NextGen PhD Student Visits Cornell for training on Prediction Modeling

Olumide Alabi, NextGen Cassava PhD student with the International Institute for Tropical Agriculture (IITA) in Ibadan, Nigeria, recently visited Jean-Luc Jannink’s laboratory group at Cornell University for training on prediction modeling. Olumide reports on his visit here:

Date: 8th March to 6th April, 2016

Location: Dr. Jean-Luc Jannink’s Research group, Plant breeding and genetics department, Bradfield Hall, Cornell University, Ithaca, NY

Practical skill acquisition in genomic prediction modeling forms the basis of my brief visit to Cornell. I got handy explanation on prediction modeling processes as they apply to past and present genomic selection cycles as being implemented in IITA-NextGen Cassava Breeding Project.

Three major objective activities included:

  1. The prediction modeling for the IITA-Genomic Selection

Marnin Wolfe, postdoctoral associate at Cornell, was able to guide me from the known in Genomic predictions in general to the unknown with practical step-by-step activities using the IITA-NextGen cassava dataset. I received concrete training on the use of single step model and information on the limitation to it, as it could be computationally intensive with large datasets. Also, I was trained on two-step model, formation of the kinship matrix using the “A.mat” function, model.matrix, kin.blup phenotype dataset curation for prediction modeling, G-BLUP model, RR-BLUP model, the inclusion of multiple random effects in prediction modeling using the EMMREML model and general theories and coding syntaxes associated with these above-mentioned models. One of the newest concepts to me in all was when I was guided through the IITA-Cycle 3 prediction, de-regressed BLUPs, especially with the theory and concept of reliability estimation, PEV,  and how these influence the accuracy of our predictions. Marnin did well in guiding me through these concepts both theoretically and practically, coupled with exercises, reading assignments, brainstorming sessions. To wrap it up, I was guided through the entire IITA-GS Cycle 3 prediction model; the code was provided to me by Marnin with detailed explanations.

  1. Fitting the appropriate model for the genetic gain estimation

Estimating the “Expected Gain” in GS application in cassava is not a straight-forward thing, as the selection of the parents is based on selection index built from the GEBVs of traits and individuals. In the gain estimation using the conventional breeder’s equation, there is a little adjustment in GS concept, which is basically the selection accuracy factor in the model. To obtain this, we had to correlate the S.I_GEBVs (Predicted) of lines and the S.I_BLUPs (Observed). In my brainstorming with Marnin, we came up with the concept highlighted below:

rA = corr(S.I_GEBVs, S.I_BLUPs)

Where S.I_GEBVs = wtGEBVT1 + wtGEBVT2 + wtGEBVT2…+ wtGEBVTN

wt = the economic weight used for trait T in the selection index model

S.I_BLUPs = wtBLUPT1 + wtBLUPT2 + wtBLUPT2…+ wtBLUPTN

Hence, the rA could be appropriately fitted in the breeder’s equation for the expected gain estimation.

  1. GWAS exploration on the plant type dataset

Dunia (Research Associate) guided me through GWA-studies with the use of datasets on plant type and the associated SNP data. For better handling of the categorical nature of the Plant Type trait (compact_1, open_2, umbrella_3 and cylinderica_4), Marnin suggested the classification of the trait as binomial scores (E.g. Compact: 0_absent, 1_present), hence coding the scores as a trait per time. It was to enable us to fit a GLIMMIX model with the flexibility of a link function for variance components.

  1. I participated in the research group and graduate student seminars and symposiums.

Skills acquired

I can practically implement Genomic prediction with more confidence on availability of appropriate dataset. I got a detailed understanding of the past IITA GS Cycle selection and a first-hand understanding of the present Cycle 3 predictions (Thanks to Marnin). I got a better clue on several aspects in statistical modeling to be included in my thesis report, especially the expected gain estimation concept and some genomic prediction steps.

Acknowledgement

My appreciation goes to Dr. Jean-Luc Jannink for the time and audience given to me while I was in Ithaca; the meeting for updates in his office and facilitation of my visit; amidst other.

Many thanks to Marnin for devoting much time in coaching me. In fact, he was my tutor all through the period I was in Ithaca. Dunia did a great job as well as my NextGen graduate student colleagues, Ugo, Uche, and Alfred. Alex of BTI is appreciated for his kind gestures all through my time in Ithaca. I would not but mention the logistics from Dan’s end, Karen and the team in IP-CALS office.

I want to thank my supervisors in IITA, Drs. Peter Kulakow and Ismail Rabbi, for granting the home-support needed to visit Cornell this period. Thanks to Dr. Chiedozie Egesi and Dr. Hale Tufan. My final appreciation goes to the Cornell-NextGen Cassava project for the full support. My regards to all.

Olumide during his training at Cornell and with Marnin Wolfe, bottom left

Olumide during his training at Cornell and with Marnin Wolfe, bottom left

NextGen Cassava featured in The Economist

Dr. Chiedozie Egesi, NextGen Cassava project manager

Dr. Chiedozie Egesi, NextGen Cassava project manager

During the recent annual AAAS (American Association for the Advancement of Science) meeting in Washington, D.C., The Economist interviewed Dr. Chiedozie Egesi, NextGen Cassava project manager. Chiedozie spoke about the potential of the NextGen Cassava project to improve the cassava crop and address challenges such as disease, low yield, and vitamin deficiency.

See the full story, “Cassava-nova,” in the online edition of The Economist.

NextGen Cassava Students Test Landmark Phenotyping Tool for Cassava Breeding: Near-Infrared Spectroscopy (NIRS)

Thanks to Nkechi Ogwo, Ugochukwu N. Ikeogu, and Lilian A. Onyegbulam of the NextGen Cassava Project for the following write-up of a recent visit by NextGen students to test NIRS tools in cassava breeding:

The NextGen Cassava Project has taken significant strides to address the challenges of long breeding cycles in cassava improvement by adopting advanced breeding tools; notably, genomic selection (GS). Efficient implementation of GS in various breeding programs requires informative genotype data as well accurate and fast phenotyping tools. In addressing the phenotyping bottleneck at National Root Crops Research Institute (NRCRI), Umudike breeding program, Dr. Chiedozie Egesi, an Assistant Director, Plant Breeder, and Coordinator of the Programme acquired a hand-held version of the NIRS (Near-Infrared Spectroscopy) device for cassava breeding at the institute. This was supported by the Next Generation Cassava Breeding Project being funded by the Bill & Melinda Gates Foundation.

NIRS is a long-established technology commonly used to estimate organic constituents such as protein, starch, oil, and carotenoid in numerous agricultural products. The NIRS technology is built on the interaction of physical matter with the near-infrared spectral region of light. The sampling process involves the irradiation of a sample with light of specific known frequency or wavelength in the near-infrared region. The estimation of frequency at which specific bonds vibrate enables NIRS instruments to predict from a spectrum the composition of the molecular bonds present in a given sample. The technology has been designed in various forms and shapes.

Hands-on experience using the hand-held NIRS device

Using the hand-held NIRS device to phenotype a cassava root in the field

When compared to the traditional methods of organic components assay, such as the I-check carotene and high performance liquid chromatography (HPLC), NIRS has huge advantages. It is unusually faster than other analytical techniques. For example, for some it takes more than one day to complete the extraction of some organic components and, depending on the system, it might only accommodate fewer than 30 samples for a complete cycle. Conversely, NIRS devices can be used to sample between 500 and 900 samples in a day. The technique is non-destructive and only simple preparation, or no preparation at all, is required of samples. In the case of the hand-held version acquired by NRCRI, Umudike, the instrument can be used directly in the field, which eliminates almost completely the difficulty of sample preparation and transportation. The device is very versatile and can be used for the analysis of several traits simultaneously. More so, NIRS avoids high hazards and problems of organic and other chemical waste disposal that are likely associated with other techniques.

The adoption of this device in phenotyping became necessary because the recent adoption of GS hinged on recent advances in molecular marker technologies with the unprecedented assay of many genetic materials associated with the technologies.

Ugochukwu Ikeogu demonstrates how to use the hand-held NIRS device

Ugochukwu Ikeogu (left) and Wilfred Magangi (right) gain hands-on experience using the NIRS device

The preliminary field application and chemometric process for quantifying important cassava root parameters—namely, starch, dry matter, carotenoid, and cyanide—took off in summer 2015 in NRCRI’s breeding program. The team is led by one of the PhD students, Ugochukwu Ikeogu from Cornell University, Ithaca, USA. For prospective extension of the technology to other breeding programs across Africa, a representative, Mr. Wilfred Abincha Magangi, who is a Master’s student from Makerere University, Uganda, East Africa visited Nigeria to witness the field application of the device.

The adoption of NIRS devices in cassava root component assay promises to increase the accuracy and efficiency of phenotyping and further hasten cassava breeding efforts being undertaken by the biotechnology program of NRCRI, Umudike.

Relating his experiences at the institute, Mr. Magangi during his two-week study visit shared that over and above accommodating huge samples per day, NIRS could be one of the most efficient tools for phenotyping in cassava breeding programmes. It is easy to handle, saves time and costs, and at the same time generates accurate results, as opposed to the other conventional tools used in East Africa. He also added that the NIRS device is less expensive to maintain.

NRCRI staff interviewing Mr. Magangi

NRCRI staff interview Mr. Magangi

The field visits and facility tour presented a knowledge exchange and networking opportunity for both groups. Mr. Magangi, the visiting student from Makerere University, Uganda said, “this experience has been an eye opener; learning a better way to phenotype by trying this unique tool for the first time, communicating with colleagues from West Africa, and learning from their experiences will help East Africa in the future.” It could be anticipated that this huge improvement in cassava breeding will go a long way to reduce the length of cassava breeding cycles and foster early release of improved varieties towards food security. Based on its numerous advantages, one could tell that the adoption of the NIRS tool in Africa is an environmentally friendly and accuracy-enhancing option for cassava breeding programmes when compared with the traditional phenotyping techniques.

This study visit forms part of a wider capacity building initiative of the NextGen Cassava Project.

Less stress, good results and lots of fun in the field using the NIRS device

Good results and fun in the field using the NIRS device

 

 

NEXTGEN Sends 58 Team Members to Nanning, China for World Congress on Root and Tuber Crops

World Congress on Root and Tuber CropsFifty-eight NEXTGEN scientists representing NEXTGEN partners from Africa, North America, and South America will attend the first World Congress on Root and Tuber Crops (WCRTC) in Nanning, China January 18-22. A 5-day conference drawing more than 500 scientists from across the globe, WCRTC represents the merger of the 3rd Scientific Conference of the Global Cassava Partnership for the 21st Century (GCP21) & the 17th Symposium of the International Society for Tropical Root Crops (ISTRC). During the conference, dedicated to adding value to root and tuber crops, more than twenty NEXTGEN scientists will give presentations on their current research on topics ranging from diseases threatening cassava to breeding to biodiversity. Additionally, 17 NEXTGEN Masters and PhD students will present posters on their research at Cornell University and Makerere University in Kampala, Uganda.

NEXTGEN is a proud sponsor of the World Congress on Root and Tuber Crops and is honored to support four outstanding female cassava researchers with NEXTGEN Cassava Early Career Female Scientist travel awards to attend the conference. These awards, presented to Teddy Amuge from Uganda; Sally Mallowa-Nyawanda from Kenya; Sarah Nanyiti from Uganda; and Nneka Okereke from Nigeria, will provide an opportunity for the awardees to meet with cassava experts from around the world and to present their research to a large and influential audience.

World Congress on Root and Tuber Crops

Joy Adiele Attends AWARD’s Enhancing Negotiation Skills Course

AWARD logoJoy Adiele, PhD student at Wageningen University and researcher at National Root Crops Research Institute (NRCRI), Umudike, Nigeria, recently attended the African Women in Agricultural Research and Development (AWARD) course, Enhancing Negotiation Skills, in Nairobi, Kenya, supported by NEXTGEN Cassava. Below is Joy’s report on the course:

The course began with a lecture from Deborah M. Kolb, the founder of the Center for Gender in Organizations at the Simmons College School of Management and former executive director of the Program on Negotiation at Harvard Law School.

Joy Adiele receives AWARD certificateThe one-week course was focused on negotiation processes and how women fare in them, including understanding the ways in which organization’s policies and practices, though appearing gender neutral, could have unintended but differential impacts on different groups of men and women. I learnt how to adopt negotiation skills in different capacities that could directly initiate other changes and help realize joint gains, especially in gender-related issues. I got to develop some practical skills on how to identify potential wins and craft strategies to achieve them. Now I understand the simple actions that oneself, people, or organizations can take that could accumulate to create substantive change.

AWARD Negotiation Skills course group photoThe Enhancing Negotiation Skills course is of essence for women who want to break the glass ceiling. The ability and confidence it impacts into one is invaluable. I am grateful to the Next Generation Cassava Breeding Project for giving me the opportunity to participate in such a life-changing course. It is a needed skill for my career success.

NEXTGEN PhD Student Roberto Lozano Attends Cold Spring Harbor Laboratory Course

NEXTGEN Cassava PhD student Roberto Lozano recently attended a two-week course on Statistical Methods for Functional Genomics at Cold Spring Harbor Laboratory (CSHL), and he reports on it here:

CSHL is considered among the leading research institutions in the world in molecular biology and genetics. Not only because of its history (considerable long list of noble laureates) but also for the current research taking place there.

Part of my research as a graduate student is focused on using high-throughput genomic data to identify functional regions across the cassava genome and try to use this information to improve Cassava GS-assisted breeding. Some of the high-throughput genomic data will come from transcriptome sequencing, chromatin footprinting and methylation profiling analysis.

Statistical Methods for Functional Genomics course attendees

Statistical Methods for Functional Genomics course attendees

High-throughput sequencing has become a major technique in biological research. However analyzing big data sets, products of these technologies, carries some challenges that are not always properly tackled. These kinds of errors can threaten the biological inferences that are made. All the techniques that I planned on using for my research carry some unique difficulties and sometimes complex statistical principles underlying their analysis methods. This course tackled all those techniques, and the instructors and speakers have wide experience working with that kind of data. That’s what initially caught my attention to apply for this course.

DNA Sculpture at CSHL

DNA Sculpture at CSHL

After taking it I have to admit that it was as good as it could get. All the instructors were great; each of them leads their own top-notch research group, and they were really helpful and resourceful. The invited speakers were great as well, showing some of the latest techniques and applications of next-gen sequencing. The attendees came from a wide variety of fields and from all around the world, working in both Academia and private companies, and the wide variety of their study fields (cancer, neurobiology, plant genomics, immunology and more) really assured lots of interesting discussions. Finally I had to mention that even the location of the Cold Spring Harbor Labs was something else, a beautiful environment that let people focus on their research.

Incorporating Women’s Needs and Preferences into RTB Breeding – Blog Post from CGIAR RTB Highlights NEXTGEN Cassava Gender Initiative

Thanks to Myriam Vitovec for highlighting the work of NEXTGEN Cassava’s Gender-Responsive Cassava Breeding Initiative in a recent post for the CGIAR Research Program on Roots, Tubers and Bananas (RTB):

There have been many cases in which improved crop varieties released by national agricultural research and extension systems (NARES) were poorly received by farmers because they lacked the flavor or another trait that farmers or consumers wanted. To ensure high adoption rates for the varieties they develop, breeding programs usually survey farmers about the traits they prefer, but all too often, those researchers rely disproportionately on the opinions of men. However, specialization of household roles means that women and men have different knowledge about and preferences for varietal traits. Women are usually responsible for food preparation and small scale processing, but their knowledge is rarely used for the varietal development process.

As RTB works to unlock the genetic potential of roots, tubers and bananas for improving food security, nutrition and incomes, it is also supporting field research to document gender-disaggregated trait preferences. The aim is to ensure that the improved RTB varieties developed in the coming years will have as widespread and gender-equitable an impact as possible.

“Next-generation breeding is helping breeders to speed up the process of developing new RTB varieties, but if we overlook the traits that farmers want, if we don’t have the right targets, then next-generation breeding could simply get us to the wrong place faster,” observed RTB Program Director Graham Thiele.

An example of this problem was discovered by CIP gender researcher Netsayi Moris Mudege in a project promoting the cultivation and consumption of nutritious orange-fleshed sweetpotato varieties in Malawi. Farmer consultations had resulted in the release of a variety that produces large roots, which men prefer because they fetch a good market price. However, most women prefer another variety that wasn’t released, because sweetpotato leaves are an important part of the local diet and the lobe-shaped leaves of that variety are better for cooking.

Cornell PhD student Paula Iragaba (fifth from the left) and her colleague (first from the left) together with adult women cassava farmers after a focus group discussion in the Arua district.

Cornell PhD student Paula Iragaba (fifth from the left) and her colleague, Winifred Candiru, (first from the left) together with adult women cassava farmers after a focus group discussion in the Arua district.

To avoid such oversights, RTB supported various initiatives in 2014 to get the trait preferences of both men and women into breeding pipelines. For example, Mudege and CIP potato breeder Asrat Amele produced an FAQ sheet on integrating gender into the participatory varietal selection of potato in Ethiopia and organized a training workshop in Addis Ababa for 20 representatives of CIP’s main partners there.

RTB and NEXTGEN Cassava have co-funded the collection of gender-disaggregated trait preference data for cassava in Nigeria, using a methodology developed by NEXTGEN Cassava Project Manager Hale Tufan and IITA Gender Focal Point Holger Kirscht. Tufan and Kirscht coordinated research in 2014 by interdisciplinary teams from IITA and NRCRI in eight farming communities in southeast and southwest Nigeria. The teams interviewed 10 women and 10 men of diverse ages and marital status in each village and conducted sex-disaggregated focus groups with 20-30 participants in most of them.

“We’re trying to bring diverse voices, including those of women and youth, into the breeding process. Because we want to tailor breeding programs for the diversity of users rather than opting for one-size-fits-all solutions,” said Tufan.

Tufan explained that traits mentioned by the farmers range from agronomic advantages such as good yield to things like ‘drawing’ when cooked, which is important for making the traditional cassava dish gari. The goal is to get those most difficult quality traits into selection indices, to translate them into standardized, measureable breeding variables, and to link them to genetic markers for genomic selection. Cassava breeders Peter Kulakow (IITA) and Chiedozie Egesi (NRCRI) have helped to tailor the data collection tools in order to ensure that they yield data that will be useful for breeding.

Paula holding two cassava roots during a visit to cassava farmer (in the white t-shirt) in the Apac district, one of her study sites.

Paula holding two cassava roots during a visit to cassava farmer (in the white T-shirt) in the Apac district, one of her study sites.

RTB and NEXTGEN Cassava are also co-funding Cornell PhD student Paula Iragaba, who returned to her native Uganda in 2015 to conduct gender-differentiated field research on cassava trait preferences.

Iragaba is working closely with Kirscht, CIRAD postharvest expert Dominique Dufour, and breeders at the National Crops Resources Research Institute (NaCRRI) to help them incorporate the preferred cassava traits that she documents into their cassava improvement program.

“This is really exciting because there is an opportunity for Paula to provide information and set up a model on how to capture and integrate gendered trait preferences into breeding programs,” said Tufan.

Paula and a farmer picking cassava leaf samples in one of the farmer's cassava gardens to be used for studying genetic diversity of cassava varieties.

Paula and a farmer picking cassava leaf samples in one of the farmer’s cassava gardens to be used for studying genetic diversity of cassava varieties.

Iragaba had an opportunity to explain her research to Bill Gates in October 2014, when Gates visited Cornell’s campus to learn about the work of NEXTGEN Cassava, which the Bill & Melinda Gates Foundation funds. Iragaba was one of several graduate students who gave short presentations about their research and answered questions from Gates.

“I talked about how women play a vital role in cassava production and processing in Uganda, and how their role needs to be considered by breeding programs in order to improve the adoption rates of new varieties,” Iragaba said. “I’m sure that if gender issues are taken into consideration by our breeding programs, we are going to have tremendous improvements in adoption rates.”

Find this and other interesting articles in the RTB Annual Report 2014