BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation

BackgroundRice quality research attracts attention worldwide. Rice chalkiness is one of the key indexes determining rice kernel quality. The traditional rice chalkiness measurement methods only use milled rice as materials and are mainly based on naked-eye observation or area-based two-dimensional (2D) image analysis and the results could not represent the three-dimensional (3D) characteristics of

BackgroundThe root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root

BackgroundDirect-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. ResultsWe used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers

BackgroundBakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development. ResultsThis study focused on investigating early defenses against

BackgroundGrain size is one of the key agronomic traits that impact grain yield. Several regulatory pathways had been reported to participate in grain size determination via cell expansion or proliferation in rice. However, little is known about cyclophilin and spliceosome participation in grain shape regulation. ResultsHere, we identified OsCYP20–2, a cyclophilin that influences spliceosome assembly

BackgroundGrain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. ResultIn this study, 14 genes related to grain size (GW2, GS2, qLGY3

BackgroundRice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main

Identification of traits strongly associated with high yield can help future gene engineering towards improvements of productivity. Here we systematically determine the major architectural and physiological features associated with high yield in two elite historical hybrid rice cultivars, i.e., YLY1 and LYP9. Data from a six-year experiment show that high yield of YLY1 are related to a number of architectural

BackgroundGlobal warming threatens rice growth and reduces yields. Proline plays important roles in plant abiotic stress tolerance. Previous research demonstrated that engineering proline metabolism-related genes can enhance tolerance to freezing and salinity in Arabidopsis. OsProDH encodes a putative proline dehydrogenase and is a single copy gene in rice. However, whether OsProDH plays roles in abiotic

BackgroundRice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability. ResultsTo characterize the genetic basis for rice rooting ability, we used

BackgroundStomata in rice control a number of physiological processes by regulating gas and water exchange between the atmosphere and plant tissues. The impact of the structural diversity of these micropores on its conductance level is an important area to explore before introducing stomatal traits into any breeding program in order to increase photosynthesis and crop yield. Therefore, an intensive

BackgroundDeveloping chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood

BackgroundUstilaginoidea virens has become one of the most devastating rice pathogens in China, as well as other rice-growing areas. Autophagy is an important process in normal cell differentiation and development among various organisms. To date, there has been no optimized experimental system introduced for the study of autophagy in U. virens. In addition, the function of autophagy in pathogenesis

BackgroundSalt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited. ResultsHere, an

BackgroundThe chloroplast signal recognition particle 54 (cpSRP54) is known for targeting the light-harvesting complex proteins to thylakoids and plays a critical role for chloroplast development in Arabidopsis, but little is known in rice. Here, we reported two homologous cpSRP54s that affect chloroplast development and plant survival in rice. ResultsTwo rice cpSRP54 homologues, OscpSRP54a and OscpSRP54b

BackgroundReproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution

BackgroundSeed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. The genetic and molecular mechanisms underlying seed dormancy in rice remain largely unknown. ResultsQuantitative trait loci (QTLs) for seed dormancy were identified in two different mapping populations, a chromosome

BackgroundChloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although many regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. ResultsIn this study, we characterized a rice mutant lethal albinic seedling 1(las1)form of a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase

BackgroundHigh soil salinity can cause significant losses in rice productivity worldwide, mainly because salt inhibits plant growth and reduces grain yield. To cope with environmental changes, plants have evolved several adaptive mechanisms that involve the regulation of many stress-responsive genes. ResultsIn this study, we identified OsSTAP1, which encodes an AP2/ERF-type transcription factor, was

BackgroundChloroplasts are essential for photosynthesis and play key roles in plant development. High temperature affects structure of chloroplasts and metabolism in plants. The seryl-tRNA synthetase plays an important role in translation of proteins. Although seryl-tRNA synthetase has been widely studied in microbes and animals, few studies have reported about its role in chloroplast development under

BackgroundSalinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali

BackgroundAroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available

BackgroundRice amylose content and amylopectin structure corporately determine rice eating and cooking qualities (ECQs). Soluble starch synthase (SS) IV-2 is a member of the soluble starch synthesis gene family but with unknown effects on ECQs. ResultsIn this study, three populations derived from a cross of two parents who possess the same major genes of starch bio-synthesis were employed to investigate

BackgroundThe plant chloroplast is essential for photosynthesis and other cellular processes, but an understanding of the biological mechanisms of plant chloroplast development are incomplete. ResultsA new temperature-sensitive white stripe leaf 9(wsl9) rice mutant is described. The mutant develops white stripes during early leaf development, but becomes green after the three-leaf stage under field

Rice (Oryza sativa. L) has been intensively studied to ensure a stable global supply of this commodity in the face of rapid global climate change. A critical factor that decreases crop yield is drought, which has been analyzed in various ways through many researches. Microbiome-based studies of rice investigate the symbiosis between rice and bacteria, which has been proposed as a way to overcome problems

BackgroundArbuscular mycorrhizal (AM) fungi form symbiotic associations with roots in most land plants. AM symbiosis provides benefits to host plants by improving nutrition and fitness. AM symbiosis has also been associated with increased resistance to pathogen infection in several plant species. In rice, the effects of AM symbiosis is less studied, probably because rice is mostly cultivated in wetland

BackgroundRice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between

BackgroundThe cell wall and chloroplast are two fundamental structures determining plant mechanical strength and grain yield. Therefore, understanding mechanisms that improve plants’ ability to develop a robust cell wall and well-developed chloroplast is of utmost importance for agricultural activities. ResultsIn this study, we report the functional characterization of a novel rice mutant, brittle

BackgroundALK is the key gene controlling rice gelatinization temperature (GT), which is closely associated with the eating and cooking quality (ECQ) in rice (Oryza sativa L.). To date, at least three ALK alleles are thought to be responsible for the diversity of GT among rice cultivars. The ALKc/SSIIai allele with high activity of the soluble starch synthase IIa (SSIIa) controls high GT, but the accurate

BackgroundGrain size affects not only rice yield but is also an important element in quality of appearance. However, the mechanism for inheritance of grain size is unclear. ResultsA rice chromosome segment substitution line Z1392, which harbors three substitution segments and produces grains of increased length, was identified. The three chromosome segments were located on chromosomes 1, 5, and 6,

MicroRNAs (miRNAs) play essential roles in rice immunity against Magnaporthe oryzae, the causative agent of rice blast disease. Here we demonstrate that Osa-miR162a fine-tunes rice immunity against M. oryzae and yield traits. Overexpression of Osa-miR162a enhances rice resistance to M. oryzae accompanying enhanced induction of defense-related genes and accumulation of hydrogen peroxide (H2O2). In contrast

BackgroundStigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution

BackgroundThe sucrose non-fermenting 1-related kinases 2 (SnRK2s) play important roles in osmotic stress responses in A. thaliana and rice (Oryza sativa L.). Osmotic stress/ABA–activated protein kinase 2 (SAPK2) is a member of SnRK2s subclass II in rice, but its function in rice yield under drought stress is unclear. ResultsCompared with wild-type (Oryza.Sativa L.spp.japonica, WT) plants, the sapk2

The utilization of heterosis has resulted in significant breakthroughs in rice breeding. However, the development of hybrid japonica has been slow in comparison with that of hybrid indica. The present review explores the history and current status of hybrid japonica breeding. With the creation of japonica cytoplasmic male sterility and photo-thermo-sensitive genic male sterile lines, both three-line

BackgroundLysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed. ResultsIn this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in

BackgroundNeo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential. However, systematic yield assessment, genome composition and functional variations associated with fertility and yield remain elusive. ResultsTwo season’s field trials of 15

Genetic transformation is one of the most important technologies for revealing or modulating gene function. It is used widely in both functional genomics and molecular breeding of rice. Demands on its use in wild Oryza species is increasing because of their high genetic diversity. Given the difficulties in genetic crosses between distantly related species, genetic transformation offers a way to alter

BackgroundRice blast is an economically important and mutable disease of rice. Using host resistance gene to breed resistant varieties has been proven to be the most effective and economical method to control rice blast and new resistance genes or quantitative trait loci (QTLs) are then needed. ResultsIn this study, we constructed two advanced backcross population to mapping blast resistance QTLs.

BackgroundLight provides the energy for photosynthesis and determines plant morphogenesis and development. Low light compromises photosynthetic efficiency and leads to crop yield loss. It remains unknown how rice responds to low light stress at a proteomic level. ResultsIn this study, the quantitative proteomic analysis with isobaric tags for relative and absolute quantitation (iTRAQ) was used and

Background Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17)

BackgroundBacterial leaf streak (BLS) and bacterial blight (BB) are two major prevalent and devastating rice bacterial diseases caused by the Gram-negative bacteria of Xanthomonas oryzae pv. oryzicola (Xoc) and Xanthomonas oryzae pv. oryzae (Xoo), respectively. Previously, we identified a defence-related (DR) gene encoding a small heat shock protein, OsHsp18.0-CI, that positively regulates BLS and

BackgroundAwns are bristle-like organs at the tips of the glumes. Wild rice has maintained long awns for successful seed propagation through seed dispersal. Seed awning is an interesting trait in rice domestication. Long awns might have been beneficial for seed gatherers in the initial phase of domestication; however, awnless phenotypes were preferably selected in a later phase with non-seed-shattering

Background Abscisic acid (ABA) acts as a signaling hormone in plants against abiotic stress, but its function in energy homeostasis under heat stress is unclear. Results Two rice genotypes, Nipponbare (wild-type, WT) with flat leaves and its mutant high temperature susceptibility (hts) plant with semi-rolled leaves, were subjected to heat stress. We found significantly higher tissue temperature, respiration

Background Rice blast is generally considered the most devastating rice disease worldwide. The development of resistant varieties has been proven to be the most economical strategy to control the disease. A cluster of resistant (R) genes on rice chromosome 12 including Pita, Pita2 and Ptr has been studies for decades. However, the relationship between these R genes has not been well established. Results

Background Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast. Results Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL - qBL3 contributing about 34% and 32% phenotypic variance towards

Xanthine dehydrogenase (XDH) is an important enzyme in purine metabolism. It is involved in regulation of the normal growth and non-biological stress-induced ageing processes in plants. The present study investigated XDH’s role in regulating rice leaf senescence. We measured physical characteristics, chlorophyll content and fluorescence parameters, active oxygen metabolism, and purine metabolism in

Background Loose Plant Architecture 1 (LPA1), an indeterminate domain (IDD) protein, exhibits almost no expression in the leaves, but the overexpression of LPA1 significantly increases the resistance of rice to sheath blight disease (ShB) via the activation of PIN-FORMED 1a (PIN1a). Results In this study, we determined that Rhizoctonia solani infection significantly induced LPA1 expression in the leaves

Background The grain number per panicle (GNP), which is one of three grain yield components, is an important trait for the genetic improvement of rice. Although the NAL1 and GNP1 genes regulating the rice GNP and grain yield have been cloned, their allelic diversity, functional differences in rice germplasms, and effects of their combination on GNP and grain yield remain unclear. Results Based on DNA

Background The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties

Abstract In this study, the cold-tolerance capacity of 133 varieties of weedy rice was evaluated based on the comprehensive evaluation index D, with Kongyu 131 used as a cold-tolerant control. A total of 39.8% of the 133 varieties were considered ‘strong’, indicating that weedy rice populations indeed have relatively strong cold-tolerance capacity as a whole, and the robust cold-tolerant varieties

Background Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations

Background Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3, that control LTG, were mapped using the BC4F8 population, which is a cross of Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491). We have characterized and analyzed the

Background Expression of either Cas9 or Cas12a and guide RNAs by a single Polymerase II (Pol II) promoter represents a compact CRISPR expression system and has many advantages for different applications. In order to make this system routine in plant biology, engineering efforts are needed for developing and optimizing such single transcript unit (STU) systems for plant genome editing. Results To develop

The breakthrough CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-mediated genome-editing technology has led to great progress in monocot research; however, several factors need to be considered for the efficient implementation of this technology. To generate genome-edited crops, single guide (sg)RNA and Cas9 DNA are delivered into plant cells and expressed, and the predicted

Background Grain size is a key agronomic trait that is directly associated with grain yield in rice. Although several genes related to grain size in rice have been identified, our understanding of the mechanism of grain development is still limited. Results In this study, we reported the characterization of a novel seed size mutant mini seed 2 (mis2), in which the grain showed reduced length, width

Multiple haplotypes at the same rice blast R-gene locus share extremely high sequence similarity, which makes the gene diagnostic method using molecular markers less effective in differentiation from one another. The composition and distribution pattern of deployed R genes/haplotypes in elite rice varieties has not been extensively analyzed. In this study, we employed PCR amplification and sequencing

BackgroundThe large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice. ResultsIn this study, we raised a mutant from tissue-culture-derived plants of Oryza sativa subsp. japonica

BackgroundRice black-streaked dwarf virus (RBSDV) causes one of the most important rice virus diseases of plants in East Asia. However, molecular mechanism(s)controlling rice resistance to infection is largely unknown. ResultsIn this paper, we showed that RBSDV infection in rice significantly induced nitric oxide (NO) production. This finding was further validated through a genetic approach using a

BackgroundGlutathione (GSH) is important for plants to resist abiotic stress, and a large amount of energy is required in the process. However, it is not clear how the energy status affects the accumulation of GSH in plants under cold stress. ResultsTwo rice pure lines, Zhongzao39 (ZZ39) and its recombinant inbred line 82 (RIL82) were subjected to cold stress for 48 h. Under cold stress, RIL82 suffered