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The physicochemical characteristics of five types of rice-based home meal replacement (HMR) products (instant rice, doshirak, kimbab, frozen fried rice, and freeze-dried rice) were measured before and after microwave cooking, and principal component analysis (PCA) was performed. HMR products contained grains from 8.42 to 8.72 mm before and after the microwave cooking. The amylose content and water absorption index (WAI) ranged from 20.10-23.15% and 0.50-2.87%, respectively. Frozen fried rice showed high amylose content but low WAI, and dry rice showed low amylose content but high WAI. There was a change in the moisture content of freeze-dried rice: moisture increased from 1.3 to 60.3% after cooking. The rehydration rate of freeze-dried rice was about twice higher than that of other HMR products, while instant rice showed a low rehydration rate. The texture profile's hardness and cohesiveness respectively were 306.1 g/cm2 and 47.9% before cooking, but 209.6 g/cm2 and 66.0% after cooking. The lightness value decreased from 72.5 to 68.9 after the microwave cooking, while there was little change in the lightness value of instant rice, and that of the frozen fried rice decreased. PCA revealed that, microwave cooking apparently affected WAI and rehydration rate in the freeze-dried rice yellowness in the frozen fried rice, and stickiness and lightness in the instant rice, respectively.

In recent years, many rice varieties with improved processing quality have been developed to promote domestic rice consumption along with the increasing preference for plant-based food and by-products. This study aimed to assess the quality characteristics of rice milk using a set of rice varieties, including saeilmi (normal brown rice, NBR; and normal white rice, NWR), milyang355 (aromatic brown rice, ABR; and aromatic white rice, AWR) and milyang365 (pigment brown rice, PBR). Among these, the amylose content ranged from 5.13-23.50%, and the highest crude protein content was recorded in ABR (7.95%). In addition, brown rice showed a higher initial pasting temperature than did white rice; however, its viscosity properties were relatively low. Our data showed that the soluble solid content of rice milk was 6.5-7.7 °Brix, and viscosity ranged from 2.8-4.8 cP. Reducing sugar and free sugar content was high in AWR (p

We investigated the germination rate, color values, physicochemical properties, antioxidant capacity, and amino acid content of germinated brown rice varieties (milyang356, nampyeong, and dasan), and their statistical correlation were analyzed. Milyang356 rice was characterized by the highest germination percentage and total color difference value (3.89) at 24 h. In all varieties, the amylose and crude protein content increased on the 1st day of germination but decreased over time (p

Rice paddies are a major source of methane emission. To meet the food demand of the growing population and to cope with global warming, reducing greenhouse gases and enhancing yield are critical. Here, we demonstrate for the first time that a novel loss-of-function rice allele, gs3, mitigates methane emission from methanogens by allocating more photosynthates to the grain and less to the root, and increases yield by enlarging grain size and weight.

The physicochemical and structural characteristics of high­yield, tongil­type mirchal glutinous rice, Milyang 328 (hereafter referred to as mirchal), were compared to those of a set of well-characterized glutinous rice varieties i.e., baegokchal, dongjinchal, and sinseonchal. The results revealed that mirchal exhibited the highest crude protein content (8.47%), water binding capacity (209.00%), and swelling power (55.82 g/g) under long term soaking. Analysis under identical conditions revealed that mirchal rice flour presented the minimum mean and median particle diameters of 50.54 μm and 22.72 μm, respectively, among the tested varieties. Furthermore, the particle diameter and onset temperature (To, 57.15°C) under these conditions were significantly lower than those under other conditions. The crystalline fraction of glutinous rice flour exhibited an A-type structure, irrespective of the soaking time. Mirchal exhibited the highest breakdown viscosity of 1,416.0 cP under short term soaking. The branch chain length distribution of the amylopectin A chain in the glutinous rice flours was arranged in the following sequence: baegokchal (30.82%) > mirchal (29.59%) > dongjinchal (28.74%) > sinseonchal (27.10%). The length distribution of the B1 chain in the glutious rice flours was arranged in the following sequence: dongjinchal (47.85%) > mirchal (47.17%) > baegokchal (45.83%) > sinseonchal (44.47%). Thus, this study revealed that mirchal possessed optimal processing characteristics owing to its high swelling power and excellent physicochemical properties, therby facilitating its application in the synthesis of yukwa and food processing materials.

In this study, we fermented ‘Makgeolli’ prepared using brown or white rice from ‘Mirchal’ for seven days to investigate the differences in their quality characteristics. Moreover, the physicochemical characteristics and antioxidant activities of ‘Makgeolli’ were assessed using principal component analysis (PCA). From the second day of fermentation, brown rice ‘Makgeolli’ exhibited a higher alcohol content (7.00%) than that of white rice ‘Makgeolli’ (3.60%). Additionally, the total polyphenol contents and antioxidant activities increased with the duration of fermentation (p

In the tropics (Southeast Asian countries), indica rice is more common than japonica. Japonica rice is mainly cultivated in temperate regions, including Korea, Japan, and China (northeast regions) due to its poor adaptation to tropical areas. To develop tropically-adapted high-yielding japonica rice, breeders should overcome the challenges, including extremely early flowering, low biomass accumulation, and inferior panicle traits. This study investigated 180 F9 recombinant inbred lines (RILs) developed from a cross between Ilpum (temperate japonica) and Zenith (indica) as a case population to identify quantitative trait loci (QTLs) that influence the said traits. Here we identified two major QTLs, qHD6-SD and qHD6- LD, conferring days to heading under short day (SD) and long day (LD) conditions, respectively. Finer mapping revealed that both qHD6-SD and qHD6-LD located in the similar 98 kb region harbored the Hd1 gene. Days to heading in the RILs harboring the Zenith allele type of qHD6-SD under SD conditions were significantly longer than those in the RILs harboring the Ilpum allele type. On the contrary, days to heading in the RILs harboring the Zenith allele type of qHD6-SD under LD conditions were significantly shorter than those in the RILs harboring the Ilpum allele type. This bi-functionality of qHD6-SD upon heading strongly support the claim that both qHD6-SD and qHD6-LD might be the Hd1 gene. Our findings further support the claim that the functional allele type of Hd1 gene delays long-day heading and promotes extremely early short-day heading. Therefore, a non-functional Hd1 type is critical to tropical adaptation of japonica rice since it delays the heading date, which is essential to attain prolonged vegetative state in order to achieve optimum biomass, increased spikelet number, and grain filling capacity.

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar ‘Hwaseong’ and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice., DNA marker-based smart breeding revealed that the ascorbate peroxidase gene APX9 of the wild rice relative Oryza rufipogon with low yield can make cultivated rice more productive and stress-tolerant.

Four near-isogenic lines (NILs) with different allele combinations of the starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1) were developed by crossing the japonica rice cultivars “Dodamssal” and “Hwayeong.” The associations between sequence variations in SBE3 and GBSS1, and starch-related traits were investigated. These sequence variations led to changes in seed morphology, starch structure, starch crystallinity, amylopectin chain length distribution, digestibility, apparent amylose content (AAC), and resistant starch content (RS). SBE3 and GBSS1 showed genetic interaction in regulating AAC and RS. Gene expression profiling of panicle tissues revealed significant differences in expression levels of GBSS1, SBE3, and other starch-related genes among the four NILs, indicating that variations in GBSS1 and SBE3 changed the expression level of starch-related genes. These variations contributed to the changes observed in AAC, RS, and physico-chemical characteristics of the rice starch from the NILs.

Nitrogen (N) is a gas and the fifth most abundant element naturally found in the atmosphere. N’s role in agriculture and plant metabolism has been widely investigated for decades, and extensive information regarding this subject is available. However, the advent of sequencing technology and the advances in plant biotechnology, coupled with the growing interest in functional genomics-related studies and the various environmental challenges, have paved novel paths to rediscovering the fundamentals of N and its dynamics in physiological and biological processes, as well as biochemical reactions under both normal and stress conditions. This work provides a comprehensive review on multiple facets of N and N-containing compounds in plants disseminated in the literature to better appreciate N in its multiple dimensions. Here, some of the ancient but fundamental aspects of N are revived and the advances in our understanding of N in the metabolism of plants is portrayed. It is established that N is indispensable for achieving high plant productivity and fitness. However, the use of N-rich fertilizers in relatively higher amounts negatively affects the environment. Therefore, a paradigm shift is important to shape to the future use of N-rich fertilizers in crop production and their contribution to the current global greenhouse gases (GHGs) budget would help tackle current global environmental challenges toward a sustainable agriculture.

Four near-isogenic lines (NILs) with different allele combinations of the

Glutinous rice is a key grain quality trait occupying an important part during rice processing in most rice growing areas. In this study, a gene pyramiding approach was used to introduce two dull genes, responsible for low amylose content, for glutinous rice breeding using marker assisted selection (MAS). The genotyping results revealed that rice cultivar Milyang319 carries both dull genes on chromosome 6, derived from cv. Milky-queen (Wx-mq) and cv. LGS-soft (du12(t)), respectively. Milyang319 had a significantly low amylose content (9.0%) compared to those observed in donor parents Milky-queen (15.7%) and LGS-soft (14.5%). In addition, the amylogram analysis of Milyang319 showed a similar pattern of glutinous rice. Originally, Milyang319 had a low hardness and more stickiness compared to those recorded in cooked rice of both dull parental lines. Therefore, Milyang319 is proposed as a promising candidate rice cultivar that could be used as a new source of waxy germplasms with same physicochemical features of glutinous rice in further breeding programs.

Grain filling is an important trait of rice that affects the yield of grain-oriented crop species with sink capacity-related traits. Here, we used a doubled haploid (DH) population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica) to investigate quantitative traits loci (QTLs) controlling grain filling in rice employing the Kompetitive allele-specific PCR (KASP) markers. The mapping population was grown under early-, normal-, and late-cultivation periods. The phenotypic evaluation revealed that spikelet number per panicle positively correlated with the grain-filling ratio under early cultivation conditions. Notably, three significant QTLs associated with the control of grain filling, qFG3, qFG5-1, and qFG5-2, were identified. Genes harbored by these QTLs are linked with diverse biological processes and molecular functions. Likewise, genes associated with abiotic stress response and transcription factor activity and redox homeostasis were detected. Genes such as MYB, WRKY60, and OsSh1 encoding transcription factor, β-catenin, and the tubulin FtsZ, as well as those encoding cytochrome P450, would play a forefront role in controlling grain filling under early cultivation conditions. Our results suggest that qFG3-related genes could mediate the transition between grain filling and abiotic stress response mechanisms. Fine-mapping these QTLs would help identify putative candidate genes for downstream functional characterization.

In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH

Developing rice varieties with increased mineral element content is the most cost-effective and efficient approach for alleviating human malnutrition and nutrient deficiencies. In this study, quantitative trait loci (QTLs) were mapped for mineral element content in 96 introgression lines derived from a cross between the elite Korean Oryza sativajaponica cultivar “Hwaseong” and the wild rice Oryza rufipogon (IRGC105491). The population was grown in two locations, and Fe, Zn, Mn, and Ca contents of the brown rice were measured. Six QTLs were identified on chromosomes 6, 8, and 10, and all O. rufipogon alleles increased trait values. The positions of qFe10 and qZn10 were further defined; higher Fe and Zn contents are related to the 375-kb O. rufipogon segment between the markers RM1873 and RM25612. The combined analysis of the whole-genome sequencing data, spatiotemporal expression profile, and gene expression suggested that a transcription factor gene, namely the rice homeobox gene 9 (LOC_Os10g33960) marks as the high potential candidate associated with Fe and/or Zn regulation. This study provides valuable information on candidate genes qFe10 and qZn10 from O. rufipogon, which may be vital in developing rice varieties with increased Fe and/or Zn content without any penalty in traits of agronomic importance.

The National Institute of Crop Science, Rural Development Administration (RDA) of Korea is presently developing new rice varieties suitable for producing Western rice-based foods, such as risotto, a well-known Italian-style product. The study considered different milled rice from five Tongil-type and six Japonica-type varieties. Besides the biometric properties, cooking behaviour, starch properties, and in vitro digestibility of Korean rice samples were compared with those of the ‘Carnaroli’ Italian variety. The physicochemical traits of the Korean varieties extended over a vast range; the amylose content stood out (from 13.0 to 41.7%), influencing the hardness and stickiness of cooked samples, and their starch digestibility. Although none of the Korean varieties seemed to guarantee cooking performances for risotto similar to the ‘Carnaroli’ one, ‘Saemimyeon’ and ‘Shingil’ cvs were judged the best for this purpose up-to-now.

The green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is one of the most important insect pests causing serious damage to rice production and yield loss in East Asia. Prior to performing RNA-Seq analysis, we conducted an electrical penetration graph (EPG) test to investigate the feeding behavior of GRH on Ilpum (recurrent parent, GRH-susceptible cultivar), a near-isogenic line (NIL carrying Grh1) compared to the Grh1 donor parent (Shingwang). Then, we conducted a transcriptome-wide analysis of GRH-responsive genes in Ilpum and NIL, which was followed by the validation of RNA-Seq data by qPCR. On the one hand, EPG results showed differential feeding behaviors of GRH between Ilpum and NIL. The phloem-like feeding pattern was detected in Ilpum, whereas the EPG test indicated a xylem-like feeding habit of GRH on NIL. In addition, we observed a high death rate of GRH on NIL (92%) compared to Ilpum (28%) 72 h post infestation, attributed to GRH failure to suck the phloem sap of NIL. On the other hand, RNA-Seq data revealed that Ilpum and NIL GRH-treated plants generated 1,766,347 and 3,676,765 counts per million mapped (CPM) reads, respectively. The alignment of reads indicated that more than 75% of reads were mapped to the reference genome, and 8859 genes and 15,815,400 transcripts were obtained. Of this number, 3424 differentially expressed genes (DEGs, 1605 upregulated in Ilpum and downregulated in NIL; 1819 genes upregulated in NIL and downregulated in Ilpum) were identified. According to the quantile normalization of the fragments per kilobase of transcript per million mapped reads (FPKM) values, followed by the Student’s t-test (p < 0.05), we identified 3283 DEGs in Ilpum (1935 upregulated and 1348 downregulated) and 2599 DEGs in NIL (1621 upregulated and 978 downregulated) with at least a log2 (logarithm base 2) twofold change (Log2FC ≥2) in the expression level upon GRH infestation. Upregulated genes in NIL exceeded by 13.3% those recorded in Ilpum. The majority of genes associated with the metabolism of carbohydrates, amino acids, lipids, nucleotides, the activity of coenzymes, the action of phytohormones, protein modification, homeostasis, the transport of solutes, and the uptake of nutrients, among others, were abundantly upregulated in NIL (carrying Grh1). However, a high number of upregulated genes involved in photosynthesis, cellular respiration, secondary metabolism, redox homeostasis, protein biosynthesis, protein translocation, and external stimuli response related genes were found in Ilpum. Therefore, all data suggest that Grh1-mediated resistance against GRH in rice would involve a transcriptome-wide reprogramming, resulting in the activation of bZIP, MYB, NAC, bHLH, WRKY, and GRAS transcription factors, coupled with the induction of the pathogen-pattern triggered immunity (PTI), systemic acquired resistance (SAR), symbiotic signaling pathway, and the activation of genes associated with the response mechanisms against viruses. This comprehensive transcriptome profile of GRH-responsive genes gives new insights into the molecular response mechanisms underlying GRH (insect pest)–rice (plant) interaction.

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.

Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). Recently the disease incidence has increased in several Asian countries and continues to spread throughout the world. No rice varieties have been developed yet to be completely resistant to this disease. With increasing need to identify various genetic resources to impart resistance to local elite varieties, this study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two SSR markers, RM1331 and RM3530 on chromosome 1.The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). The development of a rice variety with a higher level of resistance against bakanae disease is a major challenge in many rice growing countries. Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.

In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH4) due to the abundance in application of nitrogen (N)-rich fertilizers. In this study, we evaluated the root growth behavior and ROL rate of a doubled haploid (DH) population (n = 117) and parental lines 93-11 (P1, indica) and Milyang352 (P2, japonica) in response to iron (II) sulfide (FeS). In addition, we performed a linkage mapping and quantitative trait locus (QTL) analysis on the same population for the target traits. The results of the phenotypic evaluation revealed that parental lines had distinctive root growth and ROL patterns, with 93-11 (indica) and Milyang352 (japonica) showing low and high ROL rates, respectively. This was also reflected in their derived population, indicating that 93.2% of the DH lines exhibited a high ROL rate and about 6.8% had a low ROL pattern. Furthermore, the QTL and linkage map analysis detected two QTLs associated with the control of ROL and root area on chromosomes 2 (qROL-2-1, 127 cM, logarithm of the odds (LOD) 3.04, phenotypic variation explained (PVE) 11.61%) and 8 (qRA-8-1, 97 cM, LOD 4.394, PVE 15.95%), respectively. The positive additive effect (2.532) of qROL-2-1 indicates that the allele from 93-11 contributed to the observed phenotypic variation for ROL. The breakthrough is that the qROL-2-1 harbors genes proposed to be involved in stress signaling, defense response mechanisms, and transcriptional regulation, among others. The qPCR results revealed that the majority of genes harbored by the qROL-2-1 recorded a higher transcript accumulation level in Milyang352 over time compared to 93-11. Another set of genes exhibited a high transcript abundance in P1 compared to P2, while a few were differentially regulated between both parents. Therefore, OsTCP7 and OsMYB21, OsARF8 genes encoding transcription factors (TFs), coupled with OsTRX, OsWBC8, and OsLRR2 are suggested to play important roles in the positive regulation of ROL in rice. However, the recorded differential expression of OsDEF7 and OsEXPA, and the decrease in OsNIP2, Oscb5, and OsPLIM2a TF expression between parental lines proposes them as being involved in the control of oxygen flux level in rice roots.

A quantitative trait locus (QTL) gw8.1 was detected in the population derived from a cross between the elite japonica cultivar, 'Hwaseong' and Oryza rufipogon (IRGC 105491). Near isogenic lines (NILs) harboring the O. rufipogon segment on chromosome 8 showed increased grain length and weight compared to those of the recurrent parent, Hwaseong. This QTL was mapped to a 175.3-kb region containing 28 genes, of which four were considered as candidates based on the presence of mutations in their coding regions and as per the RNA expression pattern during the inflorescence stage. Leaves and panicles obtained from plants harvested 5 days after heading showed differences in gene expression between Hwaseong and gw8.1-NILs. Most genes were upregulated in O. rufipogon and gw8.1-NIL than in Hwaseong. Scanning electron microscopy analysis of the lemma inner epidermal cells indicated that cell length was higher in gw8.1 NIL than in Hwaseong, indicating that gw8.1 might regulate cell elongation. Among the candidate genes, LOC_Os08g34380 encoding a putative receptor-like kinase and LOC_Os08g34550 encoding putative RING-H2 finger protein were considered as possible candidates based on their functional similarity.

Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). This study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two RM (Rice Microsatellite) markers, RM1331 and RM3530 on chromosome 1. The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.

Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BC3F8 lines derived from an interspecific cross between the Korean japonica cultivar &ldquo, Hwaseong&rdquo, and Oryza rufipogon. In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F2 population (154 plants) along with parental lines, Hwaseong and O. rufipogon, were evaluated for LTG and coleoptile length under low-temperature conditions (13 &deg, C). Among five QTLs for LTG, two major QTLs, qLTG1 and qLTG3, were consistently detected at 6 and 7 days after incubation. Three minor QTLs were detected on chromosomes 8 and 10. Two QTLs, qLTG10.1 and qLTG10.2, showing linkage on chromosome 10, exerted opposite effects with the Hwaseong allele at qLTG10.2 and the O. rufipogon allele at qLTG10.1 respectively, in turn, increasing LTG. Interactions among QTLs were not significant, implying that the QTLs act in an additive manner. Near-isogenic line plants with the combination of favorable alleles from O. rufipogon and Hwaseong exhibited higher LTG than two introgression lines. With regard to coleoptile length, three QTLs observed on chromosomes 1, 3, and 8 were colocalized with QTLs for LTG, suggesting the pleiotropy of the single gene at each locus. According to the results, the introgression of favorable O. rufipogon alleles could hasten the development of rice with high LTG and high coleoptile elongation in japonica cultivars.