Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

Zheng, Xianfeng; Zhang, Hao; Zhang, Limei; Xu, Fangsen; Shi, Lei; Wang, Sheliang; Hong, Juan; Ding, Guangda

doi:10.3390/ijms221910354

Cited by 11 publications

(7 citation statements)

References 61 publications

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“…To better understand the biological functions of the PcNF-YAs, an exon-intron structure analysis of the PcNF-YA genes was performed and showed that the number of exons in most PcNF-YA genes was five. This finding was consistent with the results for Brassica napus [ 35 ], S. tuberosum [ 15 ], R. communis [ 14 ] and Prunus persica [ 11 ]. This evidence indicates that the structure of PcNF-YA genes is relatively stable and evolutionarily conserved.…”

Section: Discussionsupporting

confidence: 92%

Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus × canescens

Zhou

Yang

Chen

et al. 2022

IJMS

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The NF-YA gene family is a class of conserved transcription factors that play important roles in plant growth and development and the response to abiotic stress. Poplar is a model organism for studying the rapid growth of woody plants that need to consume many nutrients. However, studies on the response of the NF-YA gene family to nitrogen in woody plants are limited. In this study, we conducted a systematic and comprehensive bioinformatic analysis of the NF-YA gene family based on Populus × canescens genomic data. A total of 13 PcNF-YA genes were identified and mapped to 6 chromosomes. According to the amino acid sequence characteristics and genetic structure of the NF-YA domains, the PcNF-YAs were divided into five clades. Gene duplication analysis revealed five pairs of replicated fragments and one pair of tandem duplicates in 13 PcNF-YA genes. The PcNF-YA gene promoter region is rich in different cis-acting regulatory elements, among which MYB and MYC elements are the most abundant. Among the 13 PcNF-YA genes, 9 contained binding sites for P. × canescens miR169s. In addition, RT-qPCR data from the roots, wood, leaves and bark of P. × canescens showed different spatial expression profiles of PcNF-YA genes. Transcriptome data and RT-qPCR analysis showed that the expression of PcNF-YA genes was altered by treatment with different nitrogen forms. Furthermore, the functions of PcNF-YA genes in transgenic poplar were analyzed, and the potential roles of PcNF-YA genes in the response of poplar roots to different nitrogen forms were revealed, indicating that these genes regulate root growth and development.

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Section: Discussionsupporting

confidence: 92%

Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus × canescens

Zhou

Yang

Chen

et al. 2022

IJMS

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“…After nine days of growth, the plants were transferred to nutrient solution free of N, P or K for seven days. The same amount of NaCl were applied instead of NaNO 3 , NaH 2 PO 4 •2H 2 O and KCl in the three nutrient deficiency treatments, respectively [70]. For the ammonium toxicity treatment, plants were treated with nutrient solution containing 6 mM NH 4 Cl instead of NaNO 3 for 9 days.…”

Section: Plant Materials and Treatmentsmentioning

confidence: 99%

Nitrogen Assimilation Related Genes in Brassicanapus: Systematic Characterization and Expression Analysis Identified Hub Genes in Multiple Nutrient Stress Responses

Zhang

et al. 2021

Plants

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Nitrogen (N) is an essential macronutrient for plants. However, little is known about the molecular regulation of N assimilation in Brassica napus, one of the most important oil crops worldwide. Here, we carried out a comprehensive genome-wide analysis of the N assimilation related genes (NAGs) in B. napus. A total of 67 NAGs were identified encoding major enzymes involved in N assimilation, including asparagine synthetase (AS), glutamate dehydrogenase (GDH), glutamine oxoglutarate aminotransferase (GOGAT), glutamine synthetase (GS), nitrite reductase (NiR), nitrate reductase (NR). The syntenic analysis revealed that segmental duplication and whole-genome duplication were the main expansion pattern during gene evolution. Each NAG family showed different degrees of differentiation in characterization, gene structure, conserved motifs and cis-elements. Furthermore, diverse responses of NAG to multiple nutrient stresses were observed. Among them, more NAGs were regulated by N deficiency and ammonium toxicity than by phosphorus and potassium deprivations. Moreover, 12 hub genes responding to N starvation were identified, which may play vital roles in N utilization. Taken together, our results provide a basis for further functional research of NAGs in rapeseed N assimilation and also put forward new points in their responses to contrasting nutrient stresses.

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“…In general, homologous genes in the same species show differences in their expression in response to abiotic stress and hormonal treatment, suggesting that they may play different roles in stress resistance [ 27 , 28 , 29 ]. In this study, the MsRCI2D,-E genes in alfalfa could respond to salt and alkali stress and be regulated by ABA; the expression levels of the MsRCI2D,-E genes in roots and leaves showed an overall trend first increasing and then decreasing, but the up-regulation of the MsRCI2E gene was more rapid than that of the MsRCI2D gene ( Figure 2 ).…”

Section: Discussionmentioning

confidence: 99%

Overexpression of MsRCI2D and MsRCI2E Enhances Salt Tolerance in Alfalfa (Medicago sativa L.) by Stabilizing Antioxidant Activity and Regulating Ion Homeostasis

Zhang

et al. 2022

IJMS

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Rare cold-inducible 2 (RCI2) genes from alfalfa (Medicago sativa L.) are part of a multigene family whose members respond to a variety of abiotic stresses by regulating ion homeostasis and stabilizing membranes. In this study, salt, alkali, and ABA treatments were used to induce MsRCI2D and MsRCI2E expression in alfalfa, but the response time and the expression intensity of the MsRCI2D,-E genes were different under specific treatments. The expression intensity of the MsRCI2D gene was the highest in salt- and alkali-stressed leaves, while the MsRCI2E gene more rapidly responded to salt and ABA treatment. In addition to differences in gene expression, MsRCI2D and MsRCI2E differ in their subcellular localization. Akin to MtRCI2D from Medicago truncatula, MsRCI2D is also localized in the cell membrane, while MsRCI2E is different from MtRCI2E, localized in the cell membrane and the inner membrane. This difference might be related to an extra 20 amino acids in the C-terminal tail of MsRCI2E. We investigated the function of MsRCI2D and MsRCI2E proteins in alfalfa by generating transgenic alfalfa chimeras. Compared with the MsRCI2E-overexpressing chimera, under high-salinity stress (200 mmol·L−1 NaCl), the MsRCI2D-overexpressing chimera exhibited a better phenotype, manifested as a higher chlorophyll content and a lower MDA content. After salt treatment, the enzyme activities of SOD, POD, CAT, and GR in MsRCI2D- and -E-overexpressing roots were significantly higher than those in the control. In addition, after salt stress, the Na+ content in MsRCI2D- and -E-transformed roots was lower than that in the control; K+ was higher than that in the control; and the Na+/K+ ratio was lower than that in the control. Correspondingly, H+-ATPase, SOS1, and NHX1 genes were significantly up-regulated, and the HKT gene was significantly down-regulated after 6 h of salt treatment. MsRCI2D was also found to regulate the expression of the MsRCI2B and MsRCI2E genes, and the MsRCI2E gene could alter the expression of the MsRCI2A, MsRCI2B, and MsRCI2D genes. MsRCI2D- and -E-overexpressing alfalfa was found to have higher salt tolerance, manifested as improved activity of antioxidant enzymes, reduced content of reactive oxygen species, and sustained Na+ and K+ ion balance by regulating the expression of the H+-ATPase, SOS1, NHX1, HKT, and MsRCI2 genes.

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Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

Cited by 11 publications

References 61 publications

Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus × canescens

Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus × canescens

Nitrogen Assimilation Related Genes in Brassicanapus: Systematic Characterization and Expression Analysis Identified Hub Genes in Multiple Nutrient Stress Responses

Overexpression of MsRCI2D and MsRCI2E Enhances Salt Tolerance in Alfalfa (Medicago sativa L.) by Stabilizing Antioxidant Activity and Regulating Ion Homeostasis

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