Mining, identification, and expression analysis of the DoNPF gene family in Dendrobium officinale

doi:10.16178/j.issn.0528-9017.20240611

Abstract

Abstract:

Low temperature is one of the crucial environmental factors that limit plant productivity and geographical distribution, severely affecting plant growth and development. Mining cold-resistant germplasm and conducting in-depth research on its mechanism of action are of great significance for improving the cold resistance of crops. Dendrobium officinale is a traditional and precious Chinese medicinal herb in China, with unique effects such as promoting saliva secretion and nourishing the stomach, nourishing yin and clearing heat, and moistening the lungs and tonifying the kidneys. It is ranked first among the “nine great immortal herbs of China”. With the development of wild-simulation cultivation technology and the gradual northward expansion of Dendrobium officinale planting areas, the breeding of cold-resistant Dendrobium officinale varieties is particularly important. In this study, transcriptome data of Dendrobium officinale under low-temperature treatment were deeply mined to obtain key DoNPF genes involved in low-temperature response. Based on the published genome data and transcriptome data of Dendrobium officinale, bioinformatics methods were used to identify members of the DoNPF gene family, and their gene structures and gene expressions were analyzed. Finally, 8 DoNPF genes with significantly (p<0.05) differential expression involved in low-temperature response were screened out. This study is of great significance for improving the cold resistance of Dendrobium officinale and breeding cold-resistant Dendrobium officinale varieties.

Key words: Dendrobium officinale, DoNPF gene family, low temperature, genome-wide identification

CLC Number:

S567

FU Manman, GUO Fangqi, WU Chao. Mining, identification, and expression analysis of the DoNPF gene family in Dendrobium officinale[J]. Journal of Zhejiang Agricultural Sciences, 2025, 66(12): 2944-2951.

Figures/Tables 6

Fig.1 Differential expression genes related to low temperature in Dendrobium officinale

Fig.2 Protein-protein interactions of differential expression genes (DEG) of Dendrobium officinale

Fig.3 Phylogenetic tree of NPF gene family encoding proteins

Fig.4 Gene structure of DoNPF

Fig.5 Expression of DoNPF under normal and low-temperature treatment

Fig.6 DoNPF genes significantly differentially expressed under low-temperature treatment

References 23

[1]	YAN L, WANG X, LIU H, et al. The genome of Dendrobium officinale illuminates the biology of the important traditional Chinese orchid herb[J]. Molecular Plant, 2015, 8(6): 922-934.
[2]	邹晖, 林江波, 李海明, 等. 铁皮石斛人工栽培技术[J]. 福建农业, 2016(12): 38-39.
[3]	蒋新建, 陈玉哲. 郑州地区铁皮石斛人工种植管理技术[J]. 河南农业, 2018(30): 48-49.
[4]	DANIEL H. Molecular and integrative physiology of intestinal peptide transport[J]. Annual Review of Physiology, 2004, 66: 361-384.
[5]	NEWSTEAD S, DREW D, CAMERON A D, et al. Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2[J]. EMBO Journal, 2011, 30(2): 417-426.
[6]	FEI Y J, KANAI Y, NUSSBERGER S, et al. Expression cloning of a mammalian proton-coupled oligopeptide transporter[J]. Nature, 1994, 368(6471): 563-566.
[7]	TSAY Y F, SCHROEDER J I, FELDMANN K A, et al. The herbicide sensitivity gene CHL1 of Arabidopsis encodes a nitrate-inducible nitrate transporter[J]. Cell, 1993, 72(5): 705-713.
[8]	LÉRAN S, VARALA K, BOYER J C, et al. A unified nomenclature of nitrate transporter 1/peptide transporter family members in plants[J]. Trends in Plant Science, 2014, 19(1): 5-9.
[9]	PARKER J L, NEWSTEAD S. Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1[J]. Nature, 2014, 507(7490): 68-72.
[10]	WEN J, LI P F, RAN F, et al. Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus[J]. BMC Genomics, 2020, 21(1): 871.
[11]	LI J, LIU H L, XIA W W, et al. De novo transcriptome sequencing and the hypothetical cold response mode of Saussurea involucrata in extreme cold environments[J]. International Journal of Molecular Sciences, 2017, 18(6): 1155.
[12]	NOUR-ELDIN H H, ANDERSEN T G, BUROW M, et al. NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds[J]. Nature, 2012, 488(7412): 531-534.
[13]	ZHAO X B, HUANG J Y, YU H H, et al. Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.)[J]. BMC Plant Biology, 2010, 10: 92.
[14]	YANG X H, XIA X Z, ZENG Y, et al. Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency[J]. BMC Plant Biology, 2020, 20(1): 193.
[15]	BUCHNER P, HAWKESFORD M J. Complex phylogeny and gene expression patterns of members of the nitrate transporter 1/peptide transporter family (npf) in wheat[J]. Journal of Experimental Botany, 2014, 65(19): 5697-5710.
[16]	WANG Q, LIU C H, DONG Q L, et al. Genome-wide identification and analysis of apple nitrate transporter 1/peptide transporter family (npf) genes reveals MdNPF6.5 confers high capacity for nitrogen uptake under low-nitrogen conditions[J]. International Journal of Molecular Sciences, 2018, 19(9): 2761.
[17]	LI H, YU M, DU X Q, et al. NRT1.5/NPF7.3 functions as a proton-coupled H⁺/K⁺ antiporter for K⁺ loading into the xylem in Arabidopsis[J]. The Plant Cell, 2017, 29(8): 2016-2026.
[18]	WATANABE S, TAKAHASHI N, KANNO Y, et al. The Arabidopsis NRT1/PTR FAMILY protein NPF7.3/NRT1.5 is an indole-3-butyric acid transporter involved in root gravitropism[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(49): 31500-31509.
[19]	TONG W, IMAI A, TABATA R, et al. Polyamine resistance is increased by mutations in a nitrate transporter gene NRT1.3 (AtNPF6.4) in Arabidopsis thaliana[J]. Frontiers in Plant Science, 2016, 7: 834.
[20]	HE Y N, XI X J, ZHA Q, et al. Ectopic expression of a grape nitrate transporter VvNPF6.5 improves nitrate content and nitrogen use efficiency in Arabidopsis[J]. BMC Plant Biology, 2020, 20(1): 549.
[21]	CHEN H Y, LIN S H, CHENG L H, et al. Potential transceptor AtNRT1.13 modulates shoot architecture and flowering time in a nitrate-dependent manner[J]. The Plant Cell, 2021, 33(5): 1492-1505.
[22]	LI B, QIU J E, JAYAKANNAN M, et al. AtNPF2.5 modulates chloride (Cl^-) efflux from roots of Arabidopsis thaliana[J]. Frontiers in Plant Science, 2017, 7: 2013.
[23]	XIA X D, FAN X R, WEI J, et al. Rice nitrate transporter OsNPF2.4 functions in low-affinity acquisition and long-distance transport[J]. Journal of Experimental Botany, 2015, 66(1): 317-331.