Background: Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood. Results: We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations. Conclusions: Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies.

For the development of nanotechnology, nanomaterials are in an important position. Due to their special structure and a series of unique properties, nano-metal oxide materials are widely used in nanoelectronics, catalysis, environmental monitoring, electrochemical sensors, and many other fields. Rice, as the most important food crop in the world, has a wide range of planting areas. Therefore, in this paper, the research on the construction of rice transgenic vectors is based on nano-metal oxide materials. In this paper, particle swarm optimization is used to optimize the weights of rice-growing convolutional neural networks. Secondly, it used rice as the test plant to study the effects of seven metal oxide nanomaterials on rice seed germination and root elongation. This sheds light on the toxic effects of metal oxide nanomaterials on rice growth and discusses the factors that affect the phytotoxicity of nanomaterials. The experimental results show that before optimization, the accuracy of the small batch sample test is 87.0456%, the accuracy of the large batch sample test is 93.5876%, and the accuracy of the test is increased by 6.542%. After optimization, the accuracy of the small batch sample test is 93.5876%, the accuracy of the large batch sample test is 99.0133%, and the accuracy of the test is increased by 5.4466%. The inhibition rates of nano-CuO and ZnO on rice root length were 97.28% and 66.75%.

Pigmented rice, particularly the black and red varieties, is popular due to its better nutritional value. Anthocyanins and proanthocyanidins are two major flavonoid subcategories with broad physiological functions and therapeutic significance. However, pigment deposition is a complex process, and the molecular mechanism involved remains unknown. This review explores the metabolites responsible for the pigmentation in various rice tissues. Moreover, the current challenges, feasible strategies, and potential future directions in pigmented rice research are reported.

Maize is a globally important food crop and an industrial raw material for which nitrogen is an essential nutrient. Owing to heterosis, hybrid maize is advantageous in terms of development and stress resistance. However, the mechanisms underlying heterosis under low nitrogen availability remain poorly understood. This study aimed to investigate whether maize hybrid B73×Mo17 and its reciprocal cross show heterosis at the early seedling stage under different nitrogen availability (0.5, 1, 2, and 5 mM NO₃⁻) and to explore the corresponding physiological and gene-expression foundations. Under low nitrogen stress, the maize hybrids Mo17×B73 and B73×Mo17 exhibited superior performance in biomass production, lateral root length, root number, and root surface area compared to their parental lines, B73 and Mo17. In contrast, no significant differences were observed among these lines under normal conditions. Moreover, both hybrids showed significantly higher total nitrogen, chlorophyll, and soluble protein contents, and nitrate reductase, glutamine synthetase, and glutamate dehydrogenase activities than B73 or Mo17 under low nitrogen availability. Furthermore, the primary nitrate-response genes showed higher expression levels in both F1 hybrids than in their respective parents under low nitrate conditions; additionally, in the hybrids Mo17×B73 and B73×Mo17, the transcripts of ZmNRT3.1A and ZmNIR1 derived from the B73 allele were more abundant than those from the Mo17 allele, indicating an allelic expression bias toward the B73 parent. This study elucidates the physiological and molecular mechanisms underlying heterosis in maize under low nitrogen availability, providing a mechanistic basis for breeding maize varieties with enhanced adaptation to low-nitrogen soils.