Transcriptomic and Metabolic Profiling Reveals a Lignin Metabolism Network Involved in Mesocotyl Elongation during Maize Seed Germination

Identification of key genes involved in lignin and flavonoid accumulation during Tilia tuan seed maturation

KEY MESSAGE

Transcriptomics and phenotypic data analysis identified 24 transcription factors (TFs) that play key roles in regulating the competitive accumulation of lignin and flavonoids. Tilia tuan Szyszyl. (T. tuan) is a timber tree species with important ecological and commercial value. However, its highly lignified pericarp results in a low seed germination rate and a long dormancy period. In addition, it is unknown whether there is an interaction between the biosynthesis of flavonoids and lignin as products of the phenylpropanoid pathway during seed development. To explore the molecular regulatory mechanism of lignin and flavonoid biosynthesis, T. tuan seeds were harvested at five stages (30, 60, 90, 120, and 150 days after pollination) for lignin and flavonoid analyses. The results showed that lignin accumulated rapidly in the early and middle stages (S1, S3, and S4), and rapid accumulation of flavonoids during the early and late stages (S1 and S5). High-throughput RNA sequencing analysis of developing seeds identified 50,553 transcripts, including 223 phenylpropanoid biosynthetic pathway genes involved in lignin accumulation grouped into 3 clusters, and 106 flavonoid biosynthetic pathway genes (FBPGs) grouped into 2 clusters. Subsequent WGCNA and time-ordered gene co-expression network (TO-GCN) analysis revealed that 24 TFs (e.g., TtARF2 and TtWRKY15) were involved in flavonoids and lignin biosynthesis regulation. The transcriptome data were validated by qRT-PCR to analyze the expression profiles of key enzyme-coding genes. This study revealed that there existed a competitive relationship between flavonoid and lignin biosynthesis pathway during the development of T. tuan seeds, that provide a foundation for the further exploration of molecular mechanisms underlying lignin and flavonoid accumulation in T. tuan seeds.

ZmNAC17 Regulates Mesocotyl Elongation by Mediating Auxin and ROS Biosynthetic Pathways in Maize

The mesocotyl is of great significance in seedling emergence and in responding to biotic and abiotic stress in maize. The NAM, ATAF, and CUC2 (NAC) transcription factor family plays an important role in maize growth and development; however, its function in the elongation of the maize mesocotyl is still unclear. In this study, we found that the mesocotyl length in zmnac17 loss-of-function mutants was lower than that in the B73 wild type. By using transcriptomic sequencing technology, we identified 444 differentially expressed genes (DEGs) between zmnac17-1 and B73, which were mainly enriched in the "tryptophan metabolism" and "antioxidant activity" pathways. Compared with the control, the zmnac17-1 mutants exhibited a decrease in the content of indole acetic acid (IAA) and an increase in the content of reactive oxygen species (ROS). Our results provide preliminary evidence that ZmNAC17 regulates the elongation of the maize mesocotyl.

Effects of combined extreme cold and drought stress on growth, photosynthesis, and physiological characteristics of cool-season grasses

Abiotic stress is an important factor affecting turf establishment and limiting the sustainability of the turf industry. To alleviate the effects of combined cold and drought stress in cold- and drought-prone regions, it is essential to select and introduce turfgrass germplasms that are suitable for these conditions for successful turf establishment. Thus, we evaluated the effects of combined extreme cold and drought stress on the morphological, plant leaf functional, photosynthetic, and physiological and biochemical traits of 16 wild annual bluegrass (Poa annua) germplasms. We found that there were significant differences (P < 0.05) among different provenances, combined cold and drought stress, and the main interaction factors. Combined cold and drought stress altered the morphological characteristics of the 16 germplasms to varying degrees. Furthermore, combined cold and drought stress significantly reduced the net photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (Tr), instantaneous water use efficiency (WUE), chlorophyll content, chlorophyll fluorescence parameters, accumulated intercellular CO2 concentration (Ci), and relative electrical conductivity (REC) and malondialdehyde (MDA), proline (Pro), soluble protein (SP), soluble sugar (SS), superoxide anion (O2.-), hydrogen peroxide (H2O2), and hydroxyl radical (·OH) and other active oxygen, and increased the superoxide dismutase activity (SOD), peroxidase activity (POD), catalase activity (CAT), ascorbate peroxidase activity (APX) and glutathione reductase (GR) activities. Comprehensive evaluation using principal component analysis (PCA), membership function analysis, and clustered heatmaps indicated that the 'HZ' germplasm had stronger combined cold and drought tolerance, whereas the 'ZQ' germplasm was more sensitive to combined cold and drought, which was roughly consistent with the order of morphological damage symptoms. Therefore, it is recommended to use the 'HZ' germplasm for planting projects in cold- and drought-prone areas, while the 'ZQ' germplasm is more suitable for use under warmer and non-water-deficient conditions.

Integrated QTL Mapping, Meta-Analysis, and RNA-Sequencing Reveal Candidate Genes for Maize Deep-Sowing Tolerance

Synergetic elongation of mesocotyl and coleoptile are crucial in governing maize seedlings emergence, especially for the maize sown in deep soil. Studying the genomic regions controlling maize deep-sowing tolerance would aid the development of new varieties that are resistant to harsh conditions, such as drought and low temperature during seed germination. Using 346 F2:3 maize population families from W64A × K12 cross at three sowing depths, we identified 33 quantitative trait loci (QTLs) for the emergence rate, mesocotyl, coleoptile, and seedling lengths via composite interval mapping (CIM). These loci explained 2.89% to 14.17% of phenotypic variation in a single environment, while 12 of 13 major QTLs were identified at two or more sowing environments. Among those, four major QTLs in Bin 1.09, Bin 4.08, Bin 6.01, and Bin 7.02 supported pleiotropy for multiple deep-sowing tolerant traits. Meta-analysis identified 17 meta-QTLs (MQTLs) based on 130 original QTLs from present and previous studies. RNA-Sequencing of mesocotyl and coleoptile in both parents (W64A and K12) at 3 cm and 20 cm sowing environments identified 50 candidate genes expressed differentially in all major QTLs and MQTLs regions: six involved in the circadian clock, 27 associated with phytohormones biosynthesis and signal transduction, seven controlled lignin biosynthesis, five regulated cell wall organization formation and stabilization, three were responsible for sucrose and starch metabolism, and two in the antioxidant enzyme system. These genes with highly interconnected networks may form a complex molecular mechanism of maize deep-sowing tolerance. Findings of this study will facilitate the construction of molecular modules for deep-sowing tolerance in maize. The major QTLs and MQTLs identified could be used in marker-assisted breeding to develop elite maize varieties.

New insights into light spectral quality inhibits the plasticity elongation of maize mesocotyl and coleoptile during seed germination

The plastic elongation of mesocotyl (MES) and coleoptile (COL), which can be repressed by light exposure, plays a vital role in maize seedling emergence and establishment under adverse environmental conditions. Understanding the molecular mechanisms of light-mediated repression of MES and COL elongation in maize will allow us to develop new strategies for genetic improvement of these two crucial traits in maize. A maize variety, Zheng58, was used to monitor the transcriptome and physiological changes in MES and COL in response to darkness, as well as red, blue, and white light. The elongation of MES and COL was significantly inhibited by light spectral quality in this order: blue light > red light > white light. Physiological analyses revealed that light-mediated inhibition of maize MES and COL elongation was closely related to the dynamics of phytohormones accumulation and lignin deposition in these tissues. In response to light exposure, the levels of indole-3-acetic acid, trans-zeatin, gibberellin 3, and abscisic acid levels significantly decreased in MES and COL; by contrast, the levels of jasmonic acid, salicylic acid, lignin, phenylalanine ammonia-lyase, and peroxidase enzyme activity significantly increased. Transcriptome analysis revealed multiple differentially expressed genes (DEGs) involved in circadian rhythm, phytohormone biosynthesis and signal transduction, cytoskeleton and cell wall organization, lignin biosynthesis, and starch and sucrose metabolism. These DEGs exhibited synergistic and antagonistic interactions, forming a complex network that regulated the light-mediated inhibition of MES and COL elongation. Additionally, gene co-expression network analysis revealed that 49 hub genes in one and 19 hub genes in two modules were significantly associated with the elongation plasticity of COL and MES, respectively. These findings enhance our knowledge of the light-regulated elongation mechanisms of MES and COL, and provide a theoretical foundation for developing elite maize varieties with improved abiotic stress resistance.

Genetic Variation, DIMBOA Accumulation, and Candidate Gene Identification in Maize Multiple Insect-Resistance

Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g^-1 FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g^-1 FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.

Understanding and Comprehensive Evaluation of Cold Resistance in the Seedlings of Multiple Maize Genotypes

Maize is a cold-sensitive crop, and it exhibits severe retardation of growth and development when exposed to cold snaps during and right after seedling emergence. Although different agronomic, physiological, and molecular approaches have been tried to overcome the problems related to cold stress in recent years, the mechanisms causing cold resistance in maize are still unclear. Screening and breeding of varieties for cold resistance may be a sustainable option to boost maize production under low-temperature environments. Herein, seedlings of 39 different maize genotypes were treated under both 10 °C low temperature and 22 °C normal temperature conditions for 7 days, to assess the changes in seven growth parameters, two membrane characteristics, two reactive oxygen species (ROS) levels, and four antioxidant enzymes activities. The changes in ten photosynthetic performances, one osmotic substance accumulation, and three polyamines (PAs) metabolisms were also measured. Results indicated that significant differences among genotypes, temperature treatments, and their interactions were found in 29 studied traits, and cold–stressed seedlings were capable to enhance their cold resistance by maintaining high levels of membrane stability index (66.07%); antioxidant enzymes activities including the activity of superoxide dismutase (2.44 Unit g⁻¹ protein), peroxidase (1.65 Unit g⁻¹ protein), catalase (0.65 μM min⁻¹ g⁻¹ protein), and ascorbate peroxidase (5.45 μM min⁻¹ g⁻¹ protein); chlorophyll (Chl) content, i.e., Chl a (0.36 mg g⁻¹ FW) and Chl b (0.40 mg g⁻¹ FW); photosynthetic capacity such as net photosynthetic rate (5.52 μM m⁻² s⁻¹) and ribulose 1,5–biphosphate carboxylase activity (6.57 M m⁻² s⁻¹); PAs concentration, mainly putrescine (274.89 nM g⁻¹ FW), spermidine (52.69 nM g⁻¹ FW), and spermine (45.81 nM g⁻¹ FW), particularly under extended cold stress. Importantly, 16 traits can be good indicators for screening of cold–resistant genotypes of maize. Gene expression analysis showed that GRMZM2G059991, GRMZM2G089982, GRMZM2G088212, GRMZM2G396553, GRMZM2G120578, and GRMZM2G396856 involved in antioxidant enzymes activity and PAs metabolism, and these genes may be used for genetic modification to improve maize cold resistance. Moreover, seven strong cold–resistant genotypes were identified, and they can be used as parents in maize breeding programs to develop new varieties.