Rice (Oryza sativa L.) is one of the most important staple food crops worldwide, while its growth and productivity are threatened by various abiotic stresses, especially salt stress. Unraveling how rice adapts to salt stress at the transcription level is vital. It can provide valuable information on enhancing the salt stress tolerance performance of rice via genetic engineering technologies. Here, we conducted a meta-analysis of different rice genotypes at the seedling stage based on 96 public microarray datasets, aiming to identify the key salt-responsive genes and understand the molecular response mechanism of rice under salt stress. In total, 5559 genes were identified to be differentially expressed genes (DEGs) under salt stress, and 3210 DEGs were identified during the recovery process. The Gene Ontology (GO) enrichment results revealed that the salt-response mechanisms of shoots and roots were different. A close-knit signaling network, consisting of the Ca²⁺ signal transduction pathway, the mitogen-activated protein kinase (MAPK) cascade, multiple hormone signals, transcription factors (TFs), transcriptional regulators (TRs), protein kinases (PKs), and other crucial functional proteins, plays an essential role in rice salt stress response. In this study, many unreported salt-responsive genes were found. Besides this, MapMan results suggested that TNG67 can shift to the fermentation pathway to produce energy under salt stress and may enhance the Calvin cycle to repair a damaged photosystem during the recovery stage. Taken together, these findings provide novel insights into the salt stress molecular response and introduce numerous candidate genes for rice salt stress tolerance breeding.

Sugar transporter proteins (STPs), such as H⁺/sugar symporters, play essential roles in plants’ sugar transport, growth, and development, and possess an important potential to enhance plants’ performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.

Flavonoids as a class of important secondary metabolites are widely present in land plants, and chalcone isomerase (CHI) is the key rate-limiting enzyme that participates in catalyzing the stereospecific isomerization of chalcones to yield their corresponding flavanones. However, the phylogenetic dynamics and functional divergence of CHI family genes during the evolutionary path of green plants remains poorly understood. Here, a total of 122 CHI genes were identified by performing a genome-wide survey of 15 representative green plants from the most ancestral basal plant chlorophyte algae to higher angiosperm plants. Phylogenetic, orthologous groups (OG) classification, and genome structure analysis showed that the CHI family genes have evolved into four distinct types (types I–IV) containing eight OGs after gene duplication, and further studies indicated type III CHIs consist of three subfamilies (FAP1, FAP2, and FAP3). The phylogeny showed FAP3 CHIs as an ancestral out-group positioned on the outer layers of the main branch, followed by type IV CHIs, which are placed in an evolutionary intermediate between FAP3 CHIs and bona fide CHIs (including type I and type II). The results imply a potential intrinsic evolutionary connection between CHIs existing in the green plants. The amino acid substitutions occurring in several residues have potentially affected the functional divergence between CHI proteins. This is supported by the analysis of transcriptional divergence and cis-acting element analysis. Evolutionary dynamics analyses revealed that the differences in the total number of CHI family genes in each plant are primarily attributed to the lineage-specific expansion by natural selective forces. The current studies provide a deeper understanding of the phylogenetic relationships and functional diversification of CHI family genes in green plants, which will guide further investigation on molecular characteristics and biological functions of CHIs.

The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs’ biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of GAox genes in six Gramineae representative crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa (Os). A total of 105 GAox genes were identified in these six crop genomes, belonging to the C₁₉-GA2ox, C₂₀-GA2ox, GA3ox, and GA20ox subfamilies. Based on orthogroup (OG) analysis, GAox genes were divided into nine OGs and the number of GAox genes in each of the OGs was similar among all tested crops, which indicated that GAox genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C₁₉-GA2ox, and C₂₀-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that GAox genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more GAox genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that GAox genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that GAox genes were predominantly expressed in the panicles of the above two plants and the expression of several GAox genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into GAox genes’ evolutionary differences among six representative Gramineae and highlighted GAox genes that may play a role in abiotic stress.

Effective panicle numbers (PNs) and Tiller numbers (TNs) are important traits affecting rice (Oryza sativa L.) architecture and grain yield. However, the molecular mechanisms underlying PN and TN heterosis remain unknown in rice. In addition, new PN- or TN-related genes need to be detected and discovered. In this study, in order to detect rice quantitative trait loci (QTLs) and the heterosis-related loci of PN or TN in rice, we developed a high generation recombinant inbred line (RIL) population from a cross of two elite cultivars, Luohui9 (Xian/Indica) and RPY geng (Geng/Japonica), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines, YTA (Xian/Indica) and Z7A (Geng/Japonica). Finally, nine QTLs of PN across four seasons were identified, and two QTLs of TN in 191HB were mapped. Besides this, six heterosis-related QTLs of PN and five heterosis-related QTLs of TN were located. We found that heterosis-related QTLs of PN or TN covered multiple known genes, such as MOC1, TAC1 and OsETR2. Furthermore, homologous gene analysis identified one candidate gene of PN (LOC_10g25720). Together, these findings uncover multiple heterosis-related loci, and provide a new insight into the heterosis mechanism of PN and TN in rice.