Ubon Ratchathani Rice Research Center

Ubon Ratchathani, Thailand

Ubon Ratchathani Rice Research Center

Ubon Ratchathani, Thailand

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Korinsak S.,Kasetsart University | Sirithunya P.,Rajamangala University of Technology at Lanna | Meakwatanakarn P.,Ubon Ratchathani Rice Research Center | Sarkarung S.,IRRI ESARO | And 2 more authors.
Field Crops Research | Year: 2011

Key genomic regions associated with blast resistance against a broad spectrum of isolates could be identified in backcross introgression lines developed by conventional breeding program. In this article, eighty three BC3F2 backcross introgression lines (BILs) derived from a cross between IR68835-98-2-B-2-1-1 (a broad spectrum blast resistance variety) and KDML105 (a susceptible variety) were developed by phenotypic selection against a mixture of six virulent blast isolates (MXL) that are widely spread out in the rainfed lowland of the North and Northeast of Thailand. The resistance spectrum of the BILs was assessed by inoculating with 12 different Magnaporthe oryzae isolates that showed differential responses on the parental cultivars and the MXL that was used for phenotypic selection. All BILs showed highly resistant reactions (low disease score) to the MXL and to two blast isolates THL48 and THL149. Four markers, i.e., RM246, RM241, RM303 and RM164 completely favoring the IR68835 allele (shifting of allele frequencies from KDML105 to IR68835) were identified on chromosomes 1, 4 and 5, respectively. Therefore, these markers could be linked to the resistance genes functioning against the MXL, THL48 and THL149. Furthermore, significant shifting of alleles was identified at six markers located on chromosomes 2, 4, 8, 9 and 12. Seven DNA markers linked to specific resistance genes were identified, in which allele from IR68835 at 6 markers, i.e., RM6, RM205, RM211, RM252, RM273 and RM342 reduced disease score (DS), against blast isolates THL16, THL329, THL458, THL831, THL868 and THL96036 while allele from KDML105 at RM208 (Pi-kd on chromosomes 2) reduce DS against THL84, THL191, THL557 and THL1108. In this study, the use of DNA markers enabled the identification of specific resistance genes in the backcross breeding materials developed from routine rice breeding program through the conventional phenotypic selection. In this experiment, the usefulness of breeding materials from conventional breeding program in identifying genes corresponding to the selection was illustrated. Linked markers and their genomic location provide necessary information for further use of marker-assisted selection to improve blast resistance in rice breeding program. © 2011 Elsevier B.V.


Win K.M.,Kasetsart University | Korinsak S.,Kasetsart University | Jantaboon J.,Kasetsart University | Siangliw M.,Kasetsart University | And 7 more authors.
Field Crops Research | Year: 2012

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is one of the most devastating diseases of rainfed lowland rice in Thailand. The gene Xa21 shows broad-spectrum resistance and has been widely utilized to improve BB resistance in rice worldwide. However, Xa21 is not fully expressed in the early stages of development (seedling stage). In this study, we attempted to improve the Thai jasmine rice variety KDML105 to obtain non-age-related broad-spectrum resistance to BB. The Xa21 gene and seedling resistance genes from rice variety IR1188 (a variety with non-age-related broad-spectrum resistance to BB) were introgressed into KDML105 through three rounds of marker-assisted backcrossing (MAB) and phenotypic selection. Sixty KDML105 backcross introgression lines (KBILs) carrying the Xa21 gene were successfully developed. They were used to evaluate seedling resistance against thirteen Xoo strains. Three seedling resistance (SR) loci inherited from IR1188 were identified on rice chromosomes 1 (RM302-RM212), 8 (RM210-RM149) and 11 (RM287-RM224). The agronomic characters of the KBILs were assessed by planting these lines in the paddy field at Kasetsart University in 2003. Phenotypic variation was observed in the agronomic traits of these lines. Seven KBILs carrying the Xa21 and multiple SR loci and also having a similar plant type to the original KDML105 were chosen for testing in multi-location trials at research stations in rainfed lowland environments. The trials were conducted in 10 and 11 locations in the North and Northeast of Thailand, respectively, between 2005 and 2006. The yield, agronomic traits, cooking quality and important diseases were examined and compared with those of the original KML105. All of the 7 KBILs had a cooking quality profile (aroma, amylose content, gel consistency and alkaline spreading value) and agronomic performance similar to the original KDML105. In 2007, four KBILs were planted in farmers' fields at 5 locations. All BILs and the original KDML105 did not differ significantly in their agronomic performance. In this study, multiple loci for broad-spectrum seedling resistance were identified from the KBIL population developed by the integrated marker-assisted and phenotypic selection procedures (MAS and PS). These results facilitated the successful improvement of non-age-related broad-spectrum BB resistance in KDML105. The established non-age-related broad-spectrum BB-resistant KDML105 is currently recommended by Kasetsart University for planting in farmers' fields where the crop is vulnerable to BB. © 2012 Elsevier B.V.


PubMed | Bureau of Rice Research and Development, Mahidol University, Ubon Ratchathani Rice Research Center and Phrae Rice Research Center
Type: | Journal: Genetica | Year: 2017

The Asian rice gall midge (RGM) Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) is a major pest of rice, leading to yield losses in Thailand and many Asian countries. Despite an increasing number of reported midge outbreaks and the presence of many susceptible rice varieties, only a few studies have focused on the genetic variation of the midges. Therefore, we analyzed the phylogeography among Thai RGM populations covering north, northeast and central Thailand. Two mitochondrial DNA genes, cytochrome C oxidase I (COI) and 12S, and a non-coding repeat region (RR) situated just before COI were amplified. Overall, the haplotype diversity for COI and 12S genes of the Thai population was high, but the nucleotide diversity was quite low. Altogether, the phylogenetic tree and pairwise F


Kobayashi T.,Japan National Institute of Agrobiological Science | Yamamoto K.,Japan National Institute of Agrobiological Science | Suetsugu Y.,Japan National Institute of Agrobiological Science | Kuwazaki S.,Japan National Institute of Agrobiological Science | And 4 more authors.
Proceedings. Biological sciences / The Royal Society | Year: 2014

Host plant resistance has been widely used for controlling the major rice pest brown planthopper (BPH, Nilaparvata lugens). However, adaptation of the wild BPH population to resistance limits the effective use of resistant rice varieties. Quantitative trait locus (QTL) analysis was conducted to identify resistance-breaking genes against the anti-feeding mechanism mediated by the rice resistance gene Bph1. QTL analysis in iso-female BPH lines with single-nucleotide polymorphism (SNP) markers detected a single region on the 10th linkage group responsible for the virulence. The QTL explained from 57 to 84% of the total phenotypic variation. Bulked segregant analysis with next-generation sequencing in F2 progenies identified five SNPs genetically linked to the virulence. These analyses showed that virulence to Bph1 was controlled by a single recessive gene. In contrast to previous studies, the gene-for-gene relationship between the major resistance gene Bph1 and virulence gene of BPH was confirmed. Identified markers are available for map-based cloning of the major gene controlling BPH virulence to rice resistance. © 2014 The Author(s) Published by the Royal Society. All rights reserved.


Jairin J.,Ubon Ratchathani Rice Research Center | Jairin J.,Kyushu University | Kobayashi T.,Japan National Institute of Agrobiological Science | Yamagata Y.,Kyushu University | And 10 more authors.
DNA Research | Year: 2013

In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH. © 2012 The Author. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.


Haefele S.M.,International Rice Research Institute | Konboon Y.,Ubon Ratchathani Rice Research Center | Wongboon W.,Ubon Ratchathani Rice Research Center | Amarante S.,International Rice Research Institute | And 3 more authors.
Field Crops Research | Year: 2011

Although crop residues constitute an enormous resource, actual residue management practices in rice-based systems have various negative side effects and contribute to global warming. The concept of a combined bioenergy/biochar system could tackle these problems in a new way. Rice residues would be used for energy production, thereby reducing field burning and the use of fossil fuels, and the biochar by-product could help to improve soils, avoid methane emissions, and sequester carbon in soils. To examine some of these promises, we conducted field experiments from 2005 to 2008 in three different rice production systems. Objectives were to study the effect of biochar from rice husks on soil characteristics, assess the stability of carbonized rice residues in these different systems, and evaluate the agronomic effect of biochar applications. The results showed that application of untreated and carbonized rice husks (RH and CRH) increased total organic carbon, total soil N, the C/N ratio, and available P and K. Not significant or small effects were observed for soil reaction, exchangeable Ca, Mg, Na, and the CEC. On a fertile soil, the high C/N ratio of CRH seemed to have limited N availability, thereby slightly reducing grain yields in the first three seasons after application. On a poor soil, where the crop also suffered from water stress, soil chemical and physical improvements increased yields by 16-35%. Together with a parallel study including methane and CO2 emission measurements at one site, the results strongly suggest that CRH is very stable in various rice soils and systems, possibly for thousands of years. However, the study also showed that CRH was very mobile in some soils. Especially in poor sandy soil, about half of the applied carbon seemed to have moved below 0.30m in the soil profile within 4 years after application. We concluded that biochar from rice residues can be beneficial in rice-based systems but that actual effects on soil fertility, grain yield, and soil organic carbon will depend on site-specific conditions. Long-term studies on biochar in field trials seem essential to better understand biochar effects and to investigate its behavior in soils. © 2011 Elsevier B.V.


Boling A.A.,International Rice Research Institute | Bouman B.A.M.,International Rice Research Institute | Tuong T.P.,International Rice Research Institute | Konboon Y.,Ubon Ratchathani Rice Research Center | And 2 more authors.
NJAS - Wageningen Journal of Life Sciences | Year: 2011

Yield constraint analysis using a combination of experiments and crop growth models has been useful for quantifying the relative role of yield-limiting factors, and for prioritizing management interventions aimed at increasing the yields of non-photoperiod-sensitive rice grown under rainfed conditions. The use of a systems approach for photoperiod-sensitive varieties is constrained by the lack of crop growth models that can simulate the varieties' photoperiod response. This study used data from the literature, from a controlled-growth experiment, and from multi-location field experiments to determine the photoperiod-sensitivity parameters of Jasmine rice grown in north-east Thailand, and incorporated these in the ORYZA2000 model. Next, the model was used to analyse yield gaps by comparing yields in farmers' fields with the simulated attainable yields with an adequate N supply (60 kg ha -1) under irrigated conditions. The ORYZA2000 model adequately simulated growth, development, and yield of Jasmine rice over a 0-150 kg N ha-1 range under irrigated and normal to above-normal rainfall conditions. The simulated attainable yields ranged from 3.47 to 5.96 Mg ha -1. A simulated yield gap of 1.76 Mg ha-1 (41%) currently exists in rainfed rice farmers' fields. Yield gaps could be substantially reduced by 1.48 Mg ha-1 (34%) through improved N-management practices. The yield gap caused by water limitation was small (0.02 Mg ha -1, <1%) during the study period, when rainfall was normal to above normal. The large yield gap beyond the farmers' current fertilizer level suggests considerable scope for increasing yields through site- and time-specific nutrient management. A long-term simulation study including years with rainfall below normal is needed to comprehensively quantify yield gaps caused by water limitation. Such long-term simulation is hindered by the lack of long-term groundwater depth measurements. © 2010 Royal Netherlands Society for Agricultural Sciences. Published by Elsevier B.V. All rights reserved.


Chunta S.,Mahasarakham University | Prathepha P.,Mahasarakham University | Thiha,Mahasarakham University | Jongdee B.,Ubon Ratchathani Rice Research Center
Indian Journal of Traditional Knowledge | Year: 2014

Thailand has a large number of rice landrace varieties which are still grown by native tribes and small farmers in distant areas of the country. In these remote areas agricultural practices are primarily for food sufficiency and the farmer's livelihood. Different native rice varieties are used for different purposes. Traditional utilization of rice landraces in Northeastern Thailand include: food, medicine, rituals, wine and native whisky; agriculture and animal feed; economic purposes and exchange. This paper presents the traditional knowledge of utilization of rice landraces of farmers in four selected locations of Northeastern Thailand (Sakon Nakhon, Roi Et, Ubon Ratchathani and Nakon Rachasima Provinces).


Kato Y.,University of Tokyo | Tajima R.,Tohoku University | Homma K.,Kyoto University | Toriumi A.,Kyoto University | And 4 more authors.
Plant and Soil | Year: 2013

Background and aims: Rice plants alternately experience anaerobic and aerobic conditions during their life cycle in rainfed lowlands. Each condition affects root growth differently. Our objective was to clarify the specific rice root response to aerobic conditions in rainfed lowlands. Methods: At the Ubon Ratchathani Rice Research Center in northeastern Thailand, we obtained root samples from 17 'Surin1' (Thai variety) BC3-derived lines and 7 CT9993-5-10-1-M × IR62266-42-6-2 doubled-haploid lines from flooded and non-flooded paddy fields at the reproductive stage in 2010 and 2011. Results: In the non-flooded trial, rice was grown aerobically by draining the perched water; soil moisture at a depth of 20 cm fluctuated between -10 and -30 kPa. Deep rooting was likely promoted under aerobic conditions, but slightly drier soils under longer dry spells seemed to restrict root penetration, as the topsoil rapidly hardened during dry spells of only a few days. Fine-root development in the topsoil was inhibited under aerobic conditions. Conclusions: Even without drought stress, rice roots respond significantly to the disappearance of standing water in rainfed lowlands via deep rooting and root branching. We identified one promising 'Surin1' BC3-derived line showing an adaptive response of deep rooting under aerobic conditions, which can be used as a breeding material for rainfed lowland rice in Thailand. © 2012 Springer Science+Business Media Dordrecht.


Jairin J.,Ubon Ratchathani Rice Research Center | Sansen K.,Ubon Ratchathani Rice Research Center | Wongboon W.,Ubon Ratchathani Rice Research Center | Kothcharerk J.,Phitsanulok Rice Research Center
Breeding Science | Year: 2010

The brown planthopper (BPH) resistance gene bph4 has previously been assigned on the short arm of rice chromosome 6. However, the map position of the gene could not be determined. To detect the bph4 locus, 15 polymorphic simple sequence repeat (SSR) markers covering genetic distance of 0.0-63.4 cM on chromosome 6 were used to survey 15 BPH resistant (R) and susceptible (S) individuals from each of the 95 and 78 F2 populations derived from crosses of TN1/Babawee and Babawee/KDML105, respectively. One SSR marker, RM586, was associated with the R and S from the F2 populations. Additional markers surrounding the RM586 locus were examined to define the location of bph4. From the genetic linkage map and QTL analysis of 95 and 78 F2 individuals, the bph4 locus was mapped at the same chromosomal region of Bph3 between two flanking markers RM589 and RM586. Markers linked to the resistance gene explained 58.8-70.1% of the phenotypic variations and can be used for marker-assisted selection in BPH-resistant breeding programs. In addition, our experiment provides evidence that a recessive gene could behave as a dominant gene under different genetic backgrounds.

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