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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.

Background: 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. Results: 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).Conclusion: 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.

Increased grain yield will be critical to meet the growing demand for food, and could be achieved by delaying crop senescence. Here, via quantitative trait locus (QTL) mapping, we uncover the genetic basis underlying distinct life cycles and senescence patterns of two rice subspecies, indica and japonica. Promoter variations in the Stay-Green (OsSGR) gene encoding the chlorophyll-degrading Mg++-dechelatase were found to trigger higher and earlier induction of OsSGR in indica, which accelerated senescence of indica rice cultivars. The indica-type promoter is present in a progenitor subspecies O. nivara and thus was acquired early during the evolution of rapid cycling trait in rice subspecies. Japonica OsSGR alleles introgressed into indica-type cultivars in Korean rice fields lead to delayed senescence, with increased grain yield and enhanced photosynthetic competence. Taken together, these data establish that naturally occurring OsSGR promoter and related lifespan variations can be exploited in breeding programs to augment rice yield., Breeding crops with delayed senescence could plausibly increase grain yield. Here the authors show that variation at the rice SGR locus contributes to differences in senescence between indica and japonica subspecies and show that introgression can increase yield in an elite indica rice variety.

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.

벼 수량성 증진을 위하여 수당립수 증진 유전자로 보고된 5종의 유전자에 대한 분자표지를 검정하고 유전자원 479점에서 이들의 유전자에 대한 유전형을 검정하였다. 판독이 용이한 Gn1a 및 DEP1, Apo1 유전자의 In/del 분자표지를 각각 개발하였고 Ghd7과 Nal1 유전자에 대하여서는 기존 보고된 SNP 분자표지를 이용하여 편리성을 검정하였다. 이들 분자표지는 아가로즈젤에서 각각의 유전형 판독이 용이하기에 벼 수량성 향상을 위한 분자육종에 적용이 가능할 것으로 기대되었다. 유전자원 479점에서 수당립수 증진 유전자 5종의 유전형을 분석하였을 때 총 13개의 haplogype으로 분류되었다. 대부분의 Indica 품종과 Japonica 품종은 haploptype 1과 haplotype 13에 속하였다. 나머지 haplotype에 속한 55점의 유전자원은 수당립수 증진 유전자에 대한 유전다양성을 보유한 자원으로 유전체 분석 등을 위한 핵심집단으로 활용할 수 있을 것으로 판단되었다. 유전자원 396점의 수량구성요소를 비교하였을 때, Nal1을 제외한 4종의 수당립수 증진 유전자의 수량증진 대립유전자형에서 이삭 수가 0.6 ~ 0.8개/주 감소하였으나 수당립수는 이삭당 27 ~ 29개 증진되었다. Nal1 유전자는 유전적 배경에 따라 효과가 다르게 나타나며, Nal1-japonica 대립유전자형의 수당립수 증진 효과보다 Nal1-indica 대립유전자형이 감소효과가 큰 것으로 추측되었다. 앞으로 본 논문에서 검정된 수당립수 증진 분자표지 5종과 유전자원의 유전형을 정보를 바탕으로 벼 수량성 증진 육종에 활용하고자 한다.

Background Bakanae disease is an important fungal disease caused by Gibberella fujikuroi. Incidence of rice bakanae disease creates serious problems in the foremost rice growing countries, and no rice variety has been found to be completely resistant to this disease. However, breeding rice varieties resistant to bakanae disease may be a cost-saving solution preferable to the application of fungicides. In this study, we aimed to determine the exact position and the candidate gene for qBK1, a major resistant quantitative trait locus (QTLs) for bakanae disease. Results The genotypes/phenotypes of recombinants selected from backcrossed recombinant inbred lines of two rice varieties, Shingwang (resistant) and Ilpum (susceptible), indicated that the locus qBK1, conferring resistance to bakanae disease in Shingwang, was delimited to a 35-kb interval delimited by InDel 18 (23.637 Mbp) and InDel 19–14 (23.672 Mbp). Sequence analysis of this 35-kb region revealed four candidate genes, LOC_Os01g41770, LOC_Os01g41780, LOC_Os01g41790, and LOC_Os01g41800. There were many non-synonymous SNPs in LOC_Os01g41770 and the transcript of LOC_Os01g41790 was early terminated in Shingwang, whereas there were no differences in both LOC_Os01g41780 and LOC_Os01g41800 sequences between Ilpum and Shingwang. Expression profiling of the four candidate genes showed the up-regulation of LOC_Os01g41770, LOC_Os01g41780, and LOC_Os01g41790 in Ilpum and of LOC_Os01g41800 in Shingwang after inoculation of G. fujikuroi. Conclusion Utilization of marker-assisted selection (MAS) with a precise molecular marker on qBK1 could provide an effective tool for breeding rice varieties resistant to bakanae disease. To our knowledge, this is the first report on fine mapping and candidate gene approaches for identifying the gene for qBK1. Electronic supplementary material The online version of this article (10.1186/s12284-019-0295-9) contains supplementary material, which is available to authorized users.

We fine mapped the Xa4 locus and developed a pyramided rice line containing Xa3 and Xa4 R - alleles and a cold-tolerance QTL. This line will be valuable in rice breeding. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease of cultivated rice. Pyramiding BB resistance genes is an essential approach for increasing the resistance level of rice varieties. We selected an advanced backcross recombinant inbred line 132 (ABL132) from the BC3F7 population derived from a cross between cultivars Junam and IR72 by K3a inoculation and constructed the mapping population (BC4F6) to locate the Xa4 locus. The Xa4 locus was found to be delimited within a 60-kb interval between InDel markers InDel1 and InDel2 and tightly linked with the Xa3 gene on chromosome 11. After cold (4 °C) treatment, ABL132 with introgressions of IR72 in chromosome 11 showed lower survival rate, chlorophyll content, and relative water content compared to Junam. Genetic analysis showed that the cold stress-related quantitative trait locus (QTL) qCT11 was located in a 1.3-Mb interval close to the Xa4 locus. One line, ABL132-36, containing the Xa3 resistance allele from Junam, the Xa4 resistance allele from IR72, and the cold-tolerance QTL from Junam (qCT11), was developed from a BC4F6 population of 250 plants. This is the first report on the pyramiding of Xa3 and Xa4 genes with a cold-tolerance QTL. This region could provide a potential tool for improving resistance against BB and low-temperature stress in rice-breeding programs.

Drought caused by global climate change is one of serious problems for rice cultivation. However, it was little reported the impact of drought on rice cultivation in Korea. In here, to assess impact of drought on rice varieties in Korean climate condition, growth characteristics and yield components of rice were compared on irrigated and partially irrigated rice paddy field. First, we have chosen 11 rice varieties including `Saeilmi` and `Shindongjin` which are widely cultivated in Korea. For partially irrigated rice paddy treatment, we have withheld irrigation from 25 days after transplanting and water supply was totally dependent on rainfall for rice cultivation. When we examined early plant height and tiller number of these varieties on partially irrigated rice paddy were reduced 1.6% to 18.4% and 10.4% to 33.1%, respectively, and these reduction rate were highly correlated with yield loss in our experimental conditions. Among rice yield components, panicle number was decreased 10.5% to 30.1% according to rice varieties and reduced panicle number was highly correlated with yield loss. Grain number per panicle, grain filling rate and 1,000 seeds weight did not have correlation with yield loss of rice varieties. These result means that growth stage, especially the tillering stage, is seriously affected by drought on rice cultivation in Korea. And we suggest that `Saeilmi`, `Ilmi` and `Ilpum` are good for rice cultivation on drought prone rice field in Korea.

Chlorate resistance analysis is an effective approach commonly used to distinguish the genetic variation between Oryza sativa L. ssp. indica and japonica, and predict the nitrogen use efficiency (NUE). This study aimed at investigating the response of a doubled haploid (DH) population derived from anther culture of 93-11 &times, Milyang352 exposed to 0.1% potassium chlorate (KClO3) at the seedling stage. The results revealed that the parental rice lines 93-11 (indica) and Milyang352 (japonica) showed distinctive phenotypic responses. The parental line 93-11 scored highly sensitive (0% survival) and Milyang352 scored resistant (66.7% survival) 7 days after treatment. The DH lines reflected the differential phenotypic response observed in parental lines. Interestingly, we identified a novel quantitative trait locus (QTL) for chlorate resistance on chromosome 3 (qCHR-3, 136 cM, logarithm of the odds&mdash, LOD: 4.1) using Kompetitive Allele-Specific PCR (KASP) markers. The additive effect (&minus, 11.97) and phenotypic variation explained (PVE, 14.9%) indicated that the allele from Milyang352 explained the observed phenotypic variation. In addition, shoot growth showed a significant difference between parental lines, but not root growth. Moreover, in silico analysis identified candidate genes with diverse and interesting molecular and physiological functions. Therefore, this study suggested that the QTL qCHR-3 harbors promising candidate genes that could play a role in the regulation of nitrogen metabolism in rice.

Two recombinant inbred line F10 rice populations (IAPAR-9/Akihikari and IAPAR-9/Liaoyan241) were used to identify quantitative trait loci (QTLs) for ten drought tolerance traits at the budding and early seedling stage under polyethylene glycol-induced drought stress, and two traits of leaf rolling index (LRI) and leaf withering degree (LWD) under field drought stress. The results showed that the drought-tolerance capacity of IAPAR-9 was stronger than that of Akihikari and Liaoyan241. Thirty-four QTLs for 12 drought tolerance traits were detected, and among them, in the IAPAR-9/Akihikari population, qLRI9-1 and qLRI10-1 for LRI were repeatedly detected in RM3600-RM553 on chromosome 9 and in RM6100-RM3773 on chromosome 10, respectively, at two times points of July 31 and August 13 in 2014. The two QTLs are stable against the environmental impact, and qLRI9-1 and qLRI10-1 explained 6.77–13.66% and 5.01–8.32% of the phenotypic variance, respectively, at the two times points. qLWD9-2 for LWD in the IAPAR-9/Liaoyan241 population contributed 8.73% of variation was detected in the same marker interval with the qLRI9-1, and qLRI1-1 for LRI and qLWD1-1 for LWD were located in the same marker interval RM11054-RM5646 on chromosome 1, which contributed 18.82 and 5.78% of phenotype variation respectively. qGV3 for germination vigor and qRGV3 for relative germination vigor at the budding stage were detected in the same marker interval RM426-RM570 on chromosome 3, which explained 14.98 and 16.30% of the observed phenotypic variation respectively, representing major QTLs. The above-mentioned stable or major QTLs regions could be useful for molecular marker assisted selection breeding, fine mapping, and cloning.

The ongoing rise in temperatures caused by global climate change is a critical climatic risk factor for rice production, and enhancing rice heat tolerance is an area of particular research interest. A recombinant inbred line (RIL) mapping population was developed from heat sensitive, rice cultivar IAPAR-9 crossed with heat tolerant, Liaoyan241. RIL and parental lines were exposed to high temperature at the heating and flowering stage in experiments in 2014 and 2015. As indicators of heat tolerance, the seed setting rate under natural (NS) and heat stress (HTS) conditions were measured, and the reduction rate of seed set (RRS) was calculated. Quantitative trait loci (QTL) analysis revealed eleven heat tolerance QTLs located on chromosomes 1, 3, 4, 5, and 6. Single QTL contribution rates were 4.75–13.81% and effect values were − 5.98 to 5.00. Four major QTLs (qNS1, qNS4, qNS6, and qRRS1) were stable detected in different environments in both years. Thirteen QTLs with epistatic interactions and nine QTLs with environmental interactions were also detected. Major QTLs were all involved in epistatic and environmental interactions. Three QTLs from the SSR marker interval RM471 to RM177 region of chromosome 4 (qNS4, qHTS4, and qRRS4) were all involved in epistatic and environmental interactions and contributed to phenotypic variation, indicating that this region constituted a major QTL hotspot. The major QTL for heat tolerance identified in this study will aid in breeding tolerant cultivars and facilitating investigation of the molecular underpinnings of heat tolerance in rice.

Production of high quality pigmented rice contained with high content of anthocyanin, and polyphenol was significantly influenced by cultivation environments like transplanting date and cultivation location. This study was carried out to establish an optimum transplanting date and cultivation region to produce maximum content of anthocyanin, polyphenol and antioxidant activity of pigmented rice varieties (black, red colored). Three transplanting times (May 20, June 5, June 20) and four different sites (Miryang, Uiseong, Sangju, Bonghwa) were evaluated with five pigmented rice cultivars. Anthocyanin and total polyphenol index to average temperature during 30 days after heading (DAH) of black, red pigmented rice varieties showed that anthocyanin and total polyphenol contents were decreased by 10% and 9%, respectively, with increasing average temperature of . The optimum ripening temperature of the 30 DAH for the production of high anthocyanin and total polyphenol was 22 to for early maturity black rice, 21 to for mid-late maturity of black and red rices, respectively. On the other hand, an estimated heading date of pigmented rices in return according to the optimum ripening temperature of the 30 DAH was ranged Aug. 11 to 17 for early maturity black rice, Aug. 25 for mid-late maturity black, red rice variety in Jecheon, Aug. 27 to Sep. 2 for early maturity type, Sep. 3 to 6 for mid-late type in Daegu. It seemed that Jecheon, Boeun, Mungyeong, and Yeongju were optimum regions for cultivation of pigmented rices. The estimated sowing date of pigmented rices for high anthocyanin and total polyphenol production based on the optimum heading date was May 18 to 26 for early maturity black rice variety, April 11 for mid-late black, red variety in Jecheon, May 23 to 28 for early type, April 9 to 26 for mid-late type in Boeun, respectively.

Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedlings in seed boxes for mechanical transplanting has increased the incidence of many seedling diseases; only a few rice varieties have been reported to exhibit resistance to bakanae disease. In this study, we attempted to identify quantitative trait loci (QTLs) conferring bakanae disease resistance from the highly resistant japonica variety Wonseadaesoo. A primary QTL study using the genotypes/phenotypes of the recombinant inbred lines (RILs) indicated that the locus qBK1 WD conferring resistance to bakanae disease from Wonseadaesoo was located in a 1.59 Mb interval delimited on the physical map between chr01_13542347 (13.54 Mb) and chr01_15132528 (15.13 Mb). The log of odds (LOD) score of qBK1 WD was 8.29, accounting for 20.2% of the total phenotypic variation. We further identified a gene pyramiding effect of two QTLs, qBK WD and previously developed qBK1. The mean proportion of healthy plant for 31 F4 RILs that had no resistance genes was 35.3%, which was similar to that of the susceptible check variety Ilpum. The proportion of healthy plants for the lines with only qBK WD or qBK1 was 66.1% and 55.5%, respectively, which was significantly higher than that of the lines without resistance genes and that of Ilpum. The mean proportion of the healthy plant for 15 F4 RILs harboring both qBK WD and qBK1 was 80.2%, which was significantly higher than that of the lines with only qBK WD or qBK1. Introducing qBK WD or pyramiding the QTLs qBK WD and qBK1 could provide effective tools for breeding rice with bakanae disease resistance. To our knowledge, this is the first report on a gene pyramiding effect that provides higher resistance against bakanae disease.

Background Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedlings in seed boxes for mechanical transplanting has increased the incidence of many seedling diseases; only a few rice varieties have been reported to exhibit resistance to bakanae disease. In this study, we attempted to identify quantitative trait loci (QTLs) conferring bakanae disease resistance from the highly resistant japonica variety Wonseadaesoo. Results A primary QTL study using the genotypes/phenotypes of the recombinant inbred lines (RILs) indicated that the locus qBK1WD conferring resistance to bakanae disease from Wonseadaesoo was located in a 1.59 Mb interval delimited on the physical map between chr01_13542347 (13.54 Mb) and chr01_15132528 (15.13 Mb). The log of odds (LOD) score of qBK1WD was 8.29, accounting for 20.2% of the total phenotypic variation. We further identified a gene pyramiding effect of two QTLs, qBKWD and previously developed qBK1. The mean proportion of healthy plant for 31 F4 RILs that had no resistance genes was 35.3%, which was similar to that of the susceptible check variety Ilpum. The proportion of healthy plants for the lines with only qBKWD or qBK1 was 66.1% and 55.5%, respectively, which was significantly higher than that of the lines without resistance genes and that of Ilpum. The mean proportion of the healthy plant for 15 F4 RILs harboring both qBKWD and qBK1 was 80.2%, which was significantly higher than that of the lines with only qBKWD or qBK1. Conclusion Introducing qBKWD or pyramiding the QTLs qBKWD and qBK1 could provide effective tools for breeding rice with bakanae disease resistance. To our knowledge, this is the first report on a gene pyramiding effect that provides higher resistance against bakanae disease. Electronic supplementary material The online version of this article (10.1186/s12284-017-0197-7) contains supplementary material, which is available to authorized users.

Bakanae disease is an important fungal disease in the world. No rice (Oryza sativa L.) varieties have been found to be completely resistant to this disease. To facilitate accurate, uniform and simultaneous screening of many rice accessions, we developed an inoculation method for microconidia of Fusarium fujikuroi using a tissue embedding cassette and seedling tray. Standards for evaluating the inoculated rice seedlings as healthy or unhealthy were also established. The method was fast and reproducible for accurately evaluating resistance to bakanae disease in rice.

We obtained interesting results for genetic analysis and molecular mapping of the du12(t) gene. Control of the amylose content in rice is the major strategy for breeding rice with improved quality. In this study, we conducted genetic analysis and molecular mapping to identify the dull gene in the dull rice, Milyang262. A single recessive gene, tentatively designated as du12(t), was identified as the dull gene that leads to the low amylose character of Milyang262. To investigate the inheritance of du12(t), genetic analysis on an F2 population derived from a cross between the gene carrier, Milyang262, and a moderate amylose content variety, Junam, was conducted. A segregation ratio of 3:1 (χ 2 = 1.71, p = 0.19) was observed, suggesting that du12(t) is a single recessive factor that controls the dull character in Milyang262. Allelism tests confirmed that du12(t) is not allelic to other low amylose controlling genes, wx or du1. Recessive class analysis was performed to localize the du12(t) locus. Mapping of du12(t) was conducted on F2 and F3 populations of Baegokchal/Milyang262 cross. Linkage analysis of 120 F2 plants revealed that RM6926 and RM3509 flank du12(t) at a 2.38-Mb region. To refine the du12(t) locus position, 986 F2 and 289 F3 additional normal plants were screened by the flanking markers. Twenty-six recombinant plants were identified and later genotyped with four additional adjacent markers located between RM6926 and RM3509. Finally, du12(t) was mapped to an 840-kb region on the distal region of the long arm of chromosome 6, delimited by SSR markers RM20662 and RM412, and co-segregated by RM3765 and RM176.