Genome-wide identification of ABA receptor PYL/RCAR gene family and their response to cold stress in Medicago sativa L.

Abscisic acid (ABA) is an important phytohormone involved in plant growth, plant development, and the protection of plants against abiotic stresses. PYL/RCAR (pyrabactin resistance/pyr1-like/regulatory components of ABA receptor) is the receptor protein of ABA and the core component of the ABA signal transduction network. The PYL gene family has been identified and analyzed in many species, however, there is no report about the research on the whole genome-wide identification of the alfalfa (Medicago sativa L.) PYL gene family. Therefore, to explore the function of alfalfa PYL genes, 39 MsPYL genes were identified by analyzing the recently published genome of alfalfa. Using bioinformatics methods, we systematically analyzed the chromosome location, protein physicochemical properties, evolutionary relationship, conserved motifs, and response to low-temperature stress of the MsPYL family of alfalfa. The results showed that 39 alfalfa MsPYL genes were distributed on 24 chromosomes, and the analysis of gene duplication events showed that fragment duplication was predominant duplication in alfalfa MsPYL family gene expansion. The phylogenetic tree of MsPYL protein of alfalfa and the phylogenetic tree of PYL genes of 3 species show that the MsPYL gene family can be divided into 3 subfamilies, and the structures of the same subfamilies are relatively similar. The 39 MsPYL gene family members of alfalfa contain 10 Motifs. Motif1, Motif2, Motif3, and Motif5 are the conserved motifs shared by these genes; cis-regulatory elements in promoter regions indicate that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundantly present in the MsPYL promoter sequences; Real-time fluorescence quantitative PCR analysis showed that the expression of MsPYL genes can be induced by low-temperature treatment. This study provides a reference for further exploring the structural and functional characterization of the alfalfa PYL gene family. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01066-3.

Long-term phosphorus fertilization reveals the phosphorus limitation shaping the soil micro-food web stability in the Loess Plateau.

The intricate decomposition pathways within soil micro-food webs are vital for cycling soil organic carbon and nutrients, influencing the quality, productivity, and sustainability of soil systems. However, the impact of diverse phosphorus addition on these organic decomposition pathways still needs to be explored. In an 8-year experiment, phosphorus (P) fertilizer was added at varying levels (0 kg ha-1, CK; 60 kg ha-1, P60; 120 kg ha-1, P120; and 180 kg ha-1, P180), to investigate the response of the soil micro-food web. The results revealed a significant effect of phosphorus addition on soil microorganisms and nematodes, with P60 exerting a greater influence than other treatments. At P60, the Shannon index of nematodes and fungi surpassed other treatments, indicating higher diversity, while the Shannon index of bacteria was lower. The Chao1 index of bacteria and fungi at P60 was higher, contrasting with the lower index for nematodes. Metabolic footprints of bacterivores and omnivores-predators (BFMF and OPMF) were higher at P60, while metabolic footprints of fungivores and plant parasites (FFMF and PPMF) were lower, signifying altered energy flow. Functional metabolic footprints and energy flow analysis unveiled a stable soil micro-food web structure at P60, with enhanced energy conversion efficiency. Network analysis illustrated positive correlations between fungi, fungivorous nematodes (FF), and omnivorous-predatory nematodes (OP) at P60, while P120 and P180 showed positive correlations among bacteria, bacterivorous nematodes (BF), and OP. Path analysis underscored the higher contribution rate of BF-C, FF-C, and OP-C to soil organic carbon at P60 compared with P120 and P180. These findings suggest that nutrient interactions between fungi and nematodes regulate soil micro-food web decomposition under low phosphorus concentrations. In contrast, interactions between bacteria and nematodes dominate at high phosphorus concentrations. The study indicates that adding phosphorus has nuanced bottom-up effects, intricately shaping the structure and activity of the pathways and underscoring the need for a comprehensive understanding of nutrient dynamics in soil ecosystems.

Characterization of B-box family genes and their expression profiles under abiotic stresses in the Melilotus albus.

B-box (BBX) proteins are one of the zinc-finger transcription factor that plays a critical role in plant development, growth, and multiple stress responses. Although BBX genes have been reported in many model organisms, no comprehensive study has yet been conducted on the BBX genes in Melilotus albus, and the biological functions of this family remain unknown. In this study, a total of 20 BBX (MaBBX) genes were identified in M. albus and were phylogenetically divided into five clades. BBX members within the same clade showed similar conserved domain, suggesting similarity of potential biological function. Analysis of MaBBX conserved motifs showed that every subfamily contained two common motifs. Distribution mapping shows that BBX proteins are nonrandomly localized in eight chromosomes. The synteny showed that most homologous gene pairs of the MaBBX gene family were amplified by segmental replication, which meant segmental replication was the main way for the MaBBX gene family to evolve. Additionally, the cis-element analysis predicted light-responsive, various hormone and stress-related elements in the promoter regions of MaBBXs. Furthermore, the expression levels of all 20 MaBBX genes were detected by qRT-PCR under salt, cold, and dark stresses in M. albus. Moreover, it was observed that 16 genes had higher expression levels after 3 h of salt treatment, 10 genes were significantly upregulated after 3 h of cold treatment, and all genes were up regulated after 3 h of dark treatment, and then appeared to decline. In addition, it was also noticed that MaBBX13 may be an important candidate for improving tolerance to abiotic stress. The prediction of protein tertiary structure showed that the tertiary structures of members of the same subfamily of MaBBX proteins were highly similar. The hypothesis exhibited that most of the MaBBX proteins were predicted to be localized to the nucleus and cytoplasm and was validated by transient expression assays of MaBBX15 in tobacco leaf epidermal cells. This study provides useful information for further investigating and researching the regulatory mechanisms of BBX family genes in response to abiotic stresses in M. albus.

Spatial-Temporal Correlations between Soil pH and NPP of Grassland Ecosystems in the Yellow River Source Area, China.

In recent years, ecological concerns such as vegetation destruction, permafrost deterioration, and river drying have been paid much more attention to on the Yellow River Basin in China. Soil pH is regarded to be the fundamental variable among soil properties for vegetation growth, while net primary productivity (NPP) is also an essential indicator to reflect the healthy growth of vegetation. Due to the limitation of on-site samples, the spatial−temporal variations in soil pH and NPP, as well as their intrinsic mechanisms, remain unknown, especially in the Yellow River source area, China. Therefore, it is imperative to investigate the coupling relationship between soil pH and NPP of the area. The study coupled MODIS reflectance data (MOD09A1) with on-site soil pH to estimate spatial−temporal variations in soil pH, explore the response of NPP to soil pH, and assess the extent to which they contribute to grassland ecosystems, thus helping to fill knowledge gaps. Results indicated that the surface spectral reflectance for seven bands could express the geographic pattern of soil pH by applying a multiple linear regression equation; NPP exhibited an increasing trend while soil pH was the contrary in summer from 2000 to 2021. In summer, NPP was negatively correlated with soil pH and there was a lag effect in the response of NPP to soil pH, revealing a correlation between temperate steppes > montane meadows > alpine meadows > swamps in different grassland ecosystems. In addition, contribution indices for temperate steppes and montane meadows were positive whereas they were negative for swamps and alpine meadows, which are apparent findings. The contribution index of montane and alpine meadows was greater than that of temperate steppes and swamps. The approach of the study can enable managers to easily identify and rehabilitate alkaline soil and provides an important reference and practical value for ecological restoration and sustainable development of grassland ecosystems in alpine regions.

Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions.

The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.

Genome-Wide Identification and Expression Analysis of the SRS Gene Family in Medicago sativa.

SHI-related sequence (SRS) transcription factors, specific to plants, act as crucial regulators of plant organ growth and development. Here, we examined the Medicago sativa (alfalfa) SRS gene family (MsSRSs) to analyze the structure and function of MsSRSs using bioinformatics methods, and verify their abiotic stress responses through growth experiments. Twenty-seven MsSRS genes were identified from the genome-wide data of nontransgenic alfalfa. MsSRSs were distributed on 16 chromosomes and classified into seven different subfamilies by phylogenetic analysis. Forty-five cis-regulatory elements related to stress and phytohormone responsiveness, and tissue-specific expression occurred in the promoter sequences of MsSRSs. Ks values and Ka/Ks ratios of duplicate gene pairs showed that purifying selection affected most duplicate genes during their evolutionary history, while rapid recent positive selection strongly influenced MsSRS25 and MsSRS01. Real-time fluorescence quantitative PCR results showed that MsSRS genes could be induced by cold and salt stress. Within 12 h of salt stress exposure, the expression levels of seven and nine MsSRSs showed significant upregulation and downregulation, respectively. Within 12 h of cold stress exposure, the expression levels of the 3 and 13 selected MsSRSs showed significant upregulation and downregulation, respectively. Thus, this study provides novel comprehensive information on the MsSRS gene family, helpful for the study of SRS-mediated tolerance in alfalfa and the functional characteristics of SRS genes in other plants.

Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L.

The LIM (Lin-11, Isl-1 and Mec-3 domains) family is a key transcription factor widely distributed in animals and plants. The LIM proteins in plants are involved in the regulation of a variety of biological processes, including cytoskeletal organization, the development of secondary cell walls, and cell differentiation. It has been identified and analyzed in many species. However, the systematic identification and analysis of the LIM genes family have not yet been reported in alfalfa (Medicago sativa L.). Based on the genome-wide data of alfalfa, a total of 21 LIM genes were identified and named MsLIM01-MsLIM21. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the LIM gene family in alfalfa using bioinformatics methods. The results showed that these MsLIM genes were distributed unequally on 21 of the 32 chromosomes in alfalfa. Gene duplication analysis showed that segmental duplications were the major contributors to the expansion of the alfalfa LIM family. Based on phylogenetic analyses, the LIM gene family of alfalfa can be divided into four subfamilies: αLIM subfamily, ßLIM subfamily, γLIM subfamily, and δLIM subfamily, and approximately all the LIM genes within the same subfamily shared similar gene structure. The 21 MsLIM genes of alfalfa contain 10 Motifs, of which Motif1 and Motif3 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of MsLIM genes. Real-time quantitative PCR demonstrated that MsLIM gene expression is induced by low temperature and salt. The present study serves as a basic foundation for future functional studies on the alfalfa LIM family.