Difference between revisions of "IC4R004-GWAS-2015-25371505"
(→Plant Culture & Treatment) |
(→Plant Culture & Treatment) |
||
| Line 7: | Line 7: | ||
==Plant Culture & Treatment== | ==Plant Culture & Treatment== | ||
* The experiment was conducted in a greenhouse at the University of Bonn, Germany, from May to November 2013. A mapping population consisting of 328 rice cultivars was obtained from the International Rice Research Institute (The Philippines). The seeds were germinated in the dark for 3 d at 28 °C and then transferred to a greenhouse under natural light. Three-week-old seedlings were transplanted into 2 × 6 m ponds filled with soil (a local luvisol: 16% clay, 77% silt, 7% sand, 1.2% organic carbon, pH 6.3; Schneider, 2005) at 16.5 × 19 cm spacing. A constant water level of at least 3 cm was maintained from 10 d after transplanting throughout the growth season. Each of the six plots contained one replicate of all 328 cultivars in a completely randomized distribution. The plots were randomly assigned to ozone and control treatments, and open-top chambers (height 1.3 m) were built around all plots to ensure an identical microclimate. To avoid nutrient limitations, 107 g of K 2 SO 4 and 98 g of Ca(H 2 PO 4 ) 2 were applied to each plot as basal fertilizer at the beginning of the season, and 155 g of urea was applied in three splits during the season. Temperature, air humidity, and CO 2 concentration were constantly monitored at 12 min intervals using sensors installed at 2 m height in the greenhouse. The average temperature was 25/19 °C (day/night), the average humidity was 60/80% (day/night), and the average CO 2 concentration was 460/600 ppm (day/night). Supplementary lighting was installed above the plots to ensure a minimum light intensity of 12.5 klux even on cloudy days. Water was removed from the ponds in week 19, and the plants were harvested in week 21. Panicles were separated from the shoots and dried at 50 °C for at least 72 h to complete dryness. The shoot samples were dried for 10 weeks in the greenhouse until they reached a constant moisture content of around 11% and then weighed. | * The experiment was conducted in a greenhouse at the University of Bonn, Germany, from May to November 2013. A mapping population consisting of 328 rice cultivars was obtained from the International Rice Research Institute (The Philippines). The seeds were germinated in the dark for 3 d at 28 °C and then transferred to a greenhouse under natural light. Three-week-old seedlings were transplanted into 2 × 6 m ponds filled with soil (a local luvisol: 16% clay, 77% silt, 7% sand, 1.2% organic carbon, pH 6.3; Schneider, 2005) at 16.5 × 19 cm spacing. A constant water level of at least 3 cm was maintained from 10 d after transplanting throughout the growth season. Each of the six plots contained one replicate of all 328 cultivars in a completely randomized distribution. The plots were randomly assigned to ozone and control treatments, and open-top chambers (height 1.3 m) were built around all plots to ensure an identical microclimate. To avoid nutrient limitations, 107 g of K 2 SO 4 and 98 g of Ca(H 2 PO 4 ) 2 were applied to each plot as basal fertilizer at the beginning of the season, and 155 g of urea was applied in three splits during the season. Temperature, air humidity, and CO 2 concentration were constantly monitored at 12 min intervals using sensors installed at 2 m height in the greenhouse. The average temperature was 25/19 °C (day/night), the average humidity was 60/80% (day/night), and the average CO 2 concentration was 460/600 ppm (day/night). Supplementary lighting was installed above the plots to ensure a minimum light intensity of 12.5 klux even on cloudy days. Water was removed from the ponds in week 19, and the plants were harvested in week 21. Panicles were separated from the shoots and dried at 50 °C for at least 72 h to complete dryness. The shoot samples were dried for 10 weeks in the greenhouse until they reached a constant moisture content of around 11% and then weighed. | ||
| + | |||
| + | * Five weeks after transplanting, ozone fumigation was initiated to induce chronic stress at a target level of 60 ppb for 7 h every day. Comparable concentrations are already being observed in some areas and are expected to be reached in many countries in the future. Ozone was produced using custom-made ozone generators (UB 01; Gemke TechnikGmbH, Ennepetal, Germany) with dried air passing through silica gels as input. Ozone output was regulated by an ozone monitor (K100 W; Dr A. Kuntze GmbH, Meerbusch, Germany) with an ozonesensor (GE 760 O3; Dr A. Kuntze GmbH) placed inside the chambers. The generated ozone was blown into a central pipe running above the plant canopy, from which three parallel perforated side pipes for ozone distribution branched off at a distance of 40 cm from each other. The pipes were calibrated for even ozone distribution prior to transplanting of rice seedlings using a handheld ozone monitor (series 500; Aeroqual Ltd, Auckland, New Zealand). The fumigation lasted from 9:00 until 16:00 each day for 15 weeks until the end of the growth season. During the growth season, acute ozone stress was applied three times in weeks 8, 10, and 14 after transplanting. The average concentration of acute stress was 150 ppb and it lasted for 7 h (9:00 to 16:00). The ozone concentration was constantly monitored by the handheld ozone monitor placed within the canopy during the fumigation. The average ozone con-centration recorded was 63 ppb in the ozone treatment (excluding the episodes of acute stress), while in the control the concentration was 12 ppb on average. | ||
==Research Findings== | ==Research Findings== | ||
Revision as of 13:07, 21 June 2016
Contents
Project Title
Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study
The Background of This Project
- Tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. Here, we report a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with ozone tolerance. A diversity panel consisting of 328 accessions representing all subgroups of O. sativa was exposed to ozone stress at 60 nl l –1 for 7 h every day throughout the growth season, or to control conditions. Averaged over all genotypes, ozone significantly affected biomass-related traits (plant height –1.0%, shoot dry weight –15.9%, tiller number –8.3%, grain weight –9.3%, total panicle weight –19.7%, single panicle weight –5.5%) and biochemical/physiological traits (symptom formation, SPAD value –4.4%, foliar lignin content +3.4%). A wide range of genotypic variance in response to ozone stress were observed in all phenotypes. Association mapping based on more than 30 000 single-nucleotide polymorphism(SNP) markers yielded 16 significant markers throughout the genome by applying a significance threshold of P<0.0001. Furthermore, by determining linkage disequilibrium blocks associated with significant SNPs, we gained a total of 195 candidate genes for these traits. The following sequence analysis revealed a number of novel polymorphisms in two candidate genes for the formation of visible leaf symptoms, a RING and an EREBP gene, both of which are involved in cell death and stress defence reactions. This study demonstrated substantial natural variation of responses to ozone in rice and the possibility of using GWAS in elucidating the genetic factors underlying ozone tolerance.
Plant Culture & Treatment
- The experiment was conducted in a greenhouse at the University of Bonn, Germany, from May to November 2013. A mapping population consisting of 328 rice cultivars was obtained from the International Rice Research Institute (The Philippines). The seeds were germinated in the dark for 3 d at 28 °C and then transferred to a greenhouse under natural light. Three-week-old seedlings were transplanted into 2 × 6 m ponds filled with soil (a local luvisol: 16% clay, 77% silt, 7% sand, 1.2% organic carbon, pH 6.3; Schneider, 2005) at 16.5 × 19 cm spacing. A constant water level of at least 3 cm was maintained from 10 d after transplanting throughout the growth season. Each of the six plots contained one replicate of all 328 cultivars in a completely randomized distribution. The plots were randomly assigned to ozone and control treatments, and open-top chambers (height 1.3 m) were built around all plots to ensure an identical microclimate. To avoid nutrient limitations, 107 g of K 2 SO 4 and 98 g of Ca(H 2 PO 4 ) 2 were applied to each plot as basal fertilizer at the beginning of the season, and 155 g of urea was applied in three splits during the season. Temperature, air humidity, and CO 2 concentration were constantly monitored at 12 min intervals using sensors installed at 2 m height in the greenhouse. The average temperature was 25/19 °C (day/night), the average humidity was 60/80% (day/night), and the average CO 2 concentration was 460/600 ppm (day/night). Supplementary lighting was installed above the plots to ensure a minimum light intensity of 12.5 klux even on cloudy days. Water was removed from the ponds in week 19, and the plants were harvested in week 21. Panicles were separated from the shoots and dried at 50 °C for at least 72 h to complete dryness. The shoot samples were dried for 10 weeks in the greenhouse until they reached a constant moisture content of around 11% and then weighed.
- Five weeks after transplanting, ozone fumigation was initiated to induce chronic stress at a target level of 60 ppb for 7 h every day. Comparable concentrations are already being observed in some areas and are expected to be reached in many countries in the future. Ozone was produced using custom-made ozone generators (UB 01; Gemke TechnikGmbH, Ennepetal, Germany) with dried air passing through silica gels as input. Ozone output was regulated by an ozone monitor (K100 W; Dr A. Kuntze GmbH, Meerbusch, Germany) with an ozonesensor (GE 760 O3; Dr A. Kuntze GmbH) placed inside the chambers. The generated ozone was blown into a central pipe running above the plant canopy, from which three parallel perforated side pipes for ozone distribution branched off at a distance of 40 cm from each other. The pipes were calibrated for even ozone distribution prior to transplanting of rice seedlings using a handheld ozone monitor (series 500; Aeroqual Ltd, Auckland, New Zealand). The fumigation lasted from 9:00 until 16:00 each day for 15 weeks until the end of the growth season. During the growth season, acute ozone stress was applied three times in weeks 8, 10, and 14 after transplanting. The average concentration of acute stress was 150 ppb and it lasted for 7 h (9:00 to 16:00). The ozone concentration was constantly monitored by the handheld ozone monitor placed within the canopy during the fumigation. The average ozone con-centration recorded was 63 ppb in the ozone treatment (excluding the episodes of acute stress), while in the control the concentration was 12 ppb on average.
Research Findings
Labs working on this Project
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Karlrobert-Kreiten Strasse 13, 53115 Bonn, Germany
- Key Laboratory of Crop Genetics & Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, PR China
- Campus Klein-Altendorf, University of Bonn, Klein-Altendorf 2, 53359 Rheinbach, Germany
Corresponding Author
- Michael Frei (mfrei@uni-bonn.de)
