Interview with Dr. Inez Slamet-Loedin

Hosted by Dr. Ved Prakash

Edited by Drs. Ved Prakash and Swadhin Swain


This transcript has been edited for clarity and readability. 

Ved Prakash: Hello and welcome to another episode of PlantGENE Podcast. My name is Ved Prakash, and I am a postdoctoral fellow at Department of Plant Pathology, Kansas State University in Manhattan, Kansas. The PlantGENE project centers around the enhancement of plant genetic engineering to ensure a sustainable supply of food, feed, and fiber. In each podcast episode, we welcome esteemed leaders from academia or industry to share their experiences and insights for the benefit of our listeners. Today our guest is Doctor Inez Slamet-Loedin from International Rice Research Institute (IRRI), located in Philippines. Inez is currently the head of the Rice Genetic Design and Validation Unit at IRRI and is assigned as the global lead of the CGIAR Gene Editing Initiative. Inez is also a member of the PlantGene Advisory Committee. Her research portfolio includes improving nutrition through healthier rice, disease resistance, drought, low phosphorus tolerance, and rice productivity. Inez is also an elected fellow of the World Academy of Sciences for the Advancement of Science in Developing Countries. She has published articles in reputed journals such as Nature, Nature biotechnology, Nature Plants, Nature Communication, Nature Genetics, Proceedings of National Academy of Sciences, Plant Biotechnology and many more. Welcome Inez and thank you for joining us today. 

Inez: Thank you for giving me this opportunity.

Ved Prakash: So, let’s start with the basics. Can you describe what a day in your job is like? Right.

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Inez: My days really varies, I think. Sometimes I have to go mostly to my office. Sometimes I have to travel, or I work from home. So generally, maybe I woke up, did five minutes, uh, do five minutes quiet time. And then I have to travel back one hour to my institutes because I live in between my work and my daughter’s workplace. And so I usually go to green House. First, I go, then to the, the plants and everything, and then to the lab and then have a couple of planning meetings, check emails, check labs. Greenhouses and work afternoon. I work on either I go to the lab and checking things and discussing stuff, or work on project proposal and have more problem-solving meetings, and, when I go home, I have twin daughters, one with extra chromosomes, so. But she works in, school of all abilities and the other one has just completed, her master in oncology in Oxford. And so, when I went home, we talk we love and do other activities and in the evening because I have the collaborators globally, so sometimes I have also meetings that is inevitable, I thing. And then sometimes I travel, I think every two months or every month to the different part of the world to collaborate either in the different countries or our collaborators with the national partners. I think that’s more or less my basic day.

Ved Prakash: That’s nice. Can you describe your research?

Inez: I have two major works, both in genome engineering. The, the work that we started about ten years ago or 11 years ago is basically aimed to making rice healthier, with to increase iron and zinc in the milled rice. Rice is mostly consumed milled, I think. I’m sure that you are very used to it too. And we use one gene from rice, one gene from apple to, and the rice gene is the transporter, basically. Because if you look at rice, there’s a lot of iron in, in the leaves, but it is not transported to the grain. So, and the also the gene to basically the bind the iron in the grain. So now we have already at the stage, we have finished the multi-location trials in the Philippines and in Bangladesh, with that And then the idea is to combine it with golden rice, depends on what is the market need, or we go ahead with the Iron and Zinc rice. And I also work on the photosynthesis to basically aim to improve yield with the collaborator from Oxford and Minnesota and also with the EU consortiums with different approach. One is with the transcription factor basically, and the other one is more multi gene approach. And I also work on disease resistance and this with the partner from uh multi partner as well from EU and from India and also from US and another disease resistant project which is very exciting, which is basically based on prime editing that is with CSIRO, Australia. We also do surface for gene function validation. Select a …. of the candidate genes from, GWAS work or other works. And we do like knock out and overexpression and sometimes they develop it later using marker technology. That’s covered it more or less. And both in traits though, it’s geared to climate change and also healthier rice.

Ved Prakash: You mentioned about a gene from rice and a gene from apple. So do you mean you are trying to, incorporate a gene from apple into rice, or.

Inez: That part is the transgenic. Okay. Okay. So, we when we cannot do gene editing nowadays, we do more and more gene editing. But, when you, we try it, but with the. At the moment. What we tried; we did genetic. We just we got the increase, but we also got the increase on the yield, which we tweaked the promoter to increase the expression. But with this, insertion of rice genes with the different promoters and also, basically iron binding protein from Apple. It was initially we work on soybean, but then we have also alternative, we try apple and beans. I think apples, it seems to, it also works well. So those three. Good stuff. But that has to go through all regulatory process. And so, we work both under developing the data for regulatory science and also but we work closely with the national partners. They’re both.

Ved Prakash: Really nice! Well, another question I have for you is what motivated you to pursue a career in science?

Inez: Oh, I love science. I think mainly because the innovative part of it, it’s like it’s very exciting every day, even if it’s a small, small, things you would have, what happens now, you discuss with your stuff and then you look and then if there’s something doesn’t work, then you have to tweak here and there problem solving, I think. It’s like I have been asked a couple of times to work kind of position on administration, but I eventually turn it down and consider it. But I mean, I have to do them. Of course everybody has to do some admin work, but if its 100%, I don’t think it’s not me because I love the discussion with other people, the talents and the innovative part of it. I guess.

Ved Prakash: Really nice. Yeah. Okay. So why are you interested in rice?

Inez: Rice is life. It feed more than half of the global population, mainly in, this part of the world, but is actually now even in Africa. Now we daily start to also consume rice. But on the other hand. Of course, you don’t want people to rely only on rice. The diversity is important. But then I found that also it is like. At least if you can improve, the rice with nutrition, more nutritive rice, you give the basic needs. But unfortunately, a lot of population, it consumes rice. It’s also, those in the countries under transition or different developing countries. So, they don’t always have an access to, a good diverse diets. So, I think that’s why I was like, if you can improve rice, probably you can improve a little bit of the welfare of the people. And I think another thing that I like there is the say in Indonesia is, rice cultivates nature of humanity. The more it has grains in its plants, the more it bows. But yes. So, this combination that, if you can improve a rice based-agrifood system, you probably can improve, poverty, you can do some poverty alleviation. You contributed maybe small, but you feel good because you do something.

Ved Prakash: I agree with you on that. So, what questions lately have you found interesting while working with rice?

Inez: I think the most interesting that I found this last, one year is we work with our partners in CSIRO Australia, they’ve found in barley and, other cereal that if you change this allele and the difference is only one base pair, and then they’ve found it gives a lot of improvement on fungal resistance. And we first tried the transgenic one. And it did help on the, it did improve the resistance. So, and then I thought but because we specialize on indica rice and indica rice is more and more recalcitrant in tissue culture, right. And compared to the japonica. So, I thought, what is the percentage of editing that we gonna prime, because in this case, we have to do the prime editing because of the base pair that we want to change. And we look at the publications that we did and all this tweak here and there, and I was quite first my PhD student got 50 to 80% replacement. I thought you must make a mistake. Maybe double check. And then it’s true. So, I thought if we can do allelic replacement, it’s a really game changer in the editing world, because that means that you can more and more use information of the available from land races and others. So, I was very excited about it. And also the fact that’s one part and the other things is as I mentioned that we work on improving iron and zinc, So my colleague in, Cornell University, he tested. We sent the grain, and they tested on chicken feeding assay and, improve the microbiome. So that’s another site that. Okay. First, also learn how the if you are really within 1 and 5 years, and lack of zinc. They show how the brain development of people who have sufficient It’s not stunted, you know, zinc deficiency is one of the major costs of the standing and you get a lot more complex brain development. If you have sufficient men and it’s irreversible. That’s another thing. When we tested in the field, we have no yield penalty. And the zinc that we can get is perhaps, is quite much higher from 60 to become 40 ppm. While the breeding can only do until 24 ppm in the grain. So, and then at the same time it can improve microbiome because the microbiome is big now, right. And it’s actually affecting a lot of things. So that is also two things interest me recently, the prime editing and also the chances to make rice healthier. And also, I’m with a collaborator who is in IRRI, Dr Nese, that reduce the glycemic index of rice.

Ved Prakash: Really interesting! So, what role do advanced biotechnologies such as gene editing or marker assistant selection play in your research to develop improved rice varieties?

Inez: I think, it has a very important role for gene editing and even not necessarily as to make a final product, even for the like, for example, the development of low glycemic index rice, they have a candidate gene we check, and it does together we take, and it did. It’s actually the gene responsible for it. So, they can use it as a gene-based marker. But really accelerated and is more accurate. And that is one thing like for functional, genomics part.
But but at the same time, I mentioned about, for example, the collaboration we have with Dr …. and Dr Bing Yang and, and other partner there’s that we in this case that Yang is doing the gene constructs and, but we do the editing and selection of it and then it was checked in Columbia and in both US in Colombia, they make it, they got, status for non-regulated status. And now, that in the next phase of the project, even we are not involved, but it is in the next phase, it would be more than our partner. So ICAR from India will further test it and that’s basically added the promoter’s region. So, the Tal effector from the bacteria could no longer bind to it. And also, we work before with Tungro at IRRI and also we basically edit the sequence where the virus bind And then which needed for translation initiation factor. And that is also, I mean, all of this clearly has the role to have an improved rice varieties and I think initially perhaps takes longer, but it is more and more efficient. But this can only be done through partnership because both partner in Advance Research Institute. But it’s also in the national partners and I think really best if you involve everyone at the very beginning. So, they have a sense of belonging. This is our projects, together. And because at the end, if there’s no adoption. It’s become a publication only. But if it’s adopted and you really have to work with the advance cultivars for that proposal, depends on the purpose. It will be more and more when the regulation is more towards balance approach. But I think if you look the even the map now initially only few countries regarding gene editing as the breeding lines but now it’s more and more you see countries even in the last two three months, things are moving so fast now. So, I, I really have a big hope on I mean it is not silver bullet. We also always realize that this is one of the breeding so and, but it is very potential.

Ved Prakash: I have to appreciate that you are working in so many different aspects, including resistance with virus, resistance with bacteria, resistance with fungi, and drought which is abiotic stress. So that’s very impressive. Drought is very challenging actually. I work on transgenic before on drought. But for gene editing, because drought is a complex trait, it’s challenging. I think those are the set of the challenge that we need to have. but we can do editing directly on the lines, which is already have a partial drought resistance. For sure.

Ved Prakash: okay. So, another question I have for you is that scientists have been going back to the wild relatives for incorporating various beneficial traits into cultivated varieties. What is your thought on this?

Inez: I think It is one of very important aspect on the potential of the technology. You mentioned that currently I’m responsible for CGIAR. CGIAR is a consultative group on agriculture, and it covers many crops, right? So currently there are five centers who already work on genome editing, which apart from rice, there is banana, cassava, sorghum, maize and potato would start soon. So those are among that potential and crops that we have been working on. But if I look at the CGIAR gene bank collection is recognized among the best in collection gene bank in the work, but despite of major investment on the area of genetics-genomics which a lot of sequences are now available, right, potential genetic pathway but actually in the breeding mainly use the core collections. I think because of the linkage drag and all the unknown of the land races. So, it’s not being used so much. So, I think this development of gene editing technology and available of large scale sequence data in phenotypic studies would be very important to break the yield barrier because like in rice we have the minor increase now for like we probably got 1%. It’s already very, very good. If we got an increase. It’s not like maybe cotton or something. But if we can get more and more genes from a land races and wild relatives, I think, it would potentially you break yield barrier and gene editing is very useful to speed up the breeding process in this way. And it also can be used to show for genetic information for in the pre breeding generation. If you stimulate the recombination, for example, and improve the recombination. So, transfer of the exotic information from cultivate from is it possible from gene. And also of course the domestication like right wing has a try to do or so I think I would be also next if we can do because we have a lot of wild rice collection, and you don’t know many genes unknown. So, it’s either for functional validation or domestication is a big avenue. But what they require that for example, it’s really salinity tolerance that you can grow it in the salt water. So, for the climate change, I think it’s a super important to adaptation on the climate change. And it probably also can do some mitigation things like to reduce nitrogen use or maintain production. Yeah. So, I totally agree with you that the wild rice relatives I would be. Gene editing can have a big role on getting some, important alleles from that and also to get more and more knowledge information.

Ved Prakash: Yeah. Completely agree. And in fact, I am also screening, wild relatives from wheat and screening for tolerance against the virus. So, I got interested into what is happening in rice.

Inez: That’s very exciting work.

Ved Prakash: Yeah. It is. Okay, so let’s move to the next question. So how do you collaborate with other researchers, agriculture organizations and farmers to ensure that your research findings are effectively translated into practical solutions?

Inez: I think, as I mentioned CGIAR basically most of the CGIAR center, we are like a honest broker. We work in the middle between advanced research institutes and the national partners. I mentioned before, the concept of co-development is very important. It’s not, in the past we tend to develop something, and it is something We still do that. Then we develop something we share after we develop something. But it’s also very good if you can co-develop together. So, we work with the Advanced Research Institute for the most advanced technology to apply it for, because mostly they work with the model species, right. So, we apply it in the elite germplasm because we have very good transformation facility or capacity for indica rice and basically, we can transform any indica rice with different frequency. But we have that capacity. So, it but it’s very important to link with both national agriculture and extension system and then by partnership but we also have a partnership with private sector. It’s either small medium enterprise on big private sector, which has the access on the technology. And another point that it’s very important to eventually able to share and get it adopted to actually work on the, intellectual freedom to operate for intellectual property part. And for that you need to depend on what is your product. If your product you can negotiate for humanitarian purpose. So we work supported by a diverse network. And you also need to discuss with investor because a lot of our project is supported, for example, by Bill and Melinda Gates foundations by UK FCDO or by ECR from Australia, from and USAID. And so all this year it’s quite complex things but developing network is super- important. While you are also need to work very well with the national partners, I think to really treated everybody equal was certainly very important.

Ved Prakash: Absolutely! Yeah. Okay. So, what advice would you give to students or researchers interested in pursuing their career in your field?

Inez: I think, important to have passion, perseverance because experiment would fail from time to time. And then you need to have a vision. What you want to do in future. And while you are attending conference are things you really need to develop network. So sometimes you tend to go and stick with your friends only. Don’t do that because you can, It doesn’t mean you don’t care, but that’s an opportunity. If you go to the conference, you open network because many people are open for it. And would like to share their knowledge and information, but passion is important and also do not scared for change. I moved from Indonesia to here and it make a big change on my career, move to other places. I mean it’s difficult at the beginning. But it is important. Absolutely. I think those are a few things that I think it’s. I think passion is number one.

Ved Prakash: Okay. I have a lot of questions, but time is less. So maybe I move to the last question I have. So, what impact do you hope PlantGene will have on transformation?

Inez: I think the fact that it has ideas to address global demand for plant transformation and gene editing through network is very important because more and more in this partnership, you can work on your problem solving and also access on technology, access on even sometime facilities. And, if you need to do part of your work and also probably in the future, have also avenue to negotiate on the access freedom to operate on the technology. It has a very good mission and ideas because initially people think that transformation is something very easy. But with gene editing, it’s one of a game changer. If you have a very good transformation system, including transforming wild rice, for example. Yes. And I totally supported, of course, because I think it’s very good initiative. And that’s and hopefully, of course, I hope that it has an impact. Eventually the product is adopted, and also more and more countries are open with to treat it as a breeding line, because it’s basically a mutation for breeding. By the correct communication and outreach I think it’s opened a lot of avenues and opportunities. And I think eventually your work and my work will get adopted and be useful.

Ved Prakash: That’s true. Okay, so before we wrap up, I want to extend a huge thanks to Dr Inez Slamet-Loedin for joining us today and providing such a valuable information about their groundbreaking research in improving rice nutrition and agronomic trait. Your passion for your work and dedication to addressing global food security challenges is truly inspiring. We are incredibly grateful for your time and expertise. And to our listeners, thank you for tuning in. Stay tuned for more enlightening discussions in future episodes. Until next time. I would say take care and keep exploring the wonders of science.

Inez: Thank you for the opportunity and all the best to you and all the young scientists, who listen to this discussion. Thank you so much for the opportunity.

Ved Prakash: Thank you.

Inez: All the best.