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.

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 crucial staple crop for global food security; however, its production is adversely affected by climate change-induced extreme temperatures. High and low extreme temperatures significantly impair rice development, growth, yield, and grain quality. These adverse effects are due to disruption of physiological processes at different growth stages. Rice germplasm provides great genetic diversification from wild relatives, traditional landraces, and modern cultivars. The subspecies indica and japonica include valuable alleles that can be employed for breeding rice varieties adapted to extreme temperatures. The classical methods of hybridization and phenotypic selection are the basis of breeding programs. However, developing an improved rice variety using classical breeding methods requires 8-12 years, which is inconsistent with the rapid and extreme fluctuations in climate conditions currently threatening rice production. The potential of molecular genetics and gene editing technologies, such as quantitative trait loci (QTL), marker-assisted selection (MAS), genome-wide association studies (GWAS), genomic selection (GS), transcriptomics, and genome editing (CRISPR-Cas9) can support classical methods in breeding precision, understanding transcription factors, and enables rapid modification to accelerate the development of climate-resilient cultivars. Furthermore, speed breeding combined with high-throughput phenotyping can shorten the breeding cycle by controlling environmental factors to implement multiple generations within a single year. This review discusses climate-adaptive breeding pipeline by integrating the discovery of favorable alleles from diverse germplasm, precision trait integration using genomic selection and CRISPR-Cas9 editing, and accelerated line development through speed breeding. This framework could effectively advance rice improvement to extreme temperatures and contribute to sustained rice production for ensuring global food security under climate change.

Developing rice varieties that combine high yield, disease resistance, grain quality, and climatic adaptability is critical for sustaining rice production, particularly under current climate change. Mid-altitude rice regions face severe challenges from rice blast, climate variability, lodging, and yield-quality trade-offs. This study integrated accelerated generation advancement with multi-environment selection to develop a high-yielding, adaptable rice variety suitable to a mid-altitude production system. Yunjing-60 is a novel rice variety developed through pedigree selection combined with double-cropping acceleration. The cross was applied between Shengnong-5 and Chujing-44. Shengnong-5 is a blast-resistant, compact architecture with medium maturity. Chujing-44 is high-yielding, lodging-tolerant, and high-quality grain. Double-cropping was applied at Yuanjiang, which is characterized by a hot and dry climate. Moreover, greenhouse cultivation was conducted during cooler months from November to February. This enabled multiple generations per year for accelerating breeding cycles. The variety comparison trial in 2022 demonstrated that Yunjing-60 surpassed the check variety Chujing-38 with superior agronomic performance. It exhibited higher effective panicle density (400.5 per m²), greater sink capacity (135 filled grains per panicle), and 8.62

During cold acclimation in high-latitude and high-altitude regions, japonica rice develops enhanced cold tolerance, but the underlying genetic basis remains unclear. Here, we identify CTB5, a homeodomain-leucine zipper (HD-Zip) transcription factor that confers cold tolerance at the booting stage in japonica rice. Four natural variations in the promoter and coding regions enhance cold response and transcriptional regulatory activity, enabling the favorable CTB5KM allele to improve cold tolerance. CTB5 interacts with OsHox12 and targets gibberellin (GA) metabolism genes to promote GAs accumulation in anthers and facilitate tapetum development under cold stress. Moreover, CTB5 directly regulates PYL9 and improves cold tolerance at the seedling stage by reducing reactive oxygen species (ROS) accumulation. The CTB5KM allele is selected during the cold acclimation of japonica rice to plateau habitats in Yunnan Province. Our findings provide insights into the mechanisms underlying cold adaptation in plateau japonica rice and offer potential targets for breeding cold-tolerant rice varieties. Mechanisms confer to the enhanced cold tolerance in japonica rice have not been fully elucidated. Here, the authors report a homeodomain-leucine zipper (HD-Zip) I transcription factor encode gene CTB5 is responsible for japonica rice cold tolerance by interacting with genes in gibberellin and abscisic acid pathways.

Rice is highly sensitive to cold stress, particularly at the booting stage, which significantly threatens rice production. In this study, we cloned a gene, CTB6, encoding a lipid transfer protein involved in cold tolerance at the booting stage in rice, based on our previous fine-mapped quantitative trait locus (QTL) qCTB10-2. CTB6 is mainly expressed in the tapetum and young microspores of the anther. CTB6 interacts with catalases (CATs) to maintain their stability, thereby scavenging reactive oxygen species (ROS) accumulation in anthers and facilitating tapetum development under cold stress conditions. Additionally, CTB6 has lipid-binding ability and affects the lipid content in anthers to regulate cold tolerance at the booting stage. Haplotype analysis and promoter activity assay revealed a specific single nucleotide polymorphism (SNP)-489 variation in the promoter of CTB6, which enhances its expression and results in improved cold tolerance in Hap1-K varieties. The CTB6 near-isogenic line (NIL) exhibited enhanced cold tolerance at the booting stage, with no significant effects on other agronomic traits. Our findings uncover a natural variation of CTB6 for cold tolerance at the booting stage and provide new genetic resources for cold tolerance breeding in rice.

Cold stress is one of the main abiotic stresses that affects rice growth and production worldwide. Dissection of the genetic basis is important for genetic improvement of cold tolerance in rice. In this study, a new source of cold-tolerant accession from the Yunnan plateau, Lijiangxiaoheigu, was used as the donor parent and crossed with a cold-sensitive cultivar, Deyou17, to develop recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis for cold tolerance at the early seedling and booting stages in rice. In total, three QTLs for cold tolerance at the early seedling stage on chromosomes 2 and 7, and four QTLs at the booting stage on chromosomes 1, 3, 5, and 7, were identified. Haplotype and linear regression analyses showed that QTL pyramiding based on the additive effect of these favorable loci has good potential for cold tolerance breeding. Effect assessment in the RIL and BC3F3 populations demonstrated that qCTB1 had a stable effect on cold tolerance at the booting stage in the genetic segregation populations. Under different cold stress conditions, qCTB1 was fine-mapped to a 341-kb interval between markers M3 and M4. Through the combination of parental sequence comparison, candidate gene-based association analysis, and tissue and cold-induced expression analyses, eight important candidate genes for qCTB1 were identified. This study will provide genetic resources for molecular breeding and gene cloning to improve cold tolerance in rice.

Rice is a major crop susceptible to chilling stress. The identification of quantitative trait loci and genes for cold tolerance is crucial for the rice breeding. Of 30 quantitative-trait loci affecting seedling cold tolerance identified in a genome-wide association study of 540 rice accessions, OsbZIP72 was assigned as the causative gene for one, qCTS9.1. A single-nucleotide polymorphism in its promoter accounted for variation in expression between indica and japonica subspecies. The favorable haplotype of OsbZIP72 originated in wild rice and contributed to the expansion of japonica rice to colder habitats. OsbZIP72 positively regulates genes coding reactive oxygen species (ROS)-scavenging proteins and maintains intracellular ROS homeostasis. These findings not only enhanced our understanding of environmental adaptation but also provide novel genetic resources and potential targets for molecular design breeding for cold tolerance in rice.

Yungeng48 is a new japonica rice variety with good quality,which was bred by the Institute of Food Crops of Yunnan Academy of Agricultural Sciences with high yield intermediate material Yungeng14/Yungengyou3 as maternal parent and good quality intermediate material Yungengyou3//Yungengyou4/Yungengyou12 as paternal parent after 11 generations system selection.The rice quality,high yield,disease resistance,cold resistance and other characteristics were identified simultaneously from the selection of individual plant of F3 generation.Therefor Yungeng48 has comprehensive excellent characters such as good quality,high yield,multiple resistance and wide adaptability.The variety was approved by Yunnan Province in 2021 and is suitable for planting in rice areas with an altitude of 1 450～1 850 m in Yunnan Province and similar rice areas in neighboring provinces.

The research investigated the potential of heterologous expression of the heat-shock protein PpHSP70 in enhancing high temperature and drought tolerance in rice. After screening the whole genome sequence of Physcomitrium patens in the Phytzome database, 30 members of the HSP70 gene family were obtained. Their expression and the tissue expression patterns under abiotic stressors of high temperature, drought, and salt were analyzed. During the four-leaf stage of rice, overexpressed materials were subjected to a temperature of 45 °C for 20 h and to drought conditions for one week. After processing, 5 overexpression PpHSP70 materials survived against high temperature, and 7 materials survived against drought, while all wild-type materials KY131 died after the treatment. The results demonstrated that overexpression of PpHSP70 significantly improved both high-temperature tolerance and drought. This study provides valuable insights into the utilization of heterologous expression for enhancing crop tolerance to abiotic stressors.

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.

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 The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP‐glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica . CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high‐altitude to high‐latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.

Iron is one of the essential micronutrients to rice, but the accumulation of excessive ferrous salt in soil can cause toxicity. In this study, bioinformatics method was used to mine the data of Affymetrix rice gene expression microarray to study the differentially expressed genes of rice germplasm EPAGRI 108 under control and excess Fe conditions. The results revealed that 407 genes with more than two fold difference were identified. Compared to the control group, 330 genes were up regulated and 77 genes were down regulated under excess Fe stress. Gene Ontology and pathway analysis revealed that these differentially expressed genes were mainly involved in the biological processes such as oxidoreductase activity, glucose metabolism, amino acid metabolism, etc. Through these data analysis, we preliminarily explored the gene expression patterns of rice under excess Fe conditions, and provided a theoretical basis for further investgating the molecular mechanism tolerating for rice tolerance to Fe toxicity.

In order to study the ecological adaPtability of jαpomicα rice Varieties of Plateau in local imdicα rice Planting area of Yunnan ProVince, the growth duration, agronomic characters, economic characters, yield and disease resistance of six Plateau jαpomicα rice Varieties with good-quality, high-yield, resistance to disease and cold tolerance were analyZed by using Yixiang725 (hybrid imdicα rice Variety) as control Variety. The results showed that jαpomicα rice Varieties of Plateau could mature safely, and their growth duration was the roughly same leVel or slightly less than the imdicα rice Variety controt in local imdicα rice Planting area. There was a significant PositiVe correlation between growth duration and yield. The whole growth duration of jαpomicα rice Varieties was between 155 and 161 days, and their yield was between 6 939.0 and 10 374.0 kg∕hm2. The whole growth duration of Yunjing39 was 161 days, which was similar to Yixiang725. In all tested Varieties, the yield of Yunjing39 with good comPrehensiVe ProPerties and strong stress resistance was the highest, and was significantly higher than the hybrid imdicα rice Variety control. According to the results, Yunjing39 was suitable for local imdicα rice Planting area. The yields of Chujing28 and Yunjing26 were 9 738.0 kg∕hm2 and 9 676.5 kg∕hm2, which were slightly lower than imdicα rice Variety control, but they had a certain aPPlication Value in local Production.

利用PCR从3份携带抗稻瘟病Pi40基因的粳稻材料中扩增、筛选获得特异性片段,通过测序分析比对和引物设计,开发出一个SCAR分子标记3F.该标记在15份抗稻瘟病单基因系和抗性品种中能够特异性的检出Pi40基因系.利用Pi40品系4163与丽江新团黑谷构建F2群体123株,发现3F在其中96个单株中检测到550 bp的目标条带,同时田间稻瘟病抗性鉴定结果表明该96个单株田间表现为R,另外27份未检出目标条带的单株表现S,卡方检测分离比符合3∶1.进一步利用3F在183份云南水稻育成品种中检测,结果显示仅在其中9份材料中有目标带型出现,而在其它174份云南水稻品种中没有检测到目标带型,这为有目的地开展品种抗性改良提供直接而高效的筛选标记,结果表明3F是一个具有很高的特异性,在云南稻作系统中有实际应用价值的分子标记.以3份感病粳稻材料与4163杂交,构建稻瘟病抗性改良F2群体,利用3F筛选出来的单株经稻瘟病菌喷雾接种鉴定,表现为R,而未检出目标条带的单株则表现为S.

Plants are sensitive to external environmental conditions and the mechanisms of stress tolerance in plants are complex. As one of the most significant epigenetic phenomena, DNA methylation plays a crucial role in plants’ adaptation to environmental changes. Recent research has improved our understanding of the relationship between DNA methylation and stress tolerance. Here, we review the mechanism of DNA methylation and discuss recent reports of the dynamics of DNA methylation in plants under abiotic stress conditions, including high salt concentration, drought, and extreme temperatures. The DNA methylation plays important functions during the response to stress in plants, but the differential variations of which were exhibiting in different species. The consistent or the specific mechanisms of DNA methylation need further exploration.

[Objective] A high efficient DNA extraction technology by magnetic bead methods from single milled rice grain was studied in this report.[Method]4 milled rice samples were used to carry out genomic DNA extraction through magnetic bead methods and PCR processing to check the efficient of extraction results.[Result]Twenty single milled rice grain DNA were extracted through magnetic bead methods.After electrophoresis checking,the result showed high quality of genomic DNA bands without diffusion,and the DNA concentrations above 1 ng/μl.Moreover,2 SSR markers,RM247 and RM282,were used to carry out PCR amplified with the extraction DNA solution as templates directly.And two bands with 180 and 120 bp were detected respectively as anticipated.[Conclusion] The research results demonstrated a fairly good quality of the DNA extracting,which also supported a feasibility and high-efficient method to extracted trace DNA from single milled rice grain.

哈尼梯田红米已经有几百年的种植历史.红米营养价值要高于一般白精米,但因为食味品质差,其产业一直得不到较好的发展.以配方米的形式来提高红米食味品质是一种比较直接、简单的方式.本文通过RVA谱法对5个品种和36个配方进行检测,结果显示,用RVA谱辅助筛选出的配方与食味计和人工品尝评分的结果相符,此方法准确、快速,结果重复性优于传统配比技术.利用RVA谱分析来确定配方米的配比比例在国内尚属首例.

In this research,we used four-primers allelic gene amplification mutation system PCR technique combined with KOH and chewing determination method to analyze the fragrance traits,the existence of fragrance gene and genotype of 86 main japonica rice cultivars in Yunnan and 2 control japonica rice cultivars.The results showed that ten cultivars with fragrance or fragrance gene (badh2) had been detected by these three methods,but the results of each method were different.Five cultivars were detected with fragrance and fragrance genes (badh2)by these three methods,two cultivars were detected with fragrance but without fragrance genes (badh2) by KOH,one cultivar was detected with fragrance and fragrance genes (badh2) by KOH,one cultivar was detected with fragrance and fragrance genes (badh2) by chewing,and one cultivar was detected with fragrance genes (badh2) but without fragrance by KOH and chewing.The results of PCR amplification of DNA detection showed that there were three types of fragrance genotype,which were non-fragrant type Badh2/Badh2,heterozygous type Badh2/badh2,and fragrant type badh2/badh2.The occurrence frequency of the fragrance gene badh2 in 86 main cultivars of japonica rice from Yunnan was only 8.1％,the fragrance traits were controlled by the badh2 allele gene,and all these varieties belong to the series of Yunjing japonica rice.We found that combining four-primers allelic gene amplification mutation system PCR technique with chewing determination method might improve the efficiency and accuracy in selection of fragrance traits.