Identification and Expression Analysis of the NPF Genes in Cotton

Dong, Qiang; Wang, Guoxin; Iqbal, Asif; Muhammad, Noor; Gui, Heng; Zhang, Hengheng; Kayoumu, Mirezhatijiang; Li, Xiaotong; Zhang, Xiling; Song, Meizhen

doi:10.3390/ijms232214262

Cited by 4 publications

(9 citation statements)

References 54 publications

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“…The distribution of CsNPFs in different subfamilies is as follows: NPF1 (4), NPF2 (8), NPF3 (2), NPF4 (8), NPF5 (17), NPF6 (6), NPF7 (6), and NPF8 (3). Among them, NPF1 is more closely related to the NPF2 subfamily on one branch, NPF4 is more closely related to NPF6, and NPF7 is more closely related to NPF8, which is consistent with the results of previous research [ 8 , 10 , 11 , 38 , 39 ]. To distinguish the subfamilies of NPF genes, we renamed all CsNPF genes according to the international nomenclature, based on their homology with AtNPF genes ( Table S1 ) [ 40 ].…”

Section: Resultssupporting

confidence: 91%

“…There are two classification systems for the NPF gene family, as follows: one system is based on a phylogenetic analysis of 1077 sequences from 22 plant genomes and 24 nonplant sequences, dividing the family into 10 supergroups and 32 groups [ 45 ]; and the other system divides the NRT1/PTR family into eight subfamilies (NPF1-NPF8), based on an analysis of 2398 sequences from 33 full-sequence genomes [ 40 ]. Previous studies have generally conformed to the criteria of the latter division [ 8 , 11 , 38 , 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. Recently, a new classification method appeared in Brassica napus .…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Zhang

Zheng

et al. 2023

Plants

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The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins perform an essential role in regulating plant nitrate absorption and distribution and in improving plant nitrogen use efficiency. In this study, cucumber (Cucumis sativus L.) NPF genes were comprehensively analyzed at the whole genome level, and 54 NPF genes were found to be unevenly distributed on seven chromosomes in the cucumber genome. The phylogenetic analysis showed that these genes could be divided into eight subfamilies. We renamed all CsNPF genes according to the international nomenclature, based on their homology with AtNPF genes. By surveying the expression profiles of CsNPF genes in various tissues, we found that CsNPF6.4 was specifically expressed in roots, indicating that CsNPF6.4 may play a role in N absorption; CsNPF6.3 was highly expressed in petioles, which may be related to NO3− storage in petioles; and CsNPF2.8 was highly expressed in fruits, which may promote NO3− transport to the embryos. We further examined their expression patterns under different abiotic stress and nitrogen conditions, and found that CsNPF7.2 and CsNPF7.3 responded to salt, cold, and low nitrogen stress. Taken together, our study lays a foundation for further exploration of the molecular and physiological functions of cucumber nitrate transporters.

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Section: Resultssupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Zhang

Zheng

et al. 2023

Plants

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“…Recent transcriptome and genome‐wide studies reported the expression of 47 GhNPF in all tissues in cotton plants and suggested that GhNPF6.11, −7.1 and −8.1 could be redundant in some tissues (Dong et al, 2022). GhNPF4.8, −6.10, −6.14, −7.8 , −7.10 and −7.13 are highly expressed in roots and could regulate root uptake and xylem loading, while GhNPF4.8 and GhNPF6.18 were speculated to regulate phloem loading and intracellular transport due to their high expression in the stem and leaf (Dong et al, 2022). Nitrogen starvation induces the expression of some GhNPF genes.…”

Section: Regulation Of N Allocation To Vegetative and Reproductive Br...mentioning

confidence: 99%

“…Similarly, N‐starvation induces the high expression of GhNPF6.5 , − 6.7 , – 6.9 and – 7.8 in the shoots, whereas GhNPF2.12 , – 6.13 and – 6.17 are repressed. Though VIGS‐mediated silencing of GhNPF6.14 exhibited no difference in root biomass compared to the wildtype, the shoot of ghnpf6.14 ‐mutant accumulated less N, suggesting that GhNPF6.14 could be an essential regulator of vegetative growth in cotton (Dong et al, 2022).…”

Section: Regulation Of N Allocation To Vegetative and Reproductive Br...mentioning

confidence: 99%

Genetic regulation of nitrogen use efficiency in Gossypium spp

Ninkuu

Zhixin

Sun

2023

Plant Cell & Environment

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Cotton (Gossypium spp.) is the most important fibre crop, with desirable characteristics preferred for textile production. Cotton fibre output relies heavily on nitrate as the most important source of inorganic nitrogen (N). However, nitrogen dynamics in extreme environments limit plant growth and lead to yield loss and pollution. Therefore, nitrogen use efficiency (NUE), which involves the utilisation of the ‘right rate’, ‘right source’, ‘right time’, and ‘right place’ (4Rs), is key for efficient N management. Recent omics techniques have genetically improved NUE in crops. We herein highlight the mechanisms of N uptake and assimilation in the vegetative and reproductive branches of the cotton plant while considering the known and unknown regulatory factors. The phylogenetic relationships among N transporters in four Gossypium spp. have been reviewed. Further, the N regulatory genes that participate in xylem transport and phloem loading are also discussed. In addition, the functions of microRNAs and transcription factors in modulating the expression of target N regulatory genes are highlighted. Overall, this review provides a detailed perspective on the complex N regulatory mechanism in cotton, which would accelerate the research toward improving NUE in crops.

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“…These findings suggest that plant growth and productivity under stress conditions can be best achieved by improving N use efficiency. In addition, the GhNPF6.14 gene affects growth and nitrogen uptake and accumulation of cotton ( Dong et al., 2022 ). Nevertheless, the NPF gene family has been poorly characterized in abiotic stress response of cotton.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide investigation and expression profiles of the NPF gene family provide insight into the abiotic stress resistance of Gossypium hirsutum

et al. 2023

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Membrane transporters encoded by NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NPF) genes, which play crucial roles in plant growth, development and resistance to various stresses, are involved in the transport of nitrate (NO3-) and peptides. In several plant species, NPF genes are involved in the resistance to abiotic stresses; however, whether the whole NPF gene family in cotton contributes to this resistance has not been systematically investigated. Here, 201 genes encoding NPF proteins with a peptide transporter (PTR) domain were confirmed in three different Gossypium species, namely, Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii. The NPF proteins in these three Gossypium species and Arabidopsis thaliana were classified into three different subfamilies via phylogenetic analysis. Among the genes that encode these proteins, most GhNPF genes in the same subfamily contained similar gene structures and conserved domains. Predictions of the promoters of these genes revealed that the cis-acting elements included phytohormone- and light-responsive elements, indicating that some of these genes might be expressed in response to abiotic stress. Furthermore, 52 common potential candidate genes in 98 GhNPFs were predicted to exhibit specific spatiotemporal expression patterns in different tissues based on two RNA sequencing (RNA-seq) datasets. Finally, the gene expression profiles of abiotic stress indicated that 31 GhNPF genes were upregulated in at least one treatment period. Under abiotic stress for 12 and 24 h, the expression of GhNPF8 was upregulated upon cold treatment but downregulated with heat treatment, salt treatment and drought treatment. Furthermore, the expression of genes GhNPF8, GhNPF54 and GhNPF43 peaked at 6 h after heat and salt treatment. These results indicated that these genes exhibit underlying characteristics related to responses to abiotic stress. The verification of NPFs and analysis of their expression profiles in different tissues and in response to different abiotic stresses of cotton provide a basis for further studying the relationship between abiotic stress resistance and nitrogen (N) transport in cotton, as well as identifying candidate genes to facilitate their functional identification.

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Identification and Expression Analysis of the NPF Genes in Cotton

Cited by 4 publications

References 54 publications

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Genetic regulation of nitrogen use efficiency in Gossypium spp

Genome-wide investigation and expression profiles of the NPF gene family provide insight into the abiotic stress resistance of Gossypium hirsutum

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