IRRI Final Presentation




This gallery contains 11 photos.

The IWU group had the opportunity to visit Manila, the capital of the Philippines, twice.During the first trip, Jessica, Hannah, Julia, and I visited the National Museum of Anthropology and SM Mall of Asia. The National Museum of Anthropology features … Continue reading

Golden Rice Breeding and Carotenoid Extraction

At IRRI, I have been able to expand my knowledge of Golden Rice breeding and the carotenoid extraction experiments that are utilized to calculate its levels of beta-carotene.

This week, I along with 2 undergraduate interns from San Pablo had the opportunity to visit the transgenic unit where Golden Rice and HIZER (high iron and zinc) varieties are grown. The first observation that comes to mind would be that there are many security measures put in place in order for the detainment of the entrance of other seed varieties and for the ceasement of Golden Rice materials extending beyond the transgenic facility. Some examples include the washing of shoe soles when entering and exiting as well as all drains having mesh. Also, for the disposal of GR2E materials, seeds are boiled beforehand for 15 minutes.

Golden Rice Fields

Kuya Dalvin, Ate Mercy, and Kuya Amery shared a bit about the history of Golden Rice and the process of breeding varieties for the expression of the GR2E gene (relation with carotenoid content). When it comes to picking wild-type varieties for such crosses, it is vital to choose varieties most well-known and preferred by farmers. For instance, GR2E was initially introgressed into 3 high-yielding varieties BR29 (Bangladesh), RC82 (Philippines), and IR64 (Philippines).

IR64 parent and IR64/GR2E (prominent yellow hue, phenotypic indication of the presence of GR2E)
RC28 parent (left) and RC28/GR2E (right)

It is not effective for progenies to only express the Gr2E gene because one instead is aiming to stack trains indicating that the traits of the wild-type parents are equally as significant. To make certain of this, parents are always planted for comparisons between progeny and wild-type parents in regards to flowering dates, number of tillers, and other agronomic parameters. There should be little to no deviation between these characteristics. Before a generation of seeds are planted in the screen house, they are dried for 3 days at 50 degrees Celsius for better germination. This process breaks dormancy. GR2E lines that are transferred from the screen house to the field are fixed (normally become fixed by generation BC5F3). The transgenic division works with IRRI’s seed health unit for the redirecting of seeds to multilocation trials.

The conduction of a field study still needs to occur by a third party group to more accurately conclude the effects of Golden Rice consumption (how much are vitamin A levels in people’s blood being elevated). There is constant coordination between Excellence Through Stewardship, the Bureau of Planting, and IRRI’s biosafety office. Currently, the public has been expressing some uncertainty regarding Golden Rice. For instance, on April 18, 2023, a Writ of Kalikasan was issued. It sought to stop the release of genetically modified rice.

The carotenoid content of Golden Rice was derived from genes of daffodil, maize, and soil bacterium E. uredovora. Golden rice provides up to 50% of the estimated average requirement for vitamin A in young children. Vitamin A deficiency can cause blindness, poor growth, or even death most oftentimes in women and children. Beta-carotene, a type of carotenoid, is a precursor of vitamin A. Carotenoids support the immune system and wound healing process, protect against UV radiation, and increased carotenoid content in the daily diet may reduce the risk of chronic conditions. They are also linked to antioxidant, anti-inflammatory, and anticancer effects. Carotenoid beta-carotene in particular is a precursor of vitamin A. The carotenoid content of Golden Rice is extracted and quantified every 2 months after harvest. By working with polished seeds in comparison to un-polished seeds, you can extract the accurate amount of carotenoid.

In the carotenoid extraction laboratory, under the supervision of Ate Crystal and Ate Elaine, I was able to work with 7-month samples and compare my results to accurate results completed in the past. There is much preparation that occurs before samples are taken out of a -20 degree C storage unit. 15 ml tubes and microtubules are placed in holders and labeled in accordance with the number of samples being tested plus the number of replicates. A water bath is turned on and set to heat up to 50 degrees C. VIS682A stock dye is vortexed and then diluted (2 microliters of dye, 9.8 ml of acetone). This diluted due is utilized to set up a range that will be used later to check the accuracy of sample absorbance readings. 100 microliters of dye are placed into 3 microtubes, each tube is centrifuged, and then 1 ml of acetone is added to each. Before these samples are read by the spectrophotometer, a blank of acetone is read. For each of the 3 controls, one is aiming for an absorbance of around 0.4 at a wavelength of 680 nm. After the readings/absorbance of the samples are recorded, they are summed together. This sum is multiplied by 80% in order to establish the lower half of the range. The sum is then multiplied by 1.09% in order to establish the higher half of the range (range ex: 0.343 to 0.468).

After preparation, then samples are taken out of the freezer. However, oftentimes, if the samples one is working with are heterozygous, seed sorting may need to occur in which only yellow polished seeds are kept to be tested. Into labeled grinder tubes, about 2 grams of each sample are placed with 2 metal balls. These tubes are then put into a wood mold and grinded at 10 min intervals for a total of 30 minutes. After the samples were taken out, I noticed that they were chalky in appearance/texture and were lighter in yellow hue compared to the un-grinded seeds.

Then, each sample is weighed on an analytical balance. For the experiment, 0.5 grams of each is needed. Also, since 8 or 7-month-old Philrice samples are replicated 3 times and 2-month-old Indonesian lines are replicated 2 times, the weighing process is thus repeated according to such. The weight is written down in a spreadsheet and then the sample is placed into a corresponding 15 ml tube. Leftover samples are placed back into the grinder tube and stored.

2 ml of water is added to each 15 ml tube and sonification of each sample is conducted. Sonification is the addition of pressure and heat to a solution. When sonifying, tubes are moved upward and in a circular motion to ensure the mixing of the samples. When sonified, each sample becomes closer to a white color than yellow. The machine is cleaned in between each sample. I noticed that sonifying samples with added acetone can be a bit challenging because the solution hardens although it needs to be mixed.

Sonification machine
7 month old samples after first round of sonification

All samples are capped and then placed in the water bath for 10 minutes. After the water bath, the samples are cooled down for around 30 minutes. They are then centrifuged for 10 minutes at 3, 500 rpm. Into new 15 ml tubes, goes a yellow/clear supernatant. The carotenoid remains within the supernatant. 2 ml of acetone and 100 microliters of the dye are placed into old 15 ml tubes.

Sample with dye and acetone

Sonification then occurs and samples turn a cloudy color. Old 15 ml tubes are centrifuged for 5 minutes and supernatant is poured into new 15 ml tubes. This process is repeated 2 more times.  

Sample after second round of sonification
Sample after centrifuge

Old 15 ml tubes are discarded (the powder left in them is white signifying there is little to no carotenoid left). 2 ml of PE: DE is placed into each new 15 ml tube and then each is mixed by inversion. Water is added to these tubes until the 14 ml mark is reached and then inversion occurs again. Samples are centrifuged for 5 minutes.

Top layer indicative of carotenoid presence

This next step was tricky for me because it calls for much concentration. Each 15 ml tube is next to its designated/labeled microtube and with a pipette, the yellow/green layer at the top is gathered and dispensed into a microtube. It is vital to not suck up any water during this step. Although water within the sample had a cloudy hue while the supernatant was yellow/green in color, they often mixed slightly causing their separation to be difficult. To the 15 ml tubes, 1 ml of PE: DE is added and then they are centrifuged.

Supernatant transferred into a microtube for drying

For the drying process, microtubes are placed open in the concentrator plus for 15 minutes at 45 degrees C. Supernatant from 15 ml tubes goes into the dried sample in the microtubes. 1 ml of acetone is added to the dried sample. 

Sample after drying

Each microtube is inverted and placed in a cuvette for spectrophotometer reading. Absorbance is written down at 450 nm and 680 nm. After every sample, the cuvette is cleaned with acetone. 

Often able to see a difference in hue between samples, left will demonstrate a higher absorbance at 450 nm


This Excel spreadsheet contains my results from June 27 and June 29
Condensed results

In reference to the data analysis conducted after carotenoid extraction, not much emphasis is placed upon the content (ug/g) results, instead focus is placed upon the absorbance at 450 results. Ultimately, an absorbance of 0.4 or greater at 450 nm is most favorable. Ate Crystel and Ate Elaine mentioned that if 0.4 is not reached, they will retry such samples. 

I will continue to work with Golden Rice materials as I head to the Genotyping Services Laboratory!

Parental polymorphism, LD pruning, coordination of flowering dates in an experiment, and field seed viability testing

View walking to Genotyping Services Laboratory

Last week, the DNA of 6 parents (154, 156, 1136, 1187, 2066, and 2156) was extracted. This week, these samples were diluted in order for later use in polymerase chain reaction (PCR). Each PCR plate (10 plates in total) contained all 6 parents. To better understand, 3 microliters of parent 1 (154) were placed in the first row across (A 1-12). Parent 2 (156) was placed in the second row across (B 1-12). This pattern continued until parent 6 (2156) was placed in F 1-12. Consequently, sample designation was coordinated with the PCR plate being placed horizontally instead of vertically. After all diluted DNA was distributed in this pattern across all 10 plates, the cocktail solution was made. 

For the cocktail solution, distilled water, 10x buffer, DNTPs, Taq polymerase, forward primers, and reverse primers were combined. It is important to note that different forward primers (FR) and reverse primers (RM) were used for each PCR plate. Consequently, the cocktail solution had to be repeated for each plate with distinct primers. To better understand, plate 1 utilized FR 7475 and RM 2067 while plate 2 utilized FR 7677 and RM 2067. Once plate 7 was reached, RM changed to 2068 and FR to 8687. RM 2068 remained until plate 10. Additionally, the calculation of the amount of cocktail solution for each plate was centered around knowing that there will need to be enough for 74 wells. Extra is also needed so this led to Ate Eva calculating for 75 samples. Into each PCR well went the 6.8 microliters of designated cocktail solution and 8 microliters of mineral oil.

Preparation of cocktail solution
Multi-channel pipetting of mineral oil into each PCR well

  These plates were then put into separate PCR machines. After inserting a plate into the PCR machine, one needs to choose the following options: run, 57 °C, SSRGR, sample volume = 10, block, and save. 

PCR machine running based on information specified in file GR/SSRGR

While these plates ran for around an hour and 20 minutes, the gel solution for electrophoresis was prepared. For the gel solution, 1x TBE, syber DNA gel stain, and condalab agarose gel were combined into a 1000 ml pyrex erlenmeyer flask. The flask was then heated in the microwave for 6 minutes. After this heating, the solution was observed to be bubbling. While it cooled down, combs were placed into casting racks. The solution was then poured from the middle of the casting racks and then it began to disperse itself. One needs to make certain it is evenly distributed and then covered with aluminum foil. Once the gel completely solidified, all combs were removed and wells became visible. 

Comb placement for gel plates

To prepare for the loading of the gel, 2 microliters of loading dye was added to each PCR well. Also, 3 microliters of ladder was pipetted into the first and last well of the gel. After each row (parent), the pipette tip was washed to ensure no contamination occurred. The gel then ran for 45 minutes at 170 volts. 

Loading of each sample into a gel
Running of the gels

For the screening of the gels, a Quantum VILBER machine was used. Each gel was laid long ways or horizontally and then the following options on the computer screen were chosen: auto, 90 degrees, and crop. The brightness of the image was also increased and then each image was saved to the desktop with a label (ex. plate1 RM 2067, 7475FR 6/21/23 57 temp). Then, the gel would be removed and the machine wiped down with a kim tech wipe. 

Viewing of the gels

Zinc and yield are negatively correlated traits. The crossing of 2 parents (trait of high yield) with 4 donor parents (trait of high zinc), aims for these 2 traits to be positively correlated. From the gels, we aim to  see parental polymorphism or rather signal of samples being heterozygous. Thus, 2 bands should be present. However, when looking at the gels only plate 2 seems to contain heterozygous samples. All other plates demonstrate single bands. Consequently, more backcrossing needs to occur to create a better fixed generation.

Plate results indicating need for more backcrossing because mainly only one band is seen in each well/plates

During this third week at IRRI, I visited head house with Ate Eva. This is where the threshing, dehulling, and seed sorting of some rice samples occurs. I was able to complete these processes with brown rice and long-grain white rice samples. Threshing is when the grain is separated from the panicle. This is often done manually with the use of a wooden knife or it can be completed by a machine. After this step, comes dehulling. It is when the husk is removed from the seed. I did not witness anyone completing this step manually. If a machine was utilized for a sample, it is cleaned before the next sample goes in. This is to prevent any contamination between strains. On one of the walls of the head house are many photos of the biofortification team. I enjoyed seeing each one because this gave me a glimpse into the type of work environment that has been cultivated here at IRRI. One of friendship and teamwork. 

Threshing machines
Biofortification team wall of images/memories

In order to analyze data for the identification of lines with high yield and high zinc, Ate Nirusha conducted linkage disequilibrium (LD) pruning. Linkage disequilibrium measures non-random single nucleotide polymorphisms (SNPs). These non-random variants are concluded to have high LD, are often close to one another, and reveal similar information. On the other hand, random SNPs characterize regions that are recombinant. These random variations are concluded to have low LD, are often far apart, and reveal different information. Ate Nirusha wants to find a region of interest in the genome (quantitative trait loci) that has a direct influence on high zinc and yield. Finding such a region is easier with LD pruning because this process allows for the removal of non-random SNPs. Thus, random SNPs/ markers are left which do not pass a certain threshold called R-squared (calculated from allele frequency, 0.5 thresholds utilized by Ate Nirusha). The creation of an LD decay plot is also helpful because it demonstrates the genetic distance between markers. As genomic distance increases between markers, LD decreases. Therefore, random SNPs are better able to be pointed out. An L-shaped curve is very common for an LD decay plot. Although Ate Nirusha is pruning the data, the number of markers should still remain around 55,000. After pruning, RapDB was utilized to look for genes. This program allows one to search by chromosome, enter coordinates for a specific locus, and include keywords. Ate Nirusha believes that there may be a quantitative trait loci (QTL) on chromosome 6. So, chromosome 6 was chosen, coordinates were entered, and keywords such as meta-homeostasis, meta-transport, zinc-iron binding, zinc, and iron were typed in. However, the results were extensive and consequently signified that more LD pruning needed to occur.  

I also had the opportunity to continue working with Ate Hsu and learning about their heat stress experiment. Some obstacles had been encountered by the glass house samples. The glass house had been frequently becoming too hot, indicating a possibility that the plants could be subjected to heat stress too early. Heat stress is not to be experienced by the plants until August 15 when the plants will reach the budding stage. Consequently, fans were now routinely turned on during the day. Also, many of the plants began to demonstrate a yellow discoloration of the leaves. Some samples were sent to the pathogenic division of IRRI and the results indicated that maggots had been infesting the plants. Bulldock insecticide was applied to the plants. 

Pesticide notice of no entry until after 24 hours

Due to the various lines having different flowering dates, strains with late flowering dates were consequently transplanted first in order for the coordination of all strains to have the same heading date. This is so that heat treatment can be applied at the same time. On 6/22/23, parents and progenies with flowering dates of or near 83 days were transplanted. From each line, the 8 strongest (tall/wide panicles) were chosen. 4 pots, filled with soil and fertilizer, were designated for each line. 2 plants per pot, and the strongest was placed in the middle and the other near the edge. One can identify the parents by looking at the labeling stick placed in each container/pot. The full name of the parent strain will be written (ex. SwarnaSub1, IR2006-P12-12-2, IRRI 154, Dasan, IRRI 156, Milyang-23, Giza 178). On the other hand, the progenies which resulted from the crosses are labeled with NS, followed by a designation number for that specific line, and then followed by a number that is specific to the plant itself (ex. NS 1751-1, NS 1751-2, NS 1751-3, NS 1751-4). Looking at this experiment from a wider perspective, it is vital to note that Ate Hsu needs 2 seasons in the field for confirmation of accurate data. As of now, Ate Hsu has completed 1 season in the field and is in the process of completing 1 controlled season. The second field season will be harvested around November. This gives me insight into how long the process of data collection is and how such organized efforts are important for accurate conclusions. 

Ate Hsu observing the state of their controlled heat stress plants
Image of heat stress experiment parent strains
Image of heat stress experiment progenies

The IRRI Gene Bank monitors seed viability every 5 years (for short-term storage). If the viability of seeds falls below 85, then there is a need for field work and agro-morphological characterization. I was able to visit the viability testing of rice strains Sativa (from Asia) and Glabirmia (from Africa). Seeds are raised in seed beds and then after 21 days, they are pulled. The following day, they are transplanted. In terms of the organization of strains in the field, each strain is placed in 5 rows. Also, each plant has to be cut from the top in order for the strand to grow straight after transplanting. Irrigation pipe systems provide water to the plants. Characterization begins at the late vegetative stage. At the post-harvest stage, some examples of characterization include amylose, gel consistency, and gelatinization. Also, harvest days are highly variable due to some strains being more or less photosensitive than others (100-160 day range). 

IRRI Gene Bank seed beds
IRRI Gene Bank transplanting field

I appreciated learning about the confirmation process of parental polymorphism, LD pruning, coordination of flowering dates in an experiment, and field seed viability testing.

Genome analysis, scooping, and transplanting

Dear readers, 

Thank you for taking the time to follow along with me on this experience which I can say has already impacted me greatly. I never would have imagined that I would be able to step outside my comfort zone and develop a work-life balance within only 2 weeks of time. 

June 12, 1898, is the date on which the Philippines declared its independence from Spain. Also, on July 4, 1946, the Philippines declared its independence from the United States. Not only is there a long history of colonial powers within the Philippines but there is also a long history of Filipino resistance. Many Filipinos on Monday, June 12 take the day off and spend time with their loved ones. 

The IWU group started the week off on an unsteady foot. Since we did not have to go into the office or laboratory on Monday, we decided to visit Makiling Botanic Gardens in order to take a calm stroll. There was a bit of confusion about where to get off the shuttle but we ended up making it to the entrance. As we were walking forward, we noticed a sign which stated “Eco Trail”. I guess we simply came to the conclusion that even though we were not prepared for a hike, we would just explore the trail for a bit. In my mind, this was not going to be a hike but rather a simple stroll. Unfortunately, I was very wrong. When we noticed that this trail was actually a hike, there was a small moment in which we questioned if we should turn back. But we decided to continue forward because we were practically halfway to the end. About 30 minutes later, as I was attempting to catch up to the group, I suddenly felt my foot sliding forward upon the ground. I quickly held onto a tree trunk with all my force. Yet, still, I ended up falling flat onto my back! Luckily I did not hit my head. I got up fast in order to pretend like nothing happened but sadly the rest of the group were looking my way. I laughed, mentioned I was ok, and then we continued on. Apparently, my fall was contagious because everyone started slipping and sliding after that. Thankfully no one was injured! As we came to the end of the trail, I was exhausted but glad for the experience. We went down a couple of stairs to see a beautiful waterfall and then headed back to the IRRI campus.

Julia and I on the Eco Trail! Taken moments before my fall…
Waterfall at the very end of the hike
IWU group after the hike

On Tuesday, I spent the day reading articles recommended by Ate Hsu. You may remember that Ate Hsu is a Ph.D. student analyzing the effects of heat stress in various strains of rice. These readings gave me a better insight into the complex research Ate Hsu is conducting. The first paper I read was titled “Mapping QTL for heat tolerance at flowering stage in rice using SNP markers”. I will attempt to give a brief overview of the main points this article proposed. Rice productivity is limited by various abiotic factors such as drought, submergence, and high temperature. As we have and continue to see with global warming, these factors have only been heightened. For each 1 °C increase in global temperature, rice grain yield is expected to decline by 10%. Thus, biofortification is a vital tool that through selective breeding, resistance to abiotic stresses can be introgressed into already established and well-known lines of rice. Rice grain yield is impacted by several components which often vary in where they are present within rice stages. Some examples include pollen/spikelet sterility and anther indehiscence (tight closure of the locules and a delay in locule opening). These effects ultimately lead to a low harvest index and low grain quality. However, these negative effects which are brought about oftentimes due to heat stress do not impact all strains the same. To better explain, some strains like Indica and Japonica have been identified to be heat tolerant. But what causes this tolerance? Well, that is where Quantitative Trait Loci (QTL) come in. QTL are functionally important region(s) of the genome and within these regions are single nucleotide polymorphisms (SNPs). SNPs are a type of marker or rather a location within the genome that can be used to distinguish between individuals because there is a difference present if a comparison is conducted. These locations can be linked to important genes and can be inherited with genes of interest. Consequently, they can be useful in breeding if associations between polymorphisms and favorable traits are detected accurately. Therefore if a strain is demonstrated within the field that it is tolerant to an imposed heat stress, through QTL analysis, one can identify the region that is associated with a particular gene that is causing such tolerance. For instance, QTL for heat tolerance at flowering (the most sensitive stage to high temperature) has been mapped on all chromosomes except 6 and 7. From crossing IR64 (susceptible female, Indica) x N22 (heat tolerant male, Indica), and then through self-pollination as well as backcrossing, this study was able to find 4 SNPs associated with heat tolerance in BC1F1. Phenotyping, DNA extraction, PCR amplification, and hybridization, genotyping using SNP markers, confirmation of QTL on chromosome 4 allowed for the understanding of how spikelet fertility is controlled within the genome. 

During this second week, I have also been able to learn about the research conducted by Ate Muditha Kumari and Ate Nirusha Dissanayake who are PhD students. To start off, Ate Muditha is looking at the introgression of the beta carotene (provitamin A) compound into popular rice varieties. From Golden Rice analyses, it is known that the endosperm of rice which contains beta carotene has a yellow hue. Thus, by looking at seed color, one can phenotypically select for such a trait in terms of breeding. When the harvest comes, these samples will then be sent for character analysis. Ate Nirusha is identifying lines with high yield and high zinc through the analysis of collected MAGIC (Multi-parent advanced generation inter-cross) population data from previous seasons of field experiments. Both of their research is focused on the nutrient content of rice. There are also similarities in the methodology toward how their data sets/tables are being analyzed. To better understand, both Ate Muditha and Ate Nirusha are analyzing phenotypic and genotypic data for the establishment of a selection index, the ranking of genes, and the analysis of allelic effect (how much of the total variation is contributed by a particular locus). This compilation of data surveys is for the purpose of identifying QTLs that are in some way related to the maintaining of high levels of beta carotene and/or zinc in rice. Programs such as R and RStudio are utilized in both research studies as they pertain to statistical computing and the construction of graphics. 

Also, this week Ate Muditha and Ate Nirusha met with Ate Mona, an associated scientist within the biofortification division. Ate Mona explained that since they are both nearing the finalization of tables and graphics, it is time to find R-squared values. These values measure the proportion of phenotypic variation explained by molecular markers. Phenotypic variance refers to how much of the total variation is contributed by a particular locus. So, if there is a high phenotypic variance, it is more likely that a major QTL will be found at that locus. Furthermore, LD pruning of the data sets also has to occur. This signifies the reduction of markers or rather deciding how many SNIPS to use from a particular segment. Oftentimes, SNIPS located closely near one another reveal the same information thus instead of studying all, it can be more time efficient to study a few of those or even 1 of them. Also, when having to look into a lot of markers, it is helpful to group based on the genotype of each marker. Thus, all plants with allele A, will group and take the mean and this will then be compared with a different group to determine the significance of a marker. Software such as PLINK, GaPit, and Farmcpu aid in such genome-wide analysis methods. Farrmcpu in particular will only show you unique markers. 

On Thursday, June 15 I was able to join an experiment conducted by Ate Eva Maghirang in the genotyping services Laboratory (GSL). QTL 6.2 had been previously identified to increase zinc content in rice strains. 4 donors contain this QTL and there are 6 parents in total. This experiment is the confirmation to confirm the true heterozygotes through comparison and use of 10 primers. The first step was to extract the DNA of the 6 parents. This process began by grinding the leaf tissue of each parent using a GENO machine. After this, CTAB buffer was added to each sample. Then, the washing process with ethanol was conducted. After, the samples were centrifuged twice. These samples were stored until Monday. 

Ate Eva and I in the GSL laboratory

At IRRI’s experimental station, I met Ate Lesela Anoidem, Ate Mhyla Mantala, Ronald Adolfo Mantala, and Ate Nora. This team conducts the scooping, threshing, and transplanting of seeds/plants which resulted from specifically biofortification experiments. 

Ate Lesela Anoidem, Ate Mhyla Mantala, Ronald Adolfo Mantala, and I in scooping bio-fortified seeds

During our meryenda, we all had sapin-sapin and coffee. After this break, I was able to join the team in the scooping of seeds. Each small brown bag contains the seeds of a single plant which is further identified by a number.

Sapin-Sapin a glutinous rice flour and coconut dessert

Ate Hsu’s screen house research is conducted in BG06 within the experimental station. During my first visit, plants of IR 2006 lines with a flowering date of 88 were transplanted 21 days after they were planted. Transplanting is the process of moving a plant from one location to another 15-40 days after seeding (all dependent on flowering or heading date). This process ensures the growth of a more uniform plant. Some key procedures to follow when transplanting include transplanting only the strongest. When pulling the plants out of their previous locations, it is vital to be cautious to not rip their roots. The strongest/healthiest plant was placed in the middle of the new container and the other was placed near the side of this container. All roots were covered with moist soil and the plants were soaked with water. 

Transplanted IR 2006 lines

I was also introduced to the fertilizer that is mixed with the soil used in this experiment. It is a mixture of ammonium nitrate, phosphate (solophos), and potassium nitrate (nitrate of potash). 

Fertilizers used in Ate Hsu’s heat stress study

Also, Ate Hsu had previously replicated this screen house experiment but in the field a season prior. Therefore, the yield from this harvest is being analyzed in regard to the amount of filled and unfilled grains per every 10 particles. Filled grain weight is also being recorded. 

Field harvest characterization spreadsheet

Furthermore, this day I had the chance to practice seeding. I placed around 18 Swarna Sub-1 seeds, with the aid of tweezers, into a container filled with very fine and damp soil. 

Seeding Swarna Sub-1

This week, Kuya Froilan organized an orientation for newly arrived interns. We took a trip to the Internation Rice Genebank! This is where more than 132,000 accessions are tested for viability and saved for preserving wild rice species’ biodiversity. These accessions can be requested by countries. Also within the gene bank, there are 2 divisions. The active short-term unit which is maintained at 2-4 degrees Celsius, contains varieties that are available for distribution. The viability of these seeds is monitored every 5 years.

Short term gene bank

 On the other hand, the long-term storage unit which is maintained at -20 degrees Celsius contains samples not being withdrawn for distribution. The viability of these seeds is monitored every 10 years. Seeds are within vacuumed aluminum cans. If viability is found to be below 85% then those seeds will be planted and then the fresh seeds would be stored. 

Long term gene bank

After visiting the gene bank, I headed upstairs to attend 2 biofortification presentations. The first was titled” Boosting genetic grain through genomic selection, speed breeding, and CRISPR CAS”. Presenter Kuya Gaurav emphasized the importance of maximizing genetic gain in order to increase rice yield. The following are some practices presented to have a role in the maximizing of genetic gain:

  • Speed breeding: Manipulation of environmental conditions during breeding  
  • CRISPER: Transgene insertion
  • GEEN: The insertion, deletion, and replacement of DNA in the gene of living organisms using engineered nucleases 

The second presentation was titled “Major abiotic stresses and impact screening”. Presenter Dr. Bala explained how characteristics of interest/analysis in rice (panicle length, spikelet fertility, etc.) can be negatively impacted by poor water quality, drought, salinity, land degradation, uneven rainfall patterns, and flooding. He proposed the benefit of engaging in screening in order to better understand how specific strains react differently to these stresses. Through screening, breeders are able to isolate which strains are resistant to certain stresses and then map genes that cause such resistance. 

Dr. Bala’s presentation, submergence screening slide

On Saturday, the IWU group as well as other IRRI staff (11 people in total) took a trip to Villa Escudero. There, we participated in activities such as eating delicious coconut flavored ice-cream, bamboo rafting, swimming, and having dinner near a waterfall!

Coconut ice-cream
Bamboo rafting
IRRI interns and staff who traveled to Villa Escudero

One major takeaway from this week would be how the production, testing, and an analysis of bio-fortified rice is a process that involves many roles and perspectives. Being able to look into and join in on each step has allowed me to meet amazing, strong, and passionate individuals. 

IRRI Week 1

Hello! Thank you for being willing to embark on this journey with me as I share my experiences in the Philippines this summer at the International Rice Research Institute. 

June 3, 2023 marks the date which starts this journey. In order to arrive at Manilla, Philippines I had to embark upon 2 flights in total. The first flight traveled from O’Hare airport to Abu Dhabi airport where a layover took place. 

Semaj and I on the flight to Abu Dhabi just before take off

During this time in Abu Dhabi, we were able to explore the hotel and the city. The temperature that day was near 100 degrees Fahrenheit. I do not think I ever reached a point where I got used to these high temperatures but nevertheless I was determined to make the most of the time we had. The buildings in Abu Dhabi are extremely tall and impressive! Semaj, Jessica, and I decided to take pictures with some of these buildings in the background.

Semaj, Jessica and I attempting to do a jumping shot but sadly failing 

Us in the evening on the hotel rooftop  

Also, later that day we headed to Sheikh Zayed Grand Mosque. Mameluke, Ottoman and Fatimid architectural styles blended in the construction of this mosque. It felt surreal to be there walking through Sheikh Zayed Grand Mosque. Around 9:00 p.m. we headed back towards the hotel in order to prepare ourselves for our flight to Manilla, Phillipines which would leave at 2:50 a.m.

Images of Sheikh Zayed Grand Mosque

When we arrived at the Manila airport on 6/5/23, we met Tito Mon and Kuya Carlo. They explained that we would have to wait a couple hours in the airport in order to wait for Sam and Hannah to arrive. This allowed time for many IWU students to exchange currency. After this, I bought a mango green tea with boba and a Jollibee order of rice and fried chicken.

Mango green tea with boba

 My favorite part of the Jollibee order was the gravy! Later on, Hannah, Julia, Jessica, Sam, and I headed to IRRI in a vehicle provided by Tito Mon. When we arrived, we checked in with the front desk and were able to enter our rooms within Harar Hall. We were also given a drawstring bag which contained snacks, sanitizer, an IRRI booklet code of conduct, and a short itinerary indicating that the first part of our IRRI orientation would take place on Wednesday. As soon as I settled in, I fell fast asleep. 

IRRI draw string bag

On  6/6/23, we had the IWU orientation at around 1:15 p.m. In the morning, I had my first meal at IRRI and it was great! 

First meal at IRRI
View from IRRI cafeteria

The orientation was led by Tito Mon and Kuya Guillian. We started off by learning a couple phrases in Tagalog. Also, we learned that saying “po” is a sign of respect and should be used very often at the end of a sentence. Furthermore, “kuya” signifies older brother and “ate” signifies older sister. They come before a person’s name and demonstrate that one is showing respect to older generations. We also learned that the most common form of transportation in the Los Baños and Manila areas is the Jeepney and it costs 12 pesos to climb onto one. I plan to take a picture of a jeepney to show you what it looks like but as of now it resembles a long taxi that can fit about 20 people. We then had a “merienda” which signifies a snack. Our merienda was buko pie. This type of pie has chunks of coconut layered within with custard in between these layers. It is super “masaran” (delicious) and not very sweet. 

Slice of Buko pie

We then continued on with the presentation by playing memory games surrounding the Tagalog language. Also, we were placed into 3 groups of around 4-5 and tasked with coming up with a skit to perform and illustrate how far we have come with the Tagalog language. My group included scenes on a jeepney and within a market. After each group performed, we all headed to Kamayan at Palaisdaan, a restaurant in which we had traditional Filipino food and Halo-halo for dessert. My favorite dish from tonight would have to definitely be the coconut marinated Tilapia! 

Kamayan floating restaurant

The IRRI orientation to place 6/7/23. We headed to the IRRI Education building and met with Kuya Froilan. During the Security & Safety presentation, I took notes regarding important emergency numbers. Later, we were taken to get our pictures taken for our ID’s.  

Where we took our ID pictures

Kuya Froilan took us on a tour of the Los Baños area on an IRRI shuttle. We picked up a buko pie and also stopped at Rizal Park and saw Laguna de Bay which is the largest lake in the Philippines. 

IRRI shuttle tour of Los Baños
Laguna de Bay

When we got back from the tour, everyone was dropped off to their specific divisions in which they will be interning in. As a part of rice breeding innovations under Dr. Swamy, I am in N.C. Brady Laboratory.

Laboratory where rice breeding innovations is located

 I was nervous to meet Dr. Swamy even though I had previouslky prepared by reading his research. During this one on one meeting, Dr. Swamy gave me valuable advice. For instance, he explained that to overcome a challenge in the laboratory, one must first employ self-help and then only later should one ask others. He also emphasized the importance of creativity, consistency, and how action has to match one’s words. Dr. Swamy explained that there is a peak in rice breeding towards the end of June because higher temperatures often signify greater chance for budding. Therefore, for now my tasks are to interact with the research team and learn about their own distinct projects and read articles they recommend. 

On 6/8/23 I spent my day analyzing further readings published by Dr. Swamy at BeanHub coffee shop right next to the IRRI cafeteria.  I took notes surrounding topics such as how some quantitative trait loci in low-yielding susceptible varieties negatively affect/ lower grain yield under drought. For high-yielding varieties, this is the opposite. So, mainly these research efforts aim to deduce candidate genes that are present in drought tolerant rice varieties. Also, to produce more of such varieties through crosses, comparative genomics, and the creation of consensus maps with markers. 

Cappuccino and blueberry cheesecake

The next day, 6/9/23, I attended an online thesis defense presented by Ms. Maria Raquel L. Avanica who is an undergraduate student at the University of the Philippines Los Baños. Ms. Maria Raquel L. Avanica  presented about how high vitamin A deficiency can be combated through the biofortification of Golden Rice (GR2E). They plan to find alleles which help maintain beta carotene concentration in different GR2E introgression line populations.

Ms. Maria Raquel L. Avanica’s thesis defense

 After this, the team celebrated Raquel’s hard work by going to Beanhub cafe where I tried a Mudslide which is a frozen chocolate milk drink with vanilla ice cream on top. When we headed back to N.C. Brady Laboratory, I spoke with Ms. Hsu Myat Noe Hnin who is a PhD student at the University of the Philippines Los Baños. They are analyzing how heat stress affects rice yield. I will be learning about the transferring of rice strains to different chambers at IRRI this upcoming week. IWU students then visited Seoul Kitchen which is a Korean restaurant near the University of the Philippines. We took the IRRI shuttle to Raymundo gate and then walked about 5 minutes. I ordered Rabokki! 

Seoul Kitchen

On 6/10/23 we celebrated Hannah’s 20th birthday! We woke up early and headed to the market where businesses were selling food, drinks, clothes and more. I purchased matcha milk tea boba as well as an ube pandesal with ube jam and cream cheese filling. 

Los Baños market
Ube pandesal

We then walked to Dalcielo Restaurant & Bakeshop and shared a pizza amongst the group.

Lunch and pizza

Lastly, we sang karaoke! I sang Grenade by Bruno Mars, Hannah sang Ehu Girl by Kolohe Kai, Julia sang Rolling in the Deep by Adele, Sam sang Dancing Queen by ABBA, and Jessica sang Chandelier by Sia. My favorite part was singing happy birthday to Hannah a bit off key. 

Karaoke restaurant

Stay tuned for week 2 in which we will meet interns from New York and Korea!


Hello everyone!

My name is Jessica Navarro and I am a first-generation student at Illinois Wesleyan University studying Biology. This summer I will be traveling to Los Baños, Philippines. As an intern at the International Rice Research Institute (IRRI), I hope to learn about the role of biotechnology in global food accessibility and in particular the production of nutritious and affordable rice strains. 

Currently, I am preparing for this adventure by educating myself on Filipino culture, language, and history. I am also in the process of finalizing a VISA application. 

Looking towards the summer, I am immensely excited to learn about the several methods and techniques utilized at IRRI. Furthermore, I am thrilled to try traditional Filipino dishes and explore the Los Baños area! A couple of goals I have for my time in the Philippines include: practicing Tagalog in a social setting each day, coming prepared to the laboratory, and asking questions. 

I will be updating this blog every week starting in June! So, keep a lookout for more posts!