Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.).

BACKGROUND: Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, little information is available about WRKY transcription factors in flax (Linum usitatissimum L.). RESULTS: In this study, comprehensive genome-wide characterization of the flax WRKY gene family was conducted that led to prediction of 102 LuWRKY genes. Based on bioinformatics-based predictions of structural and phylogenetic features of encoded LuWRKY proteins, 95 LuWRKYs were classified into three main groups (Group I, II, and III); Group II LuWRKYs were further assigned to five subgroups (IIa-e), while seven unique LuWRKYs (LuWRKYs 96-102) could not be assigned to any group. Most LuWRKY proteins within a given subgroup shared similar motif compositions, while a high degree of motif composition variability was apparent between subgroups. Using RNA-seq data, expression patterns of the 102 predicted LuWRKY genes were also investigated. Expression profiling data demonstrated that most genes associated with cellulose, hemicellulose, or lignin content were predominantly expressed in stems, roots, and less in leaves. However, most genes associated with stress responses were predominantly expressed in leaves and exhibited distinctly higher expression levels in developmental stages 1 and 8 than during other stages. CONCLUSIONS: Ultimately, the present study provides a comprehensive analysis of predicted flax WRKY family genes to guide future investigations to reveal functions of LuWRKY proteins during plant growth, development, and stress responses.

Construction of a high-density genetic linkage map and QTL mapping of oleic acid content and three agronomic traits in sunflower (Helianthus annuus L.) using specific-locus amplified fragment sequencing (SLAF-seq).

High-density genetic linkage maps are particularly important for quantitative trait loci (QTL) mapping, genome assembly, and marker-assisted selection (MAS) in plants. In this study, a high-density genetic linkage map of sunflower (Helianthus annuus L.) was constructed using an F2 population generated from a cross between Helianthus annuus L. '86-1' and 'L-1-OL-1' via specific-locus amplified fragment sequencing (SLAF-seq). After sequence preprocessing, 530.50 M reads (105.60 Gb) were obtained that contained a total of 343,197 SLAFs, of which 39,589 were polymorphic. Of the polymorphic SLAFs, 6,136 were organized into a linkage map consisting of 17 linkage groups (LGs) spanning 2,221.86 cM, with an average genetic distance of 0.36 cM between SLAFs. Based on this high-density genetic map, QTL analysis was performed that focused on four sunflower phenotypic traits: oleic acid content (OAC), plant height (PH), head diameter (HD), and stem diameter (SD). Subsequently, for these four traits eight QTLs were detected that will likely be useful for increasing our understanding of genetic factors underlying these traits and for use in marker-assisted selection (MAS) for future sunflower breeding.

Kinetic study on the isothermal and nonisothermal crystallization of monoglyceride organogels.

The isothermal and nonisothermal crystallization kinetics of monoglyceride (MAG) organogels were studied by pulsed nuclear magnetic resonance (pNMR) and differential scanning calorimetry (DSC), respectively. The Avrami equation was used to describe the isothermal crystallization kinetics and experimental data fitted the equation fairly well. Results showed that the crystal growth of MAG organogels was a rod-like growth of instantaneous nuclei at higher degrees of supercooling and a plate-like form with high nucleation rate at lower degrees of supercooling. The exothermic peak in nonisothermal DSC curves for the MAG organogels became wider and shifted to lower temperature when the cooling rate increased, and nonisothermal crystallization was analyzed by Mo equation. Results indicated that at the same crystallization time, to get a higher degree of relative crystallinity, a higher cooling rate was necessary. The activation energy of nonisothermal crystallization was calculated as 739.59 kJ/mol according to the Kissinger method. Therefore, as the results of the isothermal and nonisothermal crystallization kinetics for the MAG organogels obtained, the crystallization rate, crystal nucleation, and growth during the crystallization process could be preliminarily monitored through temperature and cooling rate regulation, which laid the foundation for the real industrial manufacture and application of the MAG organogels.

Proteome Analysis of the Soybean Nodule Phosphorus Response Mechanism and Characterization of Stress-Induced Ribosome Structural and Protein Expression Changes.

In agroecosystems, a plant-usable form of nitrogen is mainly generated by legume-based biological nitrogen fixation, a process that requires phosphorus (P) as an essential nutrient. To investigate the physiological mechanism whereby phosphorus influences soybean nodule nitrogen fixation, soybean root nodules were exposed to four phosphate levels: 1 mg/L (P stress), 11 mg/L (P stress), 31 mg/L (Normal P), and 61 mg/L (High P) then proteome analysis of nodules was conducted to identify phosphorus-associated proteome changes. We found that phosphorus stress-induced ribosomal protein structural changes were associated with altered key root nodule protein synthesis profiles. Importantly, up-regulated expression of peroxidase was observed as an important phosphorus stress-induced nitrogen fixation-associated adaptation that supported two nodule-associated activities: scavenging of reactive oxygen species (ROS) and cell wall growth. In addition, phosphorus transporter (PT) and purple acid phosphatase (PAPs) were up-regulated that regulated phosphorus transport and utilization to maintain phosphorus balance and nitrogen fixation function in phosphorus-stressed root nodules.

Identification of differentially expressed genes in flax (Linum usitatissimum L.) under saline-alkaline stress by digital gene expression.

The salinization and alkalization of soil are widespread environmental problems, and alkaline salt stress is more destructive than neutral salt stress. Therefore, understanding the mechanism of plant tolerance to saline-alkaline stress has become a major challenge. However, little attention has been paid to the mechanism of plant alkaline salt tolerance. In this study, gene expression profiling of flax was analyzed under alkaline-salt stress (AS2), neutral salt stress (NSS) and alkaline stress (AS) by digital gene expression. Three-week-old flax seedlings were placed in 25 mM Na2CO3 (pH11.6) (AS2), 50mM NaCl (NSS) and NaOH (pH11.6) (AS) for 18 h. There were 7736, 1566 and 454 differentially expressed genes in AS2, NSS and AS compared to CK, respectively. The GO category gene enrichment analysis revealed that photosynthesis was particularly affected in AS2, carbohydrate metabolism was particularly affected in NSS, and the response to biotic stimulus was particularly affected in AS. We also analyzed the expression pattern of five categories of genes including transcription factors, signaling transduction proteins, phytohormones, reactive oxygen species proteins and transporters under these three stresses. Some key regulatory gene families involved in abiotic stress, such as WRKY, MAPKKK, ABA, PrxR and ion channels, were differentially expressed. Compared with NSS and AS, AS2 triggered more differentially expressed genes and special pathways, indicating that the mechanism of AS2 was more complex than NSS and AS. To the best of our knowledge, this was the first transcriptome analysis of flax in response to saline-alkaline stress. These data indicate that common and diverse features of saline-alkaline stress provide novel insights into the molecular mechanisms of plant saline-alkaline tolerance and offer a number of candidate genes as potential markers of tolerance to saline-alkaline stress.

Identification of aroma-active compounds in Jiashi muskmelon juice by GC-O-MS and OAV calculation.

To identify aromatic compounds in Jiashi melon juice, gas chromatography-mass spectrometry-olfactometry (GC-MS-O) analysis was used. Odor activity values (OAVs) were also calculated on the basis of the qualitative and quantitative analysis of volatile compounds. Results showed that 42 volatiles were identified, among which 4 compounds, namely, diethyl carbonate, isophorone, 2-butoxyethyl acetate, and menthol, were identified or tentatively identified for the first time as volatiles in melon fruit. Twelve compounds, namely, (2E,6Z)-nona-2,6-dienal, (3Z,6Z)-nona-3,6-dien-1-ol, ethyl butanoate, ethyl 2-methylbutyrate, ethyl 2-methylpropanoate, (Z)-non-6-enal, (E)-2-nonenal, heptanal, methyl 2-methylbutyrate, nonanal, hexanal, and 2-methylpropyl acetate, were identified as the potent odorants of Jiashi melon juice by both OAV and detection frequency analysis (DFA). In addition, seven odorants were detected by all of the panelists and showed higher OAVs, indicating that DFA and OAV resulted in relatively similar "Jiashi" melon aroma patterns.