Carbon (C) and nitrogen (N) are fundamental elements essential for plant growth and development, serving as the structural and functional backbone of organic compounds and driving essential biological processes such as photosynthesis, carbohydrate metabolism, and N assimilation. The metabolism and transport of C involve the movement of sugars between shoots and roots through xylem and phloem transport systems, regulated by a sugar-signaling hub. Nitrogen uptake, transport, and metabolism are equally critical, with plants assimilating nitrate and ammonium through specialized transporters and enzymes in response to varying N levels to optimize growth and development. The coordination of C and N metabolism is key to plant productivity and the maintaining of agroecosystem stability. However, inefficient utilization of N fertilizers results in substantial environmental and economic challenges, emphasizing the urgent need to improve N use efficiency (NUE) in crops. Integrating efficient photosynthesis with N uptake offers opportunities for sustainable agricultural practices. This review discusses recent advances in understanding C and N transport, metabolism, and signaling in plants, with a particular emphasis on NUE-related genes in rice, and explores breeding strategies to enhance crop efficiency and agricultural sustainability.

Diverse heterotic groups have been developed in China over several decades, but their genomic divergences have not been systematically studied after improvement. In this study, we performed Maize6H-60K array of 5,822 maize accessions and whole-genome re-sequencing of 150 inbred lines collected in China. Using multiple population structure analysis methods, we established a genetic boundary used to categorize heterotic groups and germplasm resources. We identified three chloroplast–cytoplasmic types that evolved during adaptation to diverse climatic environments in maize through phylogenetic and haplotype analyses. Comparative analyses revealed obvious genetic differences between heterotic groups and germplasm resources at both the chloroplast and nuclear genome levels, especially in the unique heterotic groups HG1 and HG2, which exhibited distinct regionality and genetic uniqueness. The divergent differentiation of heterotic groups from germplasm resources was driven by differential selection in specific genomic regions. Genome-wide selective sweep analysis identified core selected regions and candidate selected genes associated with traits between heterotic groups, highlighting that stress response- and plant defense-related genes were selected for environmental adaptation across a broad latitudinal range in China. Meanwhile, a genome-wide association study analysis provided evidence that core selected genes served as an important candidate gene pool with a potential role in genetic improvement. Gene exchanges among heterotic groups, which avoided the predominant heterotic patterns as much as possible, occurred to achieve population improvement during modern maize breeding. This study provides insights into the population differentiation and genetic characteristics of heterotic groups, which will facilitate the utilization of germplasm resources, the creation of novel maize germplasm, and the optimization of heterotic patterns during future maize breeding in China.

Maize (Zea mays L.) growth and yield are severely limited by drought stress worldwide. Stomata play crucial roles in transpiration and gas exchange and are thus essential for improving plant water-use efficiency (WUE) to help plants deal with the threat of drought. In this study, we characterized the maize dsd1 (decreased stomatal density 1) mutant, which showed defects in stomatal development, including guard mother cell differentiation, subsidiary cell formation and guard cell maturation. DSD1 encodes the basic helix-loop-helix transcription factor INDUCER OF CBF EXPRESSION b (ZmICEb) and is a homolog of ICE1 in Arabidopsis (Arabidopsis thaliana). DSD1/ZmICEb is expressed in stomatal file cells throughout stomatal development and plays a conserved role in stomatal development across maize and Arabidopsis. Mutations in DSD1/ZmICEb dramatically improved drought tolerance and WUE in maize and reduced yield losses under drought conditions. Therefore, DSD1/ZmICEb represents a promising candidate target gene for the genetic improvement of drought tolerance in maize by manipulating stomatal density.

Avena barbata, a wild oat species within the genus Avena, is a widely used model for studying plant ecological adaptation due to its strong environmental adaptability and disease resistance, serving as a valuable genetic resource for oat improvement. Here, we phased the high-quality chromosome-level genome assembly of A. barbata (6.88 Gb, contig N50 = 53.74 Mb) into A (3.57 Gb with 47,687 genes) and B (3.31 Gb with 46,029 genes) subgenomes. Comparative genomics and phylogenomic analyses clarified the evolutionary relationships and trajectories of A, B, C and D subgenomes in Avena. We inferred that the A subgenome donor of A. barbata was Avena hirtula, while the B subgenome donor was probably an extinct diploid species closely related to Avena wiestii. Genome evolution analysis revealed the dynamic transposable element (TE) content and subgenome divergence, as well as extensive structure variations across A, B, C, and D subgenomes in Avena. Population genetic analysis of 211 A. barbata accessions from distinct ecotypes identified several candidate genes related to environmental adaptability and drought resistance. Our study provides a comprehensive genetic resource for exploring the genetic basis underlying the strong environmental adaptability of A. barbata and the molecular identification of important agronomic traits for oat breeding.

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we studied dioicy-monoicy transitions in the ancient liverwort haploid-dominant plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

Successful reproduction depends on the stable germination and growth of the pollen tubes (PT). However, the molecular mechanisms involved in rice PT growth and development remain largely unknown. In a previous study, microarray transcriptome analysis identified 627 genes preferentially expressed in the tricellular and germinating pollen of rice (i.e., Oryza sativa ssp. japonica). To elucidate key genes involved in the gene transfer process facilitated by male gametophytes, we systematically screened T-DNA lines containing disrupted sequences that corresponded to these 627 genes and analyzed the genotypes of heterozygote progeny from 107 T-DNA-indexed lines covering 105 genes. We found that 42 lines exhibited a distorted segregation ratio among the wild-type (WT), heterozygote (HT), and homozygote (HM) genotypes, which deviated from the expected Mendelian ratio of 1:2:1 (WT:HT:HM). Further characterization using CRISPR/Cas9 mutants revealed that knockout mutants of certain genes that exhibited segregation distortion in the T-DNA insertion region were completely sterile. Moreover, even when T-DNA insertion lines followed Mendelian segregation patterns, sterility could be induced by simultaneously mutating functionally redundant genes, thereby overcoming genetic compensation. Interestingly, although some T-DNA insertion lines exhibited segregation ratios approximating 1:1:0, the corresponding CRISPR/Cas9 mutants produced homozygous seeds and showed partial sterility. Partial sterility suggests that despite mutant pollen grains being less competitive than WT pollen, they retain their fertilization potential under relaxed competition from WT pollen. Beyond mutant-based analysis, transcriptomic profiling of sterile mutant lines provided additional insight into the regulatory relationship between key germination regulators and the 105 target genes studied here. Overall, this study demonstrates the effectiveness of a multi-pronged strategy to accelerate the identification of defective phenotypes using mutant studies and provides valuable genetic resources for inducing novel male sterility in rice.