Amylopectin branch-chain length distribution is a key determinant of rice starch functionality and eating quality, yet the genetic basis underlying specific chain fractions remains incompletely understood in diverse germplasm. In this study, amylopectin fine structure was quantified in 137 accessions of the Korean Rice Core Selection (KRICE_Core) using HPAEC-PAD, and genome-wide association studies were conducted with 2.1 million high-quality SNPs under the FarmCPU model. The short-chain distribution (SCD, DP 6-12) varied from 26.85% to 37.20%, whereas the intermediate-chain distribution (ICD, DP 12-24) ranged from 52.57% to 61.04%, and the two fractions showed a strong inverse correlation. GWAS identified two major loci on chromosomes 4 and 6, with the chromosome 6 region showing exceptionally strong association signals and co-localizing with
This study aimed to enhance the Inpari 42 rice variety by integrating the aromatic trait through Marker-Assisted Backcrossing (MAB) while improving key agronomic characteristics in the BC1F1 generation. The aromatic gene from Merah Wangi was successfully introgressed into BC1F1 plants, confirmed through molecular analysis using the Bradbury marker, which detects mutations in the
Pre-harvest sprouting is a major physiological problem in rice caused by prolonged rainfall and high humidity during the harvest period, and it is one of the most important targets in current rice breeding programs. In this study, the effect of cold and freezing storage on the pre-harvest sprouting rate was investigated using ten rice varieties under four different treatments. The result showed storage treatments of panicle samples used for germinate evaluation had no significant influence on the pre-harvest sprouting rate. These findings may enhance the efficiency of mass screening for pre-harvest sprouting and support the development of tolerant rice varieties.
CRISPR (clustered regularly interspaced short palindromic repeats) gene-edited (GEd) crops have demonstrated significant potential to enhance global food security in the face of escalating climate challenges and rapid population growth. Since 2019, for regulatory purposes, the United States (U.S.) and several other countries have recognized transgene-free, genome-edited lines as equivalent to conventionally bred varieties. Notably, the first genome-edited food product, Calyno™ soybean oil, was commercialized in the U.S. and marketed as a non-genetically modified organism (GMO) item. Recently, regulatory frameworks, such as the enactment of the Precision Breeding Law in the United Kingdom, the European Union’s New Genomic Techniques (NGT) legislation, and the repeal of the SECURE Rule in the United States, have further established guidelines permitting the use of genome-edited lines in agriculture similar to with conventionally bred crops, provided that these lines are free of transgenic elements. In Korea, researchers and policymakers are actively engaging in discussions to establish a preliminary review committee for GEd crops to align regulatory practices with international trade standards. Thus, this study aimed to evaluate two gene-edited rice lines for generational stability in terms of molecular characteristics, focusing on edited nucleotide sequences, gene expression, target phenotypes, the presence of transgene elements, and potential off-target effects across multiple generations. Additionally, several technical challenges in nucleotide editing tracing emerged during the evaluation process that warrant further attention. The findings presented in this study are expected to offer valuable insights for shaping the regulatory framework in Korea for CRISPR-based gene-edited crops.
Citations
This research attempted to validate novel molecular markers linked to high antioxidant traits using an F2 population and a local Thai rice population. We performed total flavonoid content, total phenolic content (TPC), and ferric reducing antioxidant power (FRAP) assays to assess the antioxidant capacities of rice populations. In the F2 (“Pathum Thani 1”דHawm Mali Daeng”) population, these traits exhibited a quantitative distribution with high heritability (82.7%–98.3%) and high genetic advance (66%–94%). In validation using 10 molecular markers,
Citations
Quantitative trait locus (QTL) analysis is a powerful approach for identifying variants associated with the phenotypic variation of complex traits. However, selecting optimal methods and pre-processing steps require considerable time and effort. In this study, we demonstrated applicability and replicability of machine learning (ML) models in QTL analysis by evaluating their performance in comparison with conventional QTL analysis methods using 142 recombinant inbred lines derived from two
Citations
Rice blast, caused by the pathogenic fungus
Citations
Nitrogen is an essential nutrient for crop growth and development. Although the functions of several genes associated with nitrogen deficiency tolerance have been studied, many genetic components remain unknown. In this study, 190 North Korean (NK) rice genotypes were used to identify genes linked to nitrogen deficiency resistance. The NK population was hydroponically cultivated for 31 days under normal nitrogen (NN) and low nitrogen (LN) conditions. After this period, phenotypic evaluations were conducted on six agronomic traits (SPAD, shoot length, root length, shoot fresh weight, root fresh weight, and tiller number). A genome-wide association study (GWAS) was performed using the phenotypic values and resequencing data from 190 NK rice genotypes. As a result, 107 significant lead SNPs were identified. Among the genes related to these lead SNPs, 12 previously identified NUE-related genes for nitrogen use efficiency (NUE) and 6 unknown candidate genes exhibited significant differences in haplotype analysis. Nine of the 12 known genes (
Citations
Pigmented rice is reported have high levels of bioactive compounds, it suitable for functional food. Additionally, it has been reported that pigmented rice extract has the potential as an anti-obesity, anti-inflammatory, antioxidant, and anti-cancer agent. In Indonesia, pigmented rice is less favored by local farmers due to low public demand (limited awareness) and cultivation difficulties (prone to falling and susceptible to pests), which could lead to the extinction of the plant. Qualitative and quantitative characterization can serve as the basis for plant breeding. This study aims to analyze the morpho-agronomic traits of several pigmented rice accessions from Central Java and East Java, thus providing a source of information for local farmers in the pigmented rice breeding process. Morpho-agronomic traits observed include qualitative and quantitative characters. The grouping and its relationship between 22 rice accessions were analyzed using Principal Component Analysis (PCA)-biplots and dendrogram clustering analysis based on Unweighted Pair Group Method Using Arithmetic Averages (UPGMA). The results showed the characteristics influencing the variation of Indonesian pigmented rice, especially from East Java and Central Java, out of 22 accessions, such as leaf color, shoot color, and tiller number. The grouping based on their morpho-agronomic characters showed that there were two main clusters. Twenty out of 22 rice accession grouping in cluster 1 with diverse pigmented rice pigment type. Meanwhile, cluster 2 consists of IR Ngawi Hitam and Wojaloka. These two accessions are classified as black rice. Our findings are valuable for breeding programs, especially in rice.
Rice yield is severely affected by phosphorus (P) deficiency, and plants have evolved various strategies to cope with this limitation. While some rice genotypes are adapted to low phosphate (Pi) availability, others remain sensitive to Pi deficiency. In this study, we conducted a genome-wide association study (GWAS) using a hydroponically cultivated population of 190 North Korean (NK) rice plants to identify genes associated with phosphorus use efficiency (PUE) and Pi deficiency tolerance. The rice plants were grown in Yoshida nutrient media with either full (10 mg/L) or low-P (1 mg/L) concentrations for 40 days. The phenotypic response to Pi deficiency was assessed at the seedling stage, followed by an evaluation of eight agricultural traits: chlorophyll content (SPAD), shoot length (SL), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), root dry weight (RDW), and tiller number (TN). The GWAS analysis revealed a total of 166 significant lead SNPs, with six located near known genes for Pi deficiency tolerance:
Citations
Eight rice genotypes, including Binam, Hashemi, Deylamani, TH1, Hasani, Saleh, IR75479-199-3-3, and Gohar, were crossed in a line tester mating design to generate breeding populations, assess the general and specific combining ability (GCA and SCA) and identify suitable combinations for yield. 23 genotypes (15 F1s and eight parents) were evaluated in a randomized complete block design with three replications at the Rice Research Institute of Iran during the 2020 cropping season. Analysis of variance revealed significant genotype effects and GCA and SCA mean square values for all the investigated traits, which indicated the genetic diversity of the parental genotypes and the importance of both additive and non-additive gene effects in the inheritance of the studied traits. Results indicated that additive gene action controlled plant height. Meanwhile, non-additive gene action controlled panicle length, number of panicles per plant, heading date, hundred-grain weight, number of grains per panicle, and grain yield. Effects of general combining ability were significant for the panicle length, the number of panicles per plant, heading date, hundred-grain weight, number of grains per panicle, and plant height in all testers. Hasani and Saleh's genotypes demonstrated to be good general combiners for early maturity. Gohar was the best specific combiner to enhance yield components. Hashemi×Gohar was identified as the best combination for improving grain yield and reducing the number of days to heading. The predominance of non-additive types of gene actions related to grain yield and its components suggested that selecting the best plants should be postponed to advanced generation.
Citations
Hairs on the leaf are an important agronomic characteristic for rice growth and farming. The segregation ratio of pubescence in the F2 population showed that the pubescence on the leaf is controlled by a single dominant gene. Fine mapping for the gene was carried out by producing an Indel (insertion-deletion) primer based on BSA-Seq data. Results of the analysis revealed within the candidate site the presence of
Rice domestication has led to cultivated rice with no or short awns. Discovery of novel genes associated to awn length is of paramount importance for understanding the molecular mechanisms for the transformation of wild rice long awns to awnless cultivated rice. In this study, we employed Next-Generation Sequencing based QTL-seq approach to identify genomic regions associated with awn length using mapping population derived from a cross between awnless Tun Sart and awned Sobaekmangsudo. QTL-seq analysis identified two awn length QTLs viz.
Citations
The purity of seeds can be identified from the traits inherited from their parental lines. Hence, contamination may occur at the crossing step due to unshared similarities with their parents. This research aims to measure the genetic purity of several genotypes obtained from crosses between upland and lowland rice through the banding pattern differences among the genotype samples by using Simple Sequence Repeats (SSR) markers. Taking the leaf samples was carried out at the experimental field, while the marker analysis was conducted in the Plant Biotechnology Laboratory. In this research, 8 (eight) genotypes obtained from crossing, comprising F1, F2, and BC1 along with 4 (four) of their parents from upland rice and lowland rice, were tested using 6 (six) drought-specific SSR primers of RM5, RM211, RM232, RM249, RM255, and RM258. The banding pattern of the electrophoresis results on the 12 rice genotypes showed clear, unsmeared quality. Based on the results of distance and genetic similarities, the 12 genotypes could be classified into 4 (four) clusters in the dendrogram. Cluster I consists of the
Citations
SNP-based markers have been widely used to identify tolerant varieties harboring major genes related to abiotic stress tolerance. Here, we developed Fluidigm markers for the core set of SNPs underlying tolerance to abiotic stresses such as salinity, drought, anaerobic germination and submergence. The core set of SNPs was selected from the major genes and/or QTLs for the abiotic stresses previously reported in rice;
Citations
Rice is one of the most important sources of energy for Iranians. Currently, approximately four million tons of paddy are produced annually in 19 provinces of the country. More than 50 new rice cultivars have been introduced in Iran over the last 60 years. The average yield of rice in these years has increased from 2 t ha‒1 to nearly 5 t ha‒1 in farmers’ paddies, although some improved cultivars can produce up to 9 t ha‒1. The main strategy of rice breeding in Iran during the first 40 years was purifying local populations, introducing foreign lines, and producing high-yielding cultivars by cross-breeding and mutagenesis. Meanwhile, the production of high-quality cultivars from crosses between local varieties and high-yielding cultivars has been more emphasized recently. In this review, along with introducing improved varieties of Iranian rice and their characteristics, different improvement methods for creating these varieties are mentioned. Along with traditional breeding methods, it seems that Marker-assisted breeding and breeding by rational design can play important roles in the future of rice breeding in Iran.
Citations
A resurrection has started in haploid and double haploid research in the twenty-first century. The haploid and double haploid could be achieved through in vivo and in vitro anther and microspore culture techniques. Fixing the homozygosity is the most striking benefit of androgenesis. Various factors like genotypic dependency, growth condition, developmental stage of the microspore, pre-treatment, culture media, regeneration media, growth hormones, and various chemicals have a direct effect. Wheat, rice,
Citations
Genetic variability and correlation analysis are fundamental references for the innovative development of breeding programs to improve varieties and desirable traits. In the present study, the correlation and path analysis was conducted to understand the association among yield, micronutrients (iron and zinc), and protein content under aerobic conditions in local rice landraces from various agro ecological regions of Karnataka, India. The grain yield per plant showed a significant positive correlation with plant height, the tiller number, spikelet fertility, flag leaf length, and test weight. The zinc content was negatively correlated with grain yield per plant. The phenotypic path-coefficient analysis revealed that the total number of tillers, grain length, test weight, and harvest index exhibited a positive direct effect on grain yield per plant, while Grain protein content showed a low direct effect on this trait. This study also indicated that harvest index, flag leaf length, spikelet fertility, and test weight could be considered to make for a higher yield.
Citations
Amylose content is a key factor affecting the eating and cooking qualities of rice. In our previous study,
Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (
Citations
Cold stress is one of the serious abiotic stresses for stable rice production especially in high-latitude temperate region and high-altitude tropical area. Improving cold tolerance at seedling stage led stable seedling growth with yield stability. In this study, QTLs for cold tolerance at seedling stage were identified using the 96 introgression lines (ILs) derived from an inter-specific cross between Hwaseong (
Citations
Rice (
Citations
Rice Breeding in Bangladesh started with establishment of Bangladesh Rice Research Institute (BRRI) in 1970. It aimed at developing modern rice cultivars to benefit farmers. Among BRRI developed varieties, BR11 is considered as most popular Transplanted Aman cultivar having high yield (6.0 t/ha), bold grain and high amylose content. On the other hand, BRRI dhan28 and BRRI dhan29 are most popular Boro rice varieties for Irrigated areas. Because, they produce high yield across diverse rice growing areas. BRRI dhan29 is widely grown in haors where rice is grown once in a year. BRRI dhan28 and BRRI dhan29 accounted for 50% of total Boro rice areas. As a whole, the popularity of the cultivars BR11, BRRI dhan28 and BRRI dhan29 influenced subsequent rice breeding trends and characteristics of new rice varieties. In this review, the pedigree information revealed that IR20 and IR5 acted as key foundation parents in developing the rice cultivar BR11 and BRRI dhan29. In contrast, same parental lineage of renowned IR64 contributed in developing BRRI dhan28. The breeding history, agronomic traits, grain quality and molecular characteristics of above cultivars have been discussed briefly. Thus, the background information generated from this review might help in developing breeding lines with higher genetic diversity, improved tolerance to biotic and abiotic stresses to obtain higher genetic gain from a breeding program. Furthermore, basic studies on these varieties and their important progenies might help to disclose the complex genetic control of yield as well as other qualitative traits prioritized by farmers and consumers.
Citations
A total of 857 rice breed lines were used to evaluate rice blast resistance. Frequency of leaf spot index was skewed to the right of the 1-9 scale in bar plot, with a score of 7 showing the highest frequency. The average spot index score of 857 breed lines was 5.33. Associations showing higher than the threshold of ‒log10(P) = 5.17 were detected as significant associations. Significantly associated single nucleotide polymorphism (SNP) markers located within ± 250 kb on the lead SNP position was designated to one QTL locus of lead SNP markers. Five association loci were detected. Two associated QTLs detected on Chr. 4 were designated as qRB4.1 and qRB422, explaining 17.8% and 14.3% of total phenotypic variations, respectively. Associated QTLs detected on Chr. 1, 11, and 12 (one each) designated as qRB1, qRB11 and qRB12 explained 44.6%, 9.09%, and 13.7% of total phenotypic variations, respectively. We compared previously reported QTLs. The location of qRB4.2 was overlapped with the previously reported QTL for blast field resistance. The location of qRB12 was also overlapped with the field resistance leaf blast. The other one, qRB4.1, was overlapped with bacterial blight resistance.
Citations
Development of salt tolerance in rice through breeding program is mainly depends on the salinity responses of the potential rice germplasms. Coastal rice landraces of Bangladesh possess diverse morphological and physiological responses to salinity. Hence, our target is to identify candidate salt-tolerant coastal rice genotypes as a new source of salt tolerance (12 dS/m). Here, we annotated 20 Bangladeshi coastal
Citations
This study estimated the genetic variability and gene action of several traits in the F4 and F5 rice populations to determine a trait for selection program. The trait of date to flowering and date to harvesting had narrow genetic variability, whereas trait productive tillers, number of fertile grain, and total grains had moderate to wide genetic variability. Genetic variability in trait number of fertile grain and total grains showed decreased in F5 generation compare to the F4 generation, whereas trait productive tillers, date to flowering, and date to harvesting showed an increase. Additive gene action with duplicate and complementary epistasis was found in all traits, except for trait productive tillers only showed additive gene action with duplicate epistasis. Kurtosis less than 3 was found in all traits which indicate many genes control the traits. The number of fertile grain trait showed wide genetic variability which decreased in F5 generation compare to the F4 generation, and there is an additive gene action with duplicate epistasis. It indicates selection will be effective with the trait of number of fertile grain.
Citations
Bakanae disease is an important fungal disease caused by
Citations
Rice is a temperature-sensitive crop, its yield is severely affected by low temperature, especially cold stress at the seedling stage will delay heading. To understand the genetic basis of cold tolerance, we evaluated the cold tolerance at the seedling stage of 136 rice accessions. To evaluate cold tolerance, we treated rice seedlings with cold water irrigation for ten days and scored the cold tolerance on a 1-9 scale, based on their low-temperature response and subsequent recovery. The genome-wide association study for cold tolerance revealed seven QTLs on chromosomes 1, 3, 6, 7, 10, and 12. The genomic region of the
Citations
We conducted transcriptome profiling analysis of
Citations
Rice culm is an important trait for determining rice lodging yield, and stem diameter has been suggested as a yield-related trait; however, studies for the genetic basis of its phenotypic variation are still required. In this study, we used 160 recombination inbred lines derived from a cross of two different rice varieties [‘Milyang23’ (Tongil rice) and ‘Giho’ (
Citations
First
Prev
