Rice is the important crop for more than half of the world population. However, drought can have a devastating impact on rice growth and reduce yield drastically. Understanding the response of rice to drought stress is especially important for crop breeding. Previously we found that rice enhanced its tolerance to drought stresses via stress memory mechanisms. Numerous memory genes were identified to play important roles in the process. DNA methylation was reported to mediate tolerance via regulating gene expression and enhances the survival rate of rice encountering drought stress. However, how DNA methylation involved in stress memory is still not clear. In this study, genome-wide bisulphite sequencing at a single base resolution methylome profiling level was performed and analyzed in rice cultivar under recurrent drought stresses and recovery treatments. We found that rice drought stress memory-related differentially methylated regions (DMRs) showed dynamic and distinct patterns. The drought-memory DMRs may regulate Transposable elements and gene expression to cope with short-term repeated drought stresses. Our findings of drought-memory DMRs can explain mechanisms of rice drought stress memory in a new perspective on global methylome details. Using epigenetic markers to breed drought-resistant rice would become a feasible way in the future research.

Summary: This paper presents investigations of segregation distortion of six rice F₂populations generated from reciprocal F₁hybrids grown at three locations varied at altitudes from 400 to 2200 m. The F₁s were derived from reciprocal crosses between cv. XMG, which is ajaponicalandrace traditionally grown at 2650 m altitude, and cv. N34, which is ajaponicarestorer possessing a fertility restoring (Rf) gene and cytoplasm of male sterility (CMS) donated by anindicacultivar. Among nine morphological traits of the F₂populations, only one was in normal distribution, eight were distorted in all or at least one population. Out of 16 polymorphic PCR markers, 10 markers distributed on 7 chromosomes were significantly distorted. Among these markers, RMAN7 and RM257 were distorted in both of the reciprocal populations, which suggested that nuclear genes had strong effects on segregation distortion. The other makers were distorted only in the populations with cytoplasm donated by XMG or N34. The results indicated that segregation of DNA markers was affected by cytoplasm background. Segregation distribution was also affected by altitude, since segregation distortions of most of the markers were detected not in all the three populations generated from F₁grown at the three altitudes, but only in one population from F₁grown at one altitude. Marker M45461, which is located withinRf-1locus, was severely distorted towards N34 in all the populations with cytoplasm donated by N34, but not in the populations with cytoplasm provided by XMG. The results indicated that interaction between CMS andRfgene had strong effects on distortion. Results of this study indicated thatjaponicacytoplasm did not cause distortion favouring a special parent, butindicacytoplasm made distortion favouring a maternal parent. The results suggested thatindicacytoplasm was not well compatible withjaponicanuclear background, whilejaponicacytoplasm did not have such trouble withindicanuclei. This study also found that the six F₂populations were divergent into two groups due to difference of cytoplasm background.

Traditional breeding strategies mainly focus on the evaluation of trait performance, but pay less attention to the changing genetic background. A comprehensive understanding of the genetic diversity of germplasms is crucial for the deliberate improvement of specific traits. A collection of 154 highland rice varieties were collected as the initial genetic resource in our breeding program to improve the pathogen resistance and eating and cooking qualities. These varieties were analyzed using a whole-genome SNP array and were clustered into three groups. Further analysis revealed that the favorable alleles of pathogen resistance genes are mostly absent in our collected varieties. However, it showed that most varieties possess favorable alleles of Waxy (Wx) and ALKALI DEGENERATION (ALK), which are able to enhance the eating and cooking qualities. Moreover, only about one fifth of all varieties harbors favorable the allele of fragrance gene Betainealdehyde dehydrogenase (BADH2). Together, these results give an overall view of the genetic constitution of the target traits, which provide useful information for future genetic improvement in breeding practices.

Climate change poses a threat to global rice production by increasing the frequency and intensity of extreme weather events. The widespread cultivation of genetically uniform modern varieties has narrowed the genetic base of rice, increasing its vulnerability to these increased pressures. Rice landraces are traditional rice varieties that have been cultivated by farming communities for centuries and are considered crucial resources of genetic diversity. These landraces are adapted to a wide range of agro-ecological environments and exhibit valuable traits that provide tolerance to various biotic stresses, including drought, salinity, nutrient-deficient soils, and the increasing severity of climate-related temperature extremes. In addition, many landraces possess diverse alleles associated with resistance to biotic stresses, including pests and diseases. In addition, rice landraces exhibit great grain quality characters including high levels of essential amino acids, antioxidants, flavonoids, vitamins, and micronutrients. Hence, their preservation is vital for maintaining agricultural biodiversity and enhancing nutritional security, especially in vulnerable and resource-limited regions. However, rice landraces are increasingly threatened by genetic erosion due to widespread adoption of modern high-yielding varieties, habitat loss, and changing farming practices. This review discusses the roles of rice landraces in developing resilient and climate-smart rice cultivars. Moreover, the Pantiange Heigu landrace, cultivated at one of the highest altitudes globally in Yunnan Province, China, has been used as a case study for integrated conservation by demonstrating the successful combination of in situ and ex situ strategies, community engagement, policy support, and value-added development to sustainably preserve genetic diversity under challenging environmental and socio-economic challenges. Finally, this study explores the importance of employing advanced genomic technologies with supportive policies and economic encouragements to enhance conservation and sustainable development of rice landraces as a strategic imperative for global food security. By preserving and enhancing the utilization of rice landraces, the agricultural community can strengthen the genetic base of rice, improve crop resilience, and contribute substantially to global food security and sustainable agricultural development in the face of environmental and socio-economic challenges.

Rice is a staple food for more than half of the global population, but its production is threatened by insect pests such as planthoppers, stem borers, leafhoppers, and defoliators. The widespread use of chemical pesticides has raised concerns regarding environmental contamination, pest resistance, and negative effects on beneficial arthropods. This review examines the role of biological control and habitat management in sustainable rice pest management. It highlights the diversity and ecological roles of natural enemies, including parasitoid wasps, mirid bugs, ladybird beetles, and spiders, which help suppress pest populations in rice ecosystems. Key habitat management approaches, such as conservation biological control, ecological engineering, banker plant systems, flower strips, and the preservation of non-crop habitats, are discussed for their capacity to enhance the abundance and effectiveness of natural enemies. The review also considers integrating these approaches into IPM programs to reduce reliance on pesticides while maintaining crop productivity. Evidence from rice-growing regions demonstrates the effectiveness of habitat-based strategies in improving pest suppression and strengthening ecosystem resilience. However, challenges related to landscape complexity, farmer adoption, long-term implementation, and the need for a clear roadmap for future landscape-scale entomological research remain. Future research should focus on optimizing habitat management practices and integrating ecological approaches with modern agricultural technologies to support sustainable rice production.