 332 5.91 35.38 细胞质Cytoplasm
SlMDH10 Solyc09g091070 897 298 5.35 31.81 细胞质Cytoplasm
SlMDH11 Solyc11g007990 1329 442 6.23 48.44 叶绿体Chloroplast
SlMDH12 Solyc12g014180 1029 342 8.90 35.65 线粒体Mitochondrion

Fig. 1

Phylogenetic tree of the MDH gene family in Solanum tuberosum, Solanum lycopersicum, Arabidopsis thaliana, Oryza sativa, and Glycine max"

Fig. 2

Gene structure analysis of MDH in Solanum tuberosum"

Fig. 3

Synteny analysis of MDH genes A: synteny analysis of MDH genes in Solanum tuberosum, with red lines indicating duplicated gene pairs; B: synteny analysis of MDH genes between Solanum tuberosum and Solanum lycopersicum, Arabidopsis thaliana, Oryza sativa, and Glycine max, with colored lines indicating duplicated gene pairs."

Fig. 4

Conserved motif analysis of the MDH gene family"

Fig. 5

Prediction of cis-acting elements in the promoters of MDH gene family members The numbers indicate the copy number of specific cis-acting element in the promoter region of each gene."

Fig. 6

Expression analysis of the MDH gene family in Solanum tuberosum across different tissues and under abiotic stress and hormone treatments A: expression profile analysis of MDH genes in different tissues/organs of Solanum tuberosum; B: expression profile analysis of MDH genes in Solanum tuberosum under abiotic stress; C: expression profile analysis of MDH genes in Solanum tuberosum under hormone treatment."

Fig. 7

Cloning of StMDH2 and functional validation of salt tolerance through heterologous expression in Saccharomyces cerevisiae A: schematic diagram of the pYES2-StMDH2 recombinant vector, with numbers in parentheses indicating the positions of restriction sites or functional elements on the plasmid; B: functional validation of salt tolerance through heterologous expression of StMDH2 in Saccharomyces cerevisiae."

[1] Liu N, Zhao R M, Qiao L, et al. Growth stages classification of potato crop based on analysis of spectral response and variables optimization. Sensors, 2020, 20: 3995.
doi: 10.3390/s20143995
[2] Faried H N, Ayyub C M, Wattoo F M, et al. Assessing salt tolerance induction in potato by salicylic acid using morpho-physio- biochemical, ionic, and yield indices. Potato Res, 2022, 65: 677-691.
doi: 10.1007/s11540-021-09539-4
[3] Machado M F, Prioli A J, Mangolin C A. Malate dehydrogenase (MDH; EC1.1.1.37) isozymes in tissues and callus cultures of Cereus peruvianus (Cactaceae). Biochem Genet, 1993, 31: 167-172.
pmid: 8363555
[4] Scheibe R. Malate valves to balance cellular energy supply. Physiol Plant, 2004, 120: 21-26
doi: 10.1111/j.0031-9317.2004.0222.x pmid: 15032873
[5] Gietl C. Malate dehydrogenase isoenzymes: cellular locations and role in the flow of metabolites between the cytoplasm and cell organelles. Biochim Biophys Acta Bioenerg, 1992, 1100: 217-234.
doi: 10.1016/0167-4838(92)90476-T
[6] Selinski J, König N, Wellmeyer B, et al. The plastid-localized NAD-dependent malate dehydrogenase is crucial for energy homeostasis in developing Arabidopsis thaliana seeds. Mol Plant, 2014, 7: 170-186.
doi: 10.1093/mp/sst151
[7] Miller S S, Driscoll B T, Gregerson R G, et al. Alfalfa malate dehydrogenase (MDH): molecular cloning and characterization of five different forms reveals a unique nodule-enhanced MDH. Plant J, 1998, 15: 173-184.
doi: 10.1046/j.1365-313x.1998.00192.x pmid: 9721676
[8] Baird L M, Berndsen C E, Monroe J D. Malate dehydrogenase in plants: evolution, structure, and a myriad of functions. Essays Biochem, 2024, 68: 221-233.
doi: 10.1042/EBC20230089
[9] Huang J J, Niazi A K, Young D, et al. Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis. J Exp Bot, 2018, 69: 3491-3505.
doi: 10.1093/jxb/erx396
[10] Beeler S, Liu H C, Stadler M, et al. Plastidial NAD-dependent malate dehydrogenase is critical for embryo development and heterotrophic metabolism in Arabidopsis. Plant Physiol, 2014, 164: 1175-1190.
doi: 10.1104/pp.113.233866
[11] Tomaz T, Bagard M, Pracharoenwattana I, et al. Mitochondrial malate dehydrogenase lowers leaf respiration and alters photorespiration and plant growth in Arabidopsis. Plant Physiol, 2010, 154: 1143-1157.
doi: 10.1104/pp.110.161612
[12] Talla S K, Sunil B, Rao D E, et al. Redox basis of photosynthesis inhibition at supra-optimal bicarbonate in mesophyll protoplasts of Arabidopsis thaliana. J Plant Physiol, 2023, 287: 154047.
[13] Yokochi Y, Yoshida K, Hahn F, et al. Redox regulation of NADP-malate dehydrogenase is vital for land plants under fluctuating light environment. Proc Natl Acad Sci USA, 2021, 118: e2016903118.
[14] Chen Y Q, Fu Z Y, Zhang H, et al. Cytosolic malate dehydrogenase 4 modulates cellular energetics and storage reserve accumulation in maize endosperm. Plant Biotechnol J, 2020, 18: 2420-2435.
doi: 10.1111/pbi.v18.12
[15] Teng X, Zhong M S, Zhu X P, et al. FLOURY ENDOSPERM16 encoding a NAD-dependent cytosolic malate dehydrogenase plays an important role in starch synthesis and seed development in rice. Plant Biotechnol J, 2019, 17: 1914-1927.
doi: 10.1111/pbi.v17.10
[16] Kandoi D, Mohanty S, Tripathy B C. Overexpression of plastidic maize NADP-malate dehydrogenase (ZmNADP-MDH) in Arabidopsis thaliana confers tolerance to salt stress. Protoplasma, 2018, 255: 547-563.
doi: 10.1007/s00709-017-1168-y
[17] Tesfaye M, Temple S J, Allan D L, et al. Overexpression of malate dehydrogenase in transgenic alfalfa enhances organic acid synthesis and confers tolerance to aluminum. Plant Physiol, 2001, 127: 1836-1844.
pmid: 11743127
[18] Shi Y H, Feng J H, Wang L P, et al. OsMDH12: a peroxisomal malate dehydrogenase regulating tiller number and salt tolerance in rice. Plants, 2023, 12: 3558.
doi: 10.3390/plants12203558
[19] Jiang M, Chen Z, Ansah E O, et al. Rice NADP-dependent malate dehydrogenase gene OsMDH8.2 is involved in heat tolerance. Fundam Res, 2025, 5: 2037-2044.
doi: 10.1016/j.fmre.2023.12.010
[20] Nan N, Wang J, Shi Y J, et al. Rice plastidial NAD-dependent malate dehydrogenase 1 negatively regulates salt stress response by reducing the vitamin B6 content. Plant Biotechnol J, 2020, 18: 172-184.
doi: 10.1111/pbi.13184 pmid: 31161713
[21] Wang Z A, Li Q, Ge X Y, et al. The mitochondrial malate dehydrogenase 1 gene GhmMDH1 is involved in plant and root growth under phosphorus deficiency conditions in cotton. Sci Rep, 2015, 5: 10343.
doi: 10.1038/srep10343
[22] Li Z Q, Shi L, Lin X J, et al. Genome-wide identification and expression analysis of malate dehydrogenase gene family in sweet potato and its two diploid relatives. Int J Mol Sci, 2023, 24: 16549.
doi: 10.3390/ijms242316549
[23] Song J L, Zou X Y, Liu P D, et al. Differential expressions and enzymatic properties of malate dehydrogenases in response to nutrient and metal stresses in Stylosanthes guianensis. Plant Physiol Biochem, 2022, 170: 325-337.
doi: 10.1016/j.plaphy.2021.12.012
[24] Zhou R N, Wang S H, Liu P Y, et al. Genome-wide characterization of soybean malate dehydrogenase genes reveals a positive role for GmMDH2 in the salt stress response. J Integr Agric, 2025, 24: 2492-2510.
doi: 10.1016/j.jia.2023.12.036
[25] Zhang Y H, Wang Y L, Sun X M, et al. Genome-wide identification of MDH family genes and their association with salt tolerance in rice. Plants, 2022, 11: 1498.
doi: 10.3390/plants11111498
[26] Imran M, Tang K, Liu J Y. Comparative genome-wide analysis of the malate dehydrogenase gene families in cotton. PLoS One, 2016, 11: e0166341.
[27] Letunic I, Khedkar S, Bork P. SMART: recent updates, new developments and status in 2020. Nucleic Acids Res, 2021, 49: D458-D460.
[28] Bailey T L, Boden M, Buske F A, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, 2009, 37: W202-W208.
doi: 10.1093/nar/gkp335
[29] Liu W Z, Xie Y B, Ma J Y, et al. IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics, 2015, 31: 3359-3361.
doi: 10.1093/bioinformatics/btv362 pmid: 26069263
[30] Nakashima K, Yamaguchi-Shinozaki K. ABA signaling in stress-response and seed development. Plant Cell Rep, 2013, 32: 959-970.
doi: 10.1007/s00299-013-1418-1 pmid: 23535869
[31] Ohme-Takagi M, Shinshi H. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell, 1995, 7: 173-182.
doi: 10.1105/tpc.7.2.173 pmid: 7756828
[32] Jores T, Tonnies J, Wrightsman T, et al. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. Nat Plants, 2021, 7: 842-855.
doi: 10.1038/s41477-021-00932-y pmid: 34083762
[33] Ma B Q, Yuan Y Y, Gao M, et al. Genome-wide identification, classification, molecular evolution and expression analysis of malate dehydrogenases in apple. Int J Mol Sci, 2018, 19: 3312.
doi: 10.3390/ijms19113312
[1] Zhang Rui-Jia, Lyu Jian-Yu, Gao Yuan, Wang Hao-Yu, Wang Yu-Qi, Jiang Jia-Ning, Zhao Jian-Xiong, Wang Xue-He-Yuan, He Lin. Maize transcription factor ZmDREB53 positively regulates plant salt tolerance by scavenging reactive oxygen species [J]. Acta Agronomica Sinica, 2026, 52(9): 2660-2670.
[2] Zhao Hai-Yang, Guo Xu-Peng, Luo Yang, Yang Gang, Cai Zhen-Liang, Hu Zan-Min, Chen Yu-Hong, Fan Cheng-Ming, Zhang Xin-Yong. Regulation by zinc citrate of crop salt tolerance and soil electrical conductivity [J]. Acta Agronomica Sinica, 2026, 52(9): 2792-2808.
[3] Jiang Cun-Cang, Dou Jia-Yi, Lu Ke-Song, Xiao Si-Yun, Liu Bing, Bi Jia-Yu. Research progress on the effects and mechanisms of boron in mitigating salt stress in crops [J]. Acta Agronomica Sinica, 2026, 52(7): 1929-1942.
[4] Zou Yi-Mei, Xu Min, Wang Hai-Yang, Yao Hui, Wang Jia-Feng, Liu Hao, Ren Dai-Sheng. Analysis of transcription factor regulatory networks in two-line male sterile rice seedling roots in response to salt stress [J]. Acta Agronomica Sinica, 2026, 52(6): 1728-1742.
[5] Song Yu-Zhen, Bheel Chander Kumar, Wang Yue, Zhang Ying-Xing, Guo Juan, Khound Rituraj, Santra Dipak Kumar, Cao Xiao-Ning, Wang Rui-Yun. Genome-wide identification of the AP2 subfamily in broomcorn millet and functional characterization of PmAP2-1 and PmAP2-9 in salt tolerance [J]. Acta Agronomica Sinica, 2026, 52(4): 1127-1139.
[6] Tian Li-Tao, Ding Ning, Wang Shu-Lin, Qi En-Fang, Zhang Rong, Wang Rui-Rui, Ma Li-Wen, Li Jian-Wu, Yang Jiang-Wei. Genome-wide identification of the Argonaute gene family and its induction by late blight in potato (Solanum tuberosum L.) [J]. Acta Agronomica Sinica, 2026, 52(4): 1116-1126.
[7] Qin Yi-Yan, Fu Yao, Su Chang, Li Na, Xu Jing-Ru, Cheng Xiao-Ran, Zhang Qi, Zhao Ming-Hui. Functional analysis of OsST41 regulating salt tolerance in rice seedlings [J]. Acta Agronomica Sinica, 2026, 52(3): 802-812.
[8] Zhang Qing, Yang Yu, Guo Qian, Yue Pei-Yao, Yin Cong-Cong, Niu Jing-Ping, Zhao Jin-Zhong, Du Wei-Jun, Yue Ai-Qin. Cloning and functional analysis of the soybean GmARA6a gene in response to salt stress [J]. Acta Agronomica Sinica, 2026, 52(2): 480-493.
[9] Yang Biao, Du Shuai-Kang, Zhang Ji-Wang, Shi Ying, Zhang Li-Li. Genome-wide identification of class III POD gene family in potato and its expression profile analysis [J]. Acta Agronomica Sinica, 2026, 52(2): 405-420.
[10] Liu Ji-Chang, Li Si-Ye, Li Xue-Ting, Wang Hong-Zhang, Liu Peng, Zhang Ji-Wang, Zhao Bin, Ren Bai-Zhao, Ren Hao. Effects of salt stress on root growth and nutrient absorption efficiency of different salt-tolerant summer maize varieties [J]. Acta Agronomica Sinica, 2026, 52(2): 565-577.
[11] Jing Xiu-Qing, Cai Yong-Duo, Deng Ning, Zhao Xiao-Dong, Zhai Fei-Hong, Zeng Qun. Identification and expression pattern analysis of RopGEF family genes in Chenopodium quinoa [J]. Acta Agronomica Sinica, 2026, 52(1): 28-43.
[12] YAN Zhi-Lan, ZHAO Qin, CHANG Tian-Da, WANG Yi-Ming, WANG Bi-Hui, WANG Peng, HUANG Chun-Guo, ZHANG Hui, WANG Li-Xiang, HAO Xiao-Peng, ZHAO Bo. Genome-wide identification and characterization of Alternative oxidase (AOX) genes in leguminous crops and their expression patterns in response to abiotic stresses in common bean [J]. Acta Agronomica Sinica, 2025, 51(7): 1769-1783.
[13] PAN Ju-Zhong, WEI Ping, ZHU De-Ping, SHAO Sheng-Xue, CHEN Shan-Shan, WEI Ya-Qian, GAO Wei-Wei. Cloning and functional analysis of OsERF104 transcription factor in rice [J]. Acta Agronomica Sinica, 2025, 51(4): 900-913.
[14] LI Xue-Ting, REN Hao, WANG Hong-Zhang, ZHANG Ji-Wang, ZHAO Bin, REN Bai-Zhao, LIU Ying, YAO Hai-Yan, LIU Peng. Effects of salt stress on photosynthetic performance and dry matter accumulation and distribution in leaves of different salt-tolerant maize varieties [J]. Acta Agronomica Sinica, 2025, 51(4): 1091-1101.
[15] HUO Ru-Xue, GE Xiang-Han, SHI Jia, LI Xue-Rui, DAI Sheng-Jie, LIU Zhen-Ning, LI Zong-Yun. Functional analysis of the sweetpotato histidine kinase protein IbHK5 in response to drought and salt stresses [J]. Acta Agronomica Sinica, 2025, 51(3): 650-666.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd