The determinant factors for model resolutions obtained using CryoEM method

The CryoEM single particle imaging method has recently received broad attention in the field of structural biology for determining the structures of biological molecules. The structures can be resolved to near-atomic resolutions after rending a large number of CryoEM images measuring molecules in different orientations. However, the factors for model resolution need to be further explored. Here, we provide a theoretical framework in conjunction with numerical simulations to gauge the influence of several key factors that are determinant in model resolution. We found that the number of measured projection images and the quality of each measurement (quantified using average signal-noise-ratio) can be combined to a single factor, which is dominant to the constructed model resolution. Furthermore, the intrinsic thermal motion of the molecules and the defocus levels of the electron microscope both have significant effects on the model resolution. These effects can be quantitatively summarized using an analytical formula that provides a theoretical guideline on structure resolutions for given experimental measurements

Pure line selection for Hawm thung

Summary (Th)ประเทศไทยนับเป็นแหล่งหนึ่งที่มีความหลากหลายของพันธุกรรมข้าวที่เป็นมรดกจากบรรพบุรุษชาวนารุ่นหนึ่งไปสู่อีกรุ่นหนึ่ง แม้ว่าปัจจุบันชาวนาปลูกข้าวโดยใช้พันธุ์จากทางราชการเป็นส่วนใหญ่เพื่อขาย แต่ยังมีพื้นที่ที่มีสภาพแวดล้อมเฉพาะยังคงปลูกข้าวพันธุ์พื้นเมืองที่ปรับตัวได้ดีเหมาะสมกับสภาพแวดล้อมนั้นๆ ในจังหวัดอุบลราชธานี อำเภอเมืองและอำเภอเขื่อง มีพื้นที่นาทามติดกับลุ่มแม่น้ำที่ต้องประสบกับปัญหาน้ำท่วมทุกปี เกษตรกรหลีกเลี่ยงปัญหาโดยการปลูกข้าวเหนียวพันธุ์หอมทุ่งที่ไม่ไวต่อ ช่วงแสง ต้นสูง ลำต้นแข็ง ผลผลิตดี และคุณภาพในการรับประทานดีต่อเนื่องกันมาเป็นเวลานาน จากการเก็บรวบรวมพันธุ์ข้าว ทั้งหมด 4 หมู่บ้าน 23 ตัวอย่าง พบว่าข้าวทุกตัวอย่างมีลักษณะใกล้เคียงกันมาก แต่ยังมีความแปรปรวนบางลักษณะ ดังนั้นศูนย์วิจัยข้าวอุบลราชธานีจึงได้คัดเลือกข้าวหอมทุ่งพื้นเมืองดั้งเดิมให้เป็นสายพันธุ์บริสุทธิ์ ประเมินลักษณะประจำสายพันธุ์ ทดสอบการตอบสนองต่อความไวของช่วงแสง ที่ศูนย์วิจัยข้าวฉะเชิงเทรา พบว่าเป็นข้าวที่มีการตอบสนองต่อช่วงแสงแบบ essentially photoperiod insensitive คือ ไม่ไวต่อช่วงแสง นอกจากนี้ได้เปรียบเทียบผลผลิตในแปลงเกษตรกรและประเมินความชอบพันธุ์ข้าวโดยให้เกษตรกรในพื้นที่เป้าหมายมีส่วนร่วมในช่วงระยะก่อนเก็บเกี่ยว พบว่าข้าวหอมทุ่ง หมายเลข 2 ที่เก็บรวบรวมจาก นายเรียง สายพันธุ์บ้านเชือก ตำบลหนองขอน อำเภอเมือง ได้รับคะแนนสูงสุด และจากการทดสอบการตอบสนองต่อปุ๋ยไนโตรเจน พบว่าตอบสนองต่ออัตราปุ๋ยไนโตรเจนสูงสุด 8 กิโลกรัมไนโตรเจนต่อไร่ (ผลผลิต 279 กิโลกรัมต่อไร่) ซึ่งข้อมูลทั้งหมดนี้จะนำไปใช้เป็นประโยชน์ต่อชาวนาพื้นที่เป้าหมายให้มีเมล็ดพันธุ์ข้าวที่มีคุณภาพมากขึ้น และเป็นการอนุรักษ์พันธุ์ข้าวให้มีความหลากหลาย ส่งเสริมให้เกษตรกรเลือกใช้พันธุ์ข้าวที่เหมาะสมกับสภาพแวดล้อมนั้นๆ สอดคล้องกับปรัชญาเศรษฐกิจ พอเพียงของพระบาทสมเด็จพระเจ้าอยู่หัวของปวงชนชาวไท

The effects of cross-tolerance to oxidative stress and drought stress on rice dry matter production under aerobic conditions

Oxidative damage occurring in plant cells under drought stress is a known cause of reduced plant primary production. Decreasing oxidative damage through oxidative stress tolerance is expected to confer drought stress tolerance. In this study, we estimated cross-tolerance to oxidative stress and drought stress for breeding populations and analyzed the effects of the cross-tolerance on dry matter production in field experiments. For a total of 91 rice genotypes, including 72 backcross lines (BCLs), cross-tolerance was estimated from the first principal component score (PCS1) derived from a principal component analysis using a data set with a parameter of chlorophyll fluorescence and cell membrane stability index in both the oxidative and the drought stress treatments as the factors. The higher cross-tolerance was represented by the higher PCS1, and generally the values of PCS1 were segregated in the BCLs, suggesting that cross-tolerance is a heritable trait that can be improved by crossbreeding. The effects of positive and negative PCS1 on dry matter production under flooded and aerobic conditions were tested in field experiments. The decrease in dry matter production under aerobic conditions was smaller for the positive PCS1 genotypes. However, these genotypes also showed a lower stomatal conductance and smaller shoot biomass, especially under flooded conditions. We concluded that cross-tolerance is a useful trait for improving dry matter production, especially under severe drought stress. In view of the trade-offs between cross-tolerance and dry matter production, it is important to develop rice varieties with an optimal level of cross-tolerance for a target environment characterized by drought stress

Nuances of traditional knowledge in utilization of rice landraces by a farming community in North-Eastern Thailand

473-483Thailand 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).      </span

Quantitative Trait Loci Associated with Drought Tolerance at Reproductive Stage in Rice

Drought is a major constraint to rice (Oryza sativa) yield and its stability in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Quantitative trait loci (QTL) for grain yield and its components and other agronomic traits were identified using a subset of 154 doubled haploid lines derived from a cross between two rice cultivars, CT9993-510 to 1-M and IR62266-42 to 6-2. Drought stress treatments were managed by use of a line source sprinkler irrigation system, which provided a linearly decreasing level of irrigation coinciding with the sensitive reproductive growth stages. The research was conducted at the Ubon Rice Research Center, Ubon, Thailand. A total of 77 QTL were identified for grain yield and its components under varying levels of water stress. Out of the total of 77 QTL, the number of QTL per trait were: 7-grain yield (GY); 8-biological yield (BY); 6-harvest index (HI); 5-d to flowering after initiation of irrigation gradient (DFAIG); 10-total spikelet number (TSN); 7-percent spikelet sterility (PSS); 23-panicle number (PN); and 11-plant height (PH). The phenotypic variation explained by individual QTL ranged from 7.5% to 55.7%. Under well-watered conditions, we observed a high genetic association for BY, HI, DFAIG, PSS, TSN, PH, and GY. However, only BY and HI were found to be significantly associated with GY under drought treatments. QTL flanked by markers RG104 to RM231, EMP2_2 to RM127, and G2132 to RZ598 on chromosomes 3, 4, and 8 were associated with GY, HI, DFAIG, BY, PSS, and PN under drought treatments. The aggregate effects of these QTL on chromosomes 3, 4, and 8 resulted in higher grain yield. These QTL will be useful for rainfed rice improvement, and will also contribute to our understanding of the genetic control of GY under drought conditions at the sensitive reproductive stage. Close linkage or pleiotropy may be responsible for the coincidence of QTL detected in this experiment. Digenic interactions between QTL main effects for GY, BY, HI, and PSS were observed under irrigation treatments. Most (but not all) DH lines have the same response in measure of productivity when the intensity of water deficit was increased, but no QTL by irrigation treatment interaction was detected. The identification of genomic regions associated with GY and its components under drought stress will be useful for marker-based approaches to improve GY and its stability for farmers in drought-prone rice environments

High-yielding Crop Management by Enhancing Growth in Reproductive Stage of Direct-Seeded Rainfed Lowland Rice (Oryza sativa L.) in Northeast Thailand

Abstract: The crop management in direct-seeded rice to promote growth during the reproductive stage was evaluated in weed-controlled toposequentially intermediate fields in a small watershed in Northeast Thailand. In 2004, the effectiveness of topdressing with 21 kg ha-1 of nitrogen at the panicle initiation stage were examined using two genotypes, KDML105 and IR57514-PMI-5-B-1-2 (IR57514) seeded at the rates of 500, 250 and 125 seeds m-2. In 2005 and 2006, the effectiveness of a new management (seeding rate of 125 seeds m-2 and nitrogen application of 90-101 kg ha-1; CM2) was compared with that of conventional management (seeding rate of 500 seeds m-2 and nitrogen application of 50 kg ha-1; CM1) using 3 genotypes (KDML105, IR57514 and HY71) seeded in May and June. In 2004, the number of spikelets on the tertiary pedicel at a low seeding rate in KDML105 was greatly increased by topdressing. In 2005 and 2006, CM2 had higher grain yield than CM1 (346 vs. 235 g m-2), owing to its larger spikelet number per panicle, heavier shoot dry weight and greater nitrogen uptake. May-seeding resulted in longer non-flooded period in the seedling to tillering stage, lower SPAD reading value around heading and less shoot dry weight increase from heading to maturity, and had lower grain yield than June-seeding (253 vs. 328 g m-2). This reduction in grain yield was larger for late-heading KDML105 than in early heading IR57514. These results indicated the effectiveness of the new crop management (CM2) for direct-seeded rice in toposequentially intermediate fields with less weed infestation or weed-controlled conditions

Rainfall variability and its effects on growing period and grain yield for rainfed lowland rice under transplanting system in Northeast Thailand

Rainfall variability in Northeast Thailand during 2000-2015 was examined with objectives to determine any changes in rainfall pattern with time, and to determine its effects on duration of rice growing period and grain yield using a simulation model. Variation in mean annual rainfall over 16 years in 93 locations in the region ranged from over 1,600 to less than 1,200 mm, and the locations were grouped into 4 based on the annual rainfall. The change in annual rainfall, and early, mid and late season rainfall was analysed for the rainfall groups. There was a significant reduction in the amount of early season rainfall during the 16-year period in all groups. However, there was no significant change for annual, and mid and late season rainfall. Simulation study showed that the start of rice growing period (SGP) was delayed with reduced early rainfall during the 16 year period and the end of rice growing period (EGP) was also delayed while there was no significant change for the length of rice growing period (LGP). Simulation results showed that grain yield of KDML105, leading variety in Thailand, tended to increase during the 16 year period, as delayed planting time was optimum for achieving maximum yield in all rainfall groups. With general delay in rainfall season, occurrence of late season drought was predicted to be reduced and this helped to increase simulated grain yield. However, adaptation to changing rainfall pattern needs to be planned in advance to maximize its effect

Field phenotyping strategies and breeding for adaptation of rice to drought

This paper is a section of the book "Drought phenotyping in crops: from theory to practice" (Monneveux Philippe and Ribaut Jean-Marcel eds, published by CGIAR Generation Challenge Programme. Texcoco, Mexico). The section describes recent experience in drought phenotyping in rice which is one of the most drought-susceptible crops. The section contains genetic and genomic resources for drought adaptation and methods for selection of drought-resistant varieties in rice. In appendix, there is experience from Thailand on integration of direct selection for grain yield and physiological traits to confer drought resistance