My time at IRRI has passed and I have arrived back in the US. There are many things I will miss about the Philippines, most especially the people, the weather, and the food, but it also feels good to be back on campus. I’m glad I have some time to readjust to life on campus before my senior year begins. I have a lot of nerves going into my final year, there is so much lined up on my agenda but there is also so much to look forward to!
It’s hard to believe that this will be my final blog post for my IRRI internship experience but I’ve enjoyed every second of it and I could not be more grateful for the opportunity to participate in the IWU Freeman Asia Program. The IWU Freeman Asia Program has allowed me to visit Asia for the first time, experience my first internship, and develop personal and professional relationships which I am sure will prove to be long-lasting.
I would like to thank Dr. Teddy Amoloza, Stacey Shimizu, Tito Mon, my fellow interns, and everyone at IRRI for making this experience possible and for granting me the opportunity to take part in an adventure of a lifetime!
My duties as an intern at IRRI are officially over… Today I will be presenting my internship completion presentation to my supervisor and everyone that I worked with during my time at IRRI. I am slightly nervous because I am not the strongest presenter and I would like my IRRI colleagues to know that I have learnt so much in these passed two months and that I appreciate all of the effort that each of them have made to include me in their daily work. Below I have included my internship presentation so that you can also have a brief understanding of what I’ve been up to on the work front.
With only a week and a half left, it’s hard to believe that my time in the Philippines is already coming to a close, so I thought I’d use this post to reminisce on one of my favourite experiences that I’ve had since being here.
A few weeks ago, our group decided to spend a weekend away at the beach for some proper R&R (as one should whenever the opportunity arises!). We all took the Friday off and made our way to a beach a few hours from the IRRI campus where we stayed at a place highly recommended by one of our supervisors. None of us really knew what to expect with regards to the accommodation but , let’s just say, we couldn’t have been any closer to the shoreline if we wanted to.
On our way to our destination we met a Filipino basketball team who were on their way to a beach in the same area that we were staying to celebrate a second place win in a basketball competition. We all connected quite well and they offered for us to join them on some ocean activities the following day which we gladly accepted — we were excited to explore the area with locals who knew how to experience it in the most authentic way possible.
The upcoming days were spent enjoying what the crystal blue beaches had in store. We went snorkeling with the basketball team and saw so many beautifully tropical fish such as parrot fish, strange-looking yellow needlefish, and even clown fish. We were also able to feed bread to the fish and even got our fingers nipped a few times.
After snorkeling we were invited by the basketball team to join them for a home-cooked lunch, kamayan style — food is served on banana leaves and eaten with your bare heads, no utensils. The menu consisted of rice (of course), chicken adobo, squid adobo, grilled pork, and fish sinigang (a traditional sour soup). The food was delicious and the company was great!
During down time at our bungalow we spent a lot of time walking on the shore looking for shells and playing card games — which I can say with confidence is not my strongest suit, pun intended.
We were also introduced to Indian mangoes which i a popular snack food in the Philippines. Indian mangoes are essentially small mangoes with green skin and firm, slightly sour flesh. If you’ve never eaten them before you might think that they were unripe but they are actually meant to be eaten at this stage. Essentially, the green skin should be peeled off and the flesh cut into sections. The flesh can then be eaten as is but we were told that locals prefer to dip the flesh into salt or a fermented fish sauce, both of which I tried, but I prefer the flesh on its own. They are delicious and extremely refreshing, we even brought a few back to IRRI which I happily ate with my lunches.
Our weekend away was definitely a memorable trip that I am grateful I got to experience! We met so many new people, made new friends, ate new foods, and had the opportunity to enjoy the ocean in a way that I think many people could only dream to experience.
This past week I had the opportunity to work in the IRRI Hybridization Unit where I received hands-on experience on how hybrid rice varieties are created. In this post I’ll be giving you an insight into what hybridization is and what the process consists of. One major takeaway I had from this experience was that I was surprised by how manually laborious the hybridization process is. In other words, because of its very crucial role in rice breeding, I was expecting the hybridization process to be a lot more automated.
So, what is hybridization?
Hybridization, specifically in the world of rice breeding, is the process of combining desirable genes found in two or more existing rice varieties, known as the parents, and to go on to produce true-progeny that contain the desired genes, making it superior to the parents.
In rice breeding, hybridization has been a critical resource used to create rice varieties that have:
Increased yield potential
Better resistance to drought and other abiotic stresses
Better resistance to disease and pests
Better grain quality
IRRI provides various hybridization services such as:
Single cross hybrids, where 2 different parent types are crossed to create the first generation plants (F1), these F1 plants are allowed to self-pollinate to produce second generation (F2) seeds.
2. Double cross hybrids, where 2 different parent types are crossed to create first generation plants (F1), then 2 separate F1 plants are crossed to create the second generation (F2) seeds.
3. Top crosses, 2 different parent types are crossed to create the first generation plants (F1), then one of the F1 plants is crossed with an openly pollinated plant (non-recurrent parent) to create the second generation seeds (F2).
4. Back crosses, 2 different parent types are crossed to create the first generation plants (F1), then the F1 plant is crossed with one of the parents (recurrent parent) to create the second generation seeds (F2).
But, how is hybridization actually done?
Briefly, hybridization involves the emasculation of one of the desired parent rice plants, the pollination of this emasculated parent with the other desired parent, and the growing and harvesting of F1 seeds to go on to the next advancement.
But first there is a pre-emasculation procedure which consists of:
Choosing healthy parent plants that possess desired traits.
Isolating these plants in bowls.
Tagging of the parent plants.
Maintaining the parent plants with soil and irrigated tap water.
Keeping the parent plants in the hybridization greenhouse until mature.
The emasculation procedure is done between 3-6pm and involves:
Cutting off the top half of each spikelet to expose the anthers.
Using a vacuum and pipet to suck out the anthers from each spikelet.
Individually cover each panicle with a glassine bag to prevent the possibility of self-pollination.
The emasculated plant becomes the female parent.
Next, there is a pre-pollination procedure where:
The healthy panicles of the parent male pollinator plants are chosen.
The selected panicles are brought into the pollination chamber.
The selected panicles are placed in small clay pots filled with tap water where the panicles are left for about an hour to allow the spikelets to open and the anthers to become exposed.
The pollination stage of hybridization, which takes place between 8-11am, involves:
Bringing the emasculated female plants inside the pollination chamber.
Removing the glassine bag from the female plants.
Carefully lifting the blooming pollinator-panicles (male) above the female and gently shaking to displace the pollen and ensuring that the pollen falls onto and into cut spikelets of the female.
Covering the now pollinated female panicles with glassine bag again.
Placing the pollinated plants in the nursery area.
Allow the plant to mature.
The final stage of hybridization is harvesting and seeding which takes place 25 days after pollination. The F1 seeds are harvested and dried for 5 days, threshed, and are now ready for the next advancement.
After each cross, the resulting plants undergo genetic testing to confirm that the plants are true hybrids — contain the desired gene from the parent plants.
So far, my time in the hybridization unit has been my favourite experience at IRRI. I found it extremely interesting to experience the practical application of plant breeding for specific traits as opposed to working with theoretical crosses and punnet squares.
Believe it or not, at the time of posting this blog I am more than halfway through my internship. It’s crazy how fast time flies!
This past week was as laborious as it gets but I had such a great time! I spent my time in the rice fields where I helped with the pulling (harvesting) of rice seedlings, transplanting of the seedlings, and reseeding of rice paddies. Let’s just say it was a week full of sun, sweat, and a whole lot of mud…
On Monday and Tuesday I assisted in the harvesting of 14-day old rice seedlings which involved the careful pulling of seedlings from the soil and the tagging of them with numbered tags which would later correlate with the specific site that the seedlings would need to be transplanted to. The tagged seedlings were grouped into groups of ten and bundled together using elastic bands to make distribution at the transplantation field easier.
At IRRI many of the rice seedlings are initially grown using the ‘dry-bed method’ before being transplanted to bigger fields using the ‘wet-bed method’.
The Dry-Bed Method:
Nurseries are prepared on dry soil with beds that are 50-100cm wide and 5-10cm high. The area is free of shade and is equipped with adequate irrigation to keep the soil moist but not submerged. Right before harvesting, the dry-beds are flooded to make seedlings easier to harvest. Seedlings are usually grown in the dry-beds until they reach 15-21 days of growth, after which they are pulled and transplanted into wet-beds for further growth. The advantage of this method is that seedlings grow to be shorter and stronger, with a longer root system than those from the wet bed nursery although the pulling of the seedlings may lead to damaged roots if not done correctly.
The Wet-Bed Method:
This is the more traditional method of preparing a nursery. It is used in areas where there is sufficient water and land. Wet-beds are often much larger than dry-beds with the biggest difference being that the soil in wet-beds are almost completely submerged under water. The nurseries should be kept free from weeds, pest and disease, and nutrient deficiencies.
On Wednesday and Thursday I assisted in the transplanting of the newly harvested seedlings into a wet-bed rice paddy. Each numbered tag on the bundles of seedlings correlated to the numbered tag on a specific pole, indicating where that bundle of seedlings had to be planted.
On Friday I got a break from the field and had the opportunity to tour the Seed Processing Unit where I was shown how the rice seeds are inspected, cleaned, dried, undergo germination and moisture tests, and packaged for shipping to other rice plantations around the world.
The following Monday we worked on reseeding an empty dry-bed at the same site that the seedling harvesting took place. We used a direct seeding method in which we manually distributed/poured seeds into each row indented into the dry-beds and covered the seeds in a thin layer of dry soil afterwards.
All of the seedlings that I harvested and transplanted during my week of field work were part of a study on Zinc biofortification. Biofortification is the process of improving the nutritional quality of food crops. This can be achieved through agronomic practices, conventional breeding or biotechnology-based approaches like genetic engineering and genome editing. The seedlings have undergone genetic modifications in an attempt to create varieties of rice that contain higher levels of Zinc. This is a greatly beneficial study owing to the fact that Zinc is one of the most essential micronutrients required for healthy development in humans and more than one billion people suffer from Zinc deficiency related health problems in Asia alone. Because rice is a staple food for Asians as well as other nations, the breeding of rice varieties with high grain Zinc is a necessary operation and this is being done by exploiting several known QTLs and gene specific markers that have been identified for grain Zn and using use them in Marker-Assisted Breeding.
The past week was a great example of science in action and I have a new appreciation for the amount of work and effort that goes on ‘behind-the-scenes’.
What a weekend it has been! So many new places, new faces, and new experiences.
On Friday, all of us (including 11 students from India) spent the morning working in the rice paddies where we had the opportunity to experience traditional and automated field preparation and rice planting methods — I will make a separate post on this soon once I receive the pictures that were taken during that activity. In the afternoon, Froilan (the on-site supervisor for all IRRI students) drove the five of us around Los Baños and showed us what restaurants we should try out while we are here. We then stopped at a small vendor where I tried Carabou (water-buffalo) milk for the first time — it was delicious but it was also chocolate flavoured so maybe that doesn’t count as an honest review.
Next we drove to the outskirts of Los Baños to the biggest lake in the Philippines, Laguna de Bay, where we had great views of the water front and could even see Manila in the distance. We learnt that the lake is a huge fishing spot for Tilapia.
We then drove up Mount Makiling to buy some fruit from vendors that are considerably cheaper than vendors closer to IRRI and UPLB (University of the Philippines Los Baños). I ended up buying a Dragonfruit, which I have had before, as well as a Marang, which I have yet to try. The Marang is a strange-looking fruit that can only be eaten once the outside has turned brown and the flesh has become soft, apparently when it starts to smell like gasoline the fruit is ready to be eaten. I don’t know if I should be excited or scared but I’m sure it will be an interesting experience either way.
After our fruit-buying excursion, Froilan introduced us to the Filipino specialty of Buko Pie — Buko is the flesh of a young coconut. Buko Pie is filled with layered slices of coconut flesh surrounded by a custard, it is baked and served straight from the oven. Buko Pie is one of the most popular desserts in Los Baños and I testify that it really is delicious! If I had to describe Buko Pie I would say it is reminiscent of Apple Pie with the custard resembling that of a Melk Tert (a South African custard tart).
On Saturday, we decided to go on a hike up Mount Makiling to the Mud Spring. The Mud Spring is a type of hotspring created by the action of heat, from underlying volcanic activity, acid, and different microorganisms in the rocks and soil. They usually smell like rotting egg because of the presence of sulfur in the area. On our way to the Mud Spring we stopped at the Saturday Market at Freedom Park. I didn’t end up buying anything but it was fun to interact with the locals and have a look at what was being sold — for future reference.
Our walk up to Mud Spring and back ended up taking about 4 hours and we walked from about 20 km. It was extremely hot (34C/93F) and I’m convinced I got a month’s worth of exercise done in that day alone but luckily I had packed enough water, we had Aircons waiting for us back at IRRI, and the scenery was beautiful so it was well worth it.
An introduction to blast fungus (Magnaporthe oryzae) in rice
Today I experienced my first practical application of the science I usually only see happening in the lab or on paper. My supervisor, Dr. Swamy, introduced me to one of his current PhD students, soon-to-be Dr. Tapas Hore, who has been working on an extremely interesting project as part of his thesis. Dr. Hore has been developing a new strain of rice that is more resistant to a notoriously destructive rice disease called Blast.
Blast (Magnaporthe oryzae), also known as rice seedling blight, Johnson spot, or Imochi, is a fungal disease that can affect rice at any stage of growth. It is caused by the presence and spread of blast spores in areas that have low-moisture, high levels of rainfall, and overall cooler daytime temperatures.
The presence of blast in rice plants can be detected through physical symptoms such as white to gray-green lesions or spots, with dark green borders or diamond/spindle-shaped lesions with whitish-gray centers and red-brownish or necrotic borders on the leaf or collar of the rice plant (Figure 1 and Figure 2). These lesions can expand to kill off entire leaves of the rice plant.
Blast is a serious disease that threatens the growth of rice and, if not controlled, may cause massive reductions or even complete wipeouts of grain yields.
With the use of genetics, one can isolate genes associated with blast resistance in rice and, through varying combinations of the isolated genes, a strain of rice with desirably increased level of resistance to blast may be established — methodologies such as QTL* mapping and association mapping* may be used to accomplish this.
During my introduction to Mr. Hore’s blast project, I learnt that he had isolated 3 particular genes — Pi9, Pi35 and Pita2 — associated with blast resistance. These 3 genes were integrated into the genome of a rice breed in varying combinations — some rice seedlings contained all 3 genes, some had varying combinations of 2 out of the 3 genes, and some only contained 1 out the 3 genes.
In the screening nursery (Figure 3), where the growth and conditions of the genetically modified rice seedlings are observed and recorded, 3 rice breeds with varying susceptibilities to blast were used as controls (Figure 4) and the 3 were planted next to each other at the beginning of each experimental line which consisted of a further 20 experimental seedlings containing varying combinations of the 3 blast resistance associated genes. The experimental crops are covered every night to ensure an optimal environment is created and to control the spread of blast spores. The success of the genetically modified seedlings for blast resistance was judged by their physical condition i.e. the degree of evidence of blast (Figure 5).
Figure 5: Genetically modified seedling with varying degrees of blast resistance.
1.) Moderately resistant.
The blast resistant genes (Pi9, Pi35 and Pita2) can be isolated from the highly resistant experimental rice seedlings in order to determine what the optimal combination of these blast resistant genes may be. Dr. Hore’s target audience for his new strain of Blast resistant rice is Bangladesh and Cambodia — although the findings of his research is highly beneficial for the potential of providing other Blast affected countries with a more resistant rice strain.
The introduction I received to Dr. Hore’s project was brief but I gained a lot of insight on how a scientific idea can be translated from mind, to paper, to lab, and then to the field. Science it powerful and I’m excited for what I may learn next!
*QTL (Quantitative trait locus) analysis = a statistical method that links two types of information—phenotypic data (trait measurements) and genotypic data (usually molecular markers)—in an attempt to explain the genetic basis of variation in complex traits.
*Association mapping = also known as “linkage disequilibrium mapping”, is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering genetic associations.
I’m finally here! Well, I’ve actually been in the Philippines for just over a week now but it has been a great experience so far. I haven’t officially started my internship just yet as we had to be placed in isolation for a week to self-monitor for any possible signs of sickness from traveling — we have all now been cleared to begin our internships but we’re still waiting for our IDs to be processed in order to be able to access our respective buildings.
My first week in the Philippines was filled with exploring the area of Los Baños, Laguna. Along with the other US interns, I attended an orientation where we given a general “Survival Guide to the Philippines”, we met multiple professors from UPLB and surrounding research groups, we learnt essential Tagalog phrases, and we went out to dinner together at an amazing restaurant called Kamayan at Palaisdaan Resto and Resort where ate traditional Filipino cuisine.
The rest of the week was spent adjusting to my new environment (the heat here is no joke — and that’s coming from a South African), grocery shopping, exploring the market in the surrounding area of IRRI, and enjoying the beautiful views that Los Baños offers all day, everyday.
So far, everything has been great — the people, the food, the weather (especially the nightly thunderstorms) — and I’m excited to see what the next few weeks have in store!
Before embarking on my trip to the Philippines I decided to spend some much needed time at home in South Africa — I hadn’t seen my family in a year so I was eager to head home for a few weeks.
During my time at home, my family and I spent a weekend away in the “bushveld” — a South African term used to describe a wild savannah terrain, usually abundant with a variety of African wildlife — where we caught up, “braaied” (South African barbecue), and went on a Safari drive in search of some wildlife.
Another week at home was spent in Durban where I was able to see my grandmother for the first time in about 3 years. We went to the beach, had some famous Durban Curry, and ate WAY to much ice cream. I was also attacked by a sting-ray on the very first day that we arrived at the beach — note to self: watch where you’re walking, especially in the sea.
It was definitely a jam-packed 4 weeks at home but it was the perfect way to begin the summer and a great way to transition into my trip to the Philippines!
Look out for my next post because I will officially be in the Philippines!
I’m Katy Smit, an international student and biology major at Illinois Wesleyan University, and this blog will follow me as I take part in the IWU Freeman Asia Program. I will be participating in an internship with the International Rice Research Institute in the Philippines where I will be working in the Genetic Design and Validation Unit under the supervision of Dr. Mallikarjuna Swamy. At this moment it is T-minus 9 days until my departure day to the Philippines and all is set and ready for my first trip to Asia!
With this blog, I hope to provide regular insights and tips-and-tricks to study abroad as well as fun updates on what I have been up to during my summer abroad. The comment section is always open and you are welcome to leave in questions or suggestions!
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