DNA Fingerprinting, 2013-2015

The objective is to pilot test and validate alternate approaches to collect variety-specific adoption data against a reliable benchmark (in this instance, DNA fingerprinting) to determine which method/approach is the most cost-effective i.e. which method provides a given level of accuracy at the least cost. The idea is to come up with ‘lessons learned’ and recommendations on methods/approaches that can be used in scaling up the collection and assembly of diffusion data on improved varieties. Methods being tested against the benchmark of DNA analysis include:

  • Farmer elicitation + some basic seed source data (all CCCs)
  • Farmer elicitation based on series of photographs of plants and/or seeds (cassava and beans)
  • Trained enumerators/experts recording observations on varietal characteristics (phenotyping) by visiting the field (cassava and maize)
  • Trained expert identifying the variety based on his/her observation of varietal characteristics (phenotyping) during the field visit (cassava)
  • Taking photos of the plant in the field or harvested seeds for latter identification by experts (i.e., breeders) (beans and cassava)

This sub-activity (“Advance methodologies for tracking the update and adoption of improved varieties”) falls under Objective 1 (Methods) of the SIAC program and is managed by researchers from the Michigan State University (MSU). Three studies have been initiated and are at different stages of implementation: (1) Cassava in Ghana; (2) Maize in Uganda; and (3) Beans in East/Southern Africa.

A two-day workshop was convened by Greg Traxler and Mariana Kim from the Gates Foundation on 4th and 5th August 2014 in Seattle (USA) where findings from the Diffusion and Impact of Improved Varieties in Africa (DIIVA) study, and this MSU-led effort was presented. Objectives, brief summary of proceedings, and list of participants can be found here (PDF). Another workshop was convyened by SPIA, Michigan State University (MSU), and IFPRI in Boston on 3rd and 4th August 2016. This workshop brought together results/learning from SIAC Objectives 1 and 2 (including DNA fingerprinting pilots), and other private and public sector partners involved in finding innovative ways to collect technology adoption in developing countries (Agenda, papers, and presentations).

(1) Cassava in Ghana
This study tests the effectiveness of the following four household-based methods of tracking varietal adoption for cassava against the benchmark of DNA analysis of cassava leaf samples.

  • Method A: Elicitation from farmers by asking him/her the names of varieties planted and some basic questions for each variety planted.
  • Method B: Farmer elicitation on varietal characteristics by showing a series of photographs (or actual plants). This information will be later used by the analyst to identify varieties based on morphological characteristic data.
  • Method C: A trained enumerator recording observations on varietal characteristics by visiting the field and sharing their opinion on what the variety is (based on observations). The information collected will be also used by the analyst to identify varieties based on morphological characteristic data.
  • Method D: Enumerator taking photos of the plant in the field for latter identification by experts (i.e., breeders).

The field work for this study is jointly supported by SIAC and the RTB CRP and conducted in partnership with IITA, Crop Research Institute (CRI)-Ghana, and Agriculture Innovation Consulting (AIC) Ghana. All the data collection was completed in late Fall 2013.

Although variety-specific DNA analysis is still outstanding, the emerging results from the available data indicate that: a) there is a large variation in the estimates of adoption of improved varieties derived using different methods tested in this study; b) a large number of farmers are mistakenly identifying varieties as improved varieties when it was not, or identifying a variety as traditional when it was in fact improved; and, c) the methods of varietal identification that relied on ‘experts’ were better than the farmers’ elicitation, but not that reliable in identifying varieties by names. At least in the case of cassava in Ghana, this study has demonstrated the unreliability of both farmer and expert elicitation based methods of varietal identification. Thus, estimating the adoption of improved varieties for cassava in a setting similar to Ghana (which is typical of many developing countries in Africa), based on traditional methods is questionable.

(2) Maize in Uganda
As part of the planned DTMA adoption survey in two districts in Uganda, MSU has designed and implemented modules and protocols to test the effectiveness of the following three household-based methods of tracking varietal adoption for maize. Methods A, B and C as in the cassava in Ghana (see above) were used with slight modification.

Field data were collected in June 2014 and leaf tissues from 400 maize fields were collected for DNA analysis. The National Crops Research and Resource Institute (NaCRRI) of NARO is serving as the ‘technical’ partner for DNA analysis through their ongoing project with UGA.

Unfortunately, due to delays in transferring the leaf tissues from the field to the lab and large amounts of compacted leaf material in the tubes, all the samples collected in June 2014 were lost due to mold development. Due to the delays and difficulties experienced during this project, LGC (the firm offering DNA fingerprinting) has offered to repeat the work for this project for free of charge. The cost share of the SIAC project for this purchase order with LGC was US $40,000 (which is now available towards other activities, including re-doing the sample collection).

This offer by LGC to do the analysis without any charge is a huge incentive and discussions are currently underway with NaCRRI and CIMMYT to see if a team can be mobilized to collect the samples from the same farmers visited in June 2014. This will be most likely planned in April 2015 (which is the earliest window of opportunity to collect lead tissues from farmers’ fields in Uganda), pending the approval by the PSC. Data from other methods (A-C) to elicit information from the field to identify specific varieties have been tabulated and analysed, but in the absence of DNA results we are not able to determine the accuracy of the results of those methods.

(3) Beans in Zambia
This study tests the effectiveness of the following four household-based methods of tracking varietal adoption for common beans. Methods A, B, C and D as in the cassava in Ghana (see above) were used with slight modification.

The accuracy of adoption estimates derived from the above four methods will be evaluated against the varietal identification established through ‘DNA fingerprinting’ of seed samples collected from the farmers. This study is conducted in collaboration with CIAT and the Zambian Agricultural Research Institute (ZARI) as part of the PABRA bean adoption study (which was already planned). Seed samples and data corresponding to the four methods have been collected from 402 households that were surveyed under the PABRA study. The DNA analysis of the beans seed samples shipped to LGC has been put on hold because the bean breeder at ZARI has not been able to provide the correct sample identification information. The information that was shared by the ZARI technician does not match with the sample IDs used for testing methods A to D. Without this critical information, doing the DNA analysis will be meaningless. MSU (in consultation with SPIA) is evaluating whether they should still rely on the breeder providing the correct information and/or the remaining seeds so the work can be completed at MSU or explore new opportunity to re-do this study in another country.

Although, in the absence of the DNA analysis, we cannot assess which method of varietal identification is closer to the ‘truth’, the preliminary results from this study (analysis of Methods A-D) reinforce the importance of doing the DNA analysis to establish the benchmark to be able to test the effectiveness (or non-effectiveness) of other less costly methods. Given the unfortunate situation with the lack of response from the breeder in ZARI, MSU will discuss with SPIA on the next steps toward doing a study on beans in another country or collaborating with CIAT on their planned study in Rwanda (or Uganda).

Recent blog entries

Recent publications

illustrative photo