Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

Guard cell anion channel PbrSLAC1 regulates stomatal closure through PbrSnRK2.3 protein kinases

Stomatal pores on the leaf surface are the gateways for gas exchange between plants and the atmosphere, which is regulated mainly by the S-type anion channel SLAC1. However, the gene encoding the main S-type anion channel SLAC1 in pear and its genetic characteristics remain unknown. In this study, Pbr015894.1 was identified as the candidate for PbrSLAC1 in pear, and it was found to be expressed abundantly in leaves, particularly in the guard cells. Virus-induced gene silencing experiments indicated that stomatal closure was achieved by a change in cell turgor instigated by PbrSLAC1 channel transport of NO₃^- in pear leaves and induced by abscisic acid. Furthermore, the expression of PbrSLAC1 in Arabidopsis slac1-3 and slac1-4 rescued the defective NO₃^- transport seen in these mutants, pointing to its role in anion transport. Fluorescence microscopy suggested that PbrSLAC1 was localized in the plasma membrane, and a dual-luciferase assay system demonstrated an interaction between PbrSLAC1 and PbrSnRK2.3/2.8. Moreover, anion conductance mediated by PbrSLAC1 was activated by PbrSnRK2.3 in Xenopus laevis oocytes and the channel showed greater permeability for nitrate than chloride, sulfate, or malate ions. Taken together, these results demonstrate that PbrSLAC1, an anion channel regulated by PbrSnRK2.3, is involved in stomatal closure by mediating the efflux of NO₃^- in pear leaf.

Cassava (Manihot esculenta) Slow Anion Channel (MeSLAH4) Gene Overexpression Enhances Nitrogen Assimilation, Growth, and Yield in Rice

Nitrogen is one of the most important nutrient elements required for plant growth and development, which is also immensely related to the efficient use of nitrogen by crop plants. Therefore, plants evolved sophisticated mechanisms and anion channels to extract inorganic nitrogen (nitrate) from the soil or nutrient solutions, assimilate, and recycle the organic nitrogen. Hence, developing crop plants with a greater capability of using nitrogen efficiently is the fundamental research objective for attaining better agricultural productivity and environmental sustainability. In this context, an in-depth investigation has been conducted into the cassava slow type anion channels (SLAHs) gene family, including genome-wide expression analysis, phylogenetic relationships with other related organisms, chromosome localization, and functional analysis. A potential and nitrogen-responsive gene of cassava (MeSLAH4) was identified and selected for overexpression (OE) analysis in rice, which increased the grain yield and root growth related performance. The morpho-physiological response of OE lines was better under low nitrogen (0.01 mm NH₄NO₃) conditions compared to the wild type (WT) and OE lines under normal nitrogen (0.5 mm NH₄NO₃) conditions. The relative expression of the MeSLAH4 gene was higher (about 80-fold) in the OE line than in the wild type. The accumulation and flux assay showed higher accumulation of NO 3 - and more expansion of root cells and grain dimension of OE lines compared to the wild type plants. The results of this experiment demonstrated that the MeSLAH4 gene may play a vital role in enhancing the efficient use of nitrogen in rice, which could be utilized for high-yielding crop production.

Genome-Wide Identification and Comparative Analysis of the ASR Gene Family in the Rosaceae and Expression Analysis of PbrASRs During Fruit Development

The members of the Abscisic Acid (ABA) Stress and Ripening gene family (ASR) encode a class of plant-specific proteins with ABA/WDS domains that play important roles in fruit ripening, abiotic stress tolerance and biotic stress resistance in plants. The ASR gene family has been widely investigated in the monocotyledons and dicotyledons. Although the genome sequence is already available for eight fruit species of the Rosaceae, there is far less information about the evolutionary characteristics and the function of the ASR genes in the Rosaceae than in other plant families. Twenty-seven ASR genes were identified from species in the Rosaceae and divided into four subfamilies (I, II, III, and IV) on the basis of structural characteristics and phylogenetic analysis. Purifying selection was the primary force for ASR family gene evolution in eight Rosaceae species. qPCR experiments showed that the expression pattern of PbrASR genes from Pyrus bretschneideri was organ-specific, being mainly expressed in flower, fruit, leaf, and root. During fruit development, the mRNA abundance levels of different PbrASR genes were either down- or up-regulated, and were also induced by exogenous ABA. Furthermore, subcellular localization results showed that PbrASR proteins were mainly located in the nucleus and cytoplasm. These results provide a theoretical foundation for investigation of the evolution, expression, and functions of the ASR gene family in commercial fruit species of the Rosaceae family.

Identification and Expression Analysis of SLAC/SLAH Gene Family in Brassica napus L

Slow type anion channels (SLAC/SLAHs) play important roles during anion transport, growth and development, abiotic stress responses and hormone responses in plants. However, there is few report on SLAC/SLAHs in rapeseed (Brassica napus). Genome-wide identification and expression analysis of SLAC/SLAH gene family members were performed in B. napus. A total of 23 SLAC/SLAH genes were identified in B. napus. Based on the structural characteristics and phylogenetic analysis of these members, the SLAC/SLAHs could be classified into three main groups. Transcriptome data demonstrated that BnSLAH3 genes were detected in various tissues of the rapeseed and could be up-regulated by low nitrate treatment in roots. BnSLAC/SLAHs were exclusively localized on the plasma membrane in transient expression of tobacco leaves. These results will increase our understanding of the evolution and expression of the SLAC/SLAHs and provide evidence for further research of biological functions of candidates in B. napus.

Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

Background

The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae.

Results

A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment.

Conclusions

This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07201-w.

Genome-wide identification of lysin motif containing protein family genes in eight rosaceae species, and expression analysis in response to pathogenic fungus Botryosphaeria dothidea in Chinese white pear

BACKGROUND

Lysin motif-containing proteins (LYP), which act as pattern-recognition receptors, play central roles in growth, node formation, and responses to biotic stresses. The sequence of Chinese white pear genome (cv. 'Dangshansuli') along with the seven other species of Rosaceae has already been reported. Although, in these fruit crops, there is still a lack of clarity regarding the LYP family genes and their evolutionary history.

RESULTS

In the existing study, eight Rosaceae species i.e., Pyrus communis, Prunus persica, Fragaria vesca, Pyrus bretschneideri, Prunus avium, Prunus mume, Rubus occidentalis, and Malus × domestica were evaluated. Here, we determined a total of 124 LYP genes from the underlined Rosaceae species. While eighteen of the genes were from Chinese white pear, named as PbrLYPs. According to the LYPs structural characteristics and their phylogenetic analysis, those genes were classified into eight groups (group LYK1, LYK2, LYK3, LYK4/5, LYM1/3, LYM2, NFP, and WAKL). Dispersed duplication and whole-genome duplication (WGD) were found to be the most contributing factors of LYP family expansion in the Rosaceae species. More than half of the duplicated PbrLYP gene pairs were dated back to the ancient WGD (~ 140 million years ago (MYA)), and PbrLYP genes have experienced long-term purifying selection. The transcriptomic results indicated that the PbrLYP genes expression was tissue-specific. Most PbrLYP genes showed differential expression in leaves under fungal pathogen infection with two of them located in the plasmalemma.

CONCLUSION

A comprehensive analysis identified 124 LYP genes in eight Rosaceae species. Our findings have provided insights into the functions and characteristics of the Rosaceae LYP genes and a guide for the identification of other candidate LYPs for further genetic improvements for pathogen-resistance in higher plants.

Genome-wide identification, and characterization of the CDPK gene family reveal their involvement in abiotic stress response in Fragaria x ananassa

Calcium-dependent protein kinases (CDPKs) are encoded by a large gene family and play important roles against biotic and abiotic stresses and in plant growth and development. To date, little is known about the CDPK genes in strawberry (Fragaria x ananassa). In this study, analysis of Fragaria x ananassa CDPK gene family was performed, including gene structures, phylogeny, interactome and expression profiles. Nine new CDPK genes in Fragaria x ananassa were identified based on RNA-seq data. These identified strawberry FaCDPK genes were classified into four main groups, based on the phylogenetic analysis and structural features. FaCDPK genes were differentially expressed during fruit development and ripening, as well as in response to abiotic stress (salt and drought), and hormone (abscisic acid) treatment. In addition, the interaction network analysis pointed out proteins involved in the ABA-dependent response to plant stress via Ca2+ signaling, especially RBOHs. To our knowledge, this is the first report on CDPK families in Fragaria x ananassa, and it will provide valuable information for development of biofortified fruits and stress tolerant plants.

Lanthanum Prolongs Vase Life of Cut Tulip Flowers by Increasing Water Consumption and Concentrations of Sugars, Proteins and Chlorophylls

We evaluated the effect of separately adding two sources of lanthanum (La), LaCl₃ and La(NO₃)₃ × 6H₂O at a concentration of 40 µM each, to the preservative solution of 15 cut tulip flower varieties. Ascorbic acid (AsA; 0.2 g/L) was used as a reference solution, while distilled water was used as control. The variety Laura Fygi recorded the longest vase life with 13 days. The highest water consumption per gram of stem fresh biomass weight (FBW) (2.5 mL) was observed in the variety Violet Beauty, whereas the lowest (1.098 mL) was recorded in Pink Impression. At the end of the vase life period, higher concentrations of total soluble sugars in petals and total soluble proteins in leaves were recorded in La-treated stems, compared to the AsA treatment and the control. Additionally, La(NO₃)₃ × 6H₂O supply increased the fresh weight of stems in vase and prolonged vase life. Moreover, this treatment resulted in the highest foliar concentration of chlorophylls at the end of vase life. Therefore, La increases tulip flower vase life as a consequence of improving the concentrations of some vital biomolecules.

PbrSLAH3 is a nitrate-selective anion channel which is modulated by calcium-dependent protein kinase 32 in pear

BACKGROUND

The functional characteristics of SLAC/SLAH family members isolated from Arabidopsis thaliana, poplar, barley and rice have been comprehensively investigated. However, there are no reports regarding SLAC/SLAH family genes from Rosaceae plants.

RESULTS

In this study, the function of PbrSLAH3, which is predominately expressed in pear (Pyrus bretschneideri) root, was investigated. PbrSLAH3 can rescue the ammonium toxicity phenomenon of slah3 mutant plants under high-ammonium/low-nitrate conditions. In addition, yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that PbrSLAH3 interacts with PbrCPK32. Moreover, when PbrSLAH3 was co-expressed with either the Arabidopsis calcium-dependent protein kinase (CPK) 21 or PbrCPK32 in Xenopus oocytes, yellow fluorescence was emitted from the oocytes and typical anion currents were recorded in the presence of extracellular NO3-. However, when PbrSLAH3 alone was injected, no yellow fluorescence or anion currents were recorded, suggesting that anion channel PbrSLAH3 activity was controlled through phosphorylation. Finally, electrophysiological and transgene results showed that PbrSLAH3 was more permeable to NO3- than Cl-.

CONCLUSION

We suggest that PbrSLAH3 crossing-talk with PbrCPK32 probably participate in transporting of nitrate nutrition in pear root.