Here, we have organized the results from the user survey and the analysis of germplasm distribution starting with the four fundamental information gaps about genebanks posited by Wright (1997): (1) who uses genebanks, (2) why users want germplasm, (3) what kind of germplasm is used, and (4) what characteristics users are seeking. We added a fifth information gap following Loresto et al. (2000): contributions made to rice science. In addition, we present responses of the 2019 IRRI genebank user survey respondents to questions regarding their likely future demand for germplasm and alternate sources of germplasm. These questions are relevant for the management of crop collections at IRRI and elsewhere. Finally, we present the results from the regression analysis to establish the importance of germplasm data in promoting the use of genetic resources.
Who uses genebanks?
Between 2012 and 2018, there were a total of 2174 requests for rice germplasm from 1005 unique requestors, with an average of 247 annual requests in the last three years (Table 2). Most users (71%) requested only once in the past seven years, but some made multiple requests, ranging from 2 (14%) to more than 20 (0.9%). Approximately half of the requests came from IRRI internal users, which confirmed the integrative service provided by the genebank to IRRI’s research and breeding platforms.
Externally, IRRI distributed germplasm to requestors from universities (32%), national research programs (14%), private companies (9%), other CGIAR centers (3%), and individuals, including farmers (24%). Requests for germplasm outside IRRI were received from 63 countries in all regions of the world, mostly from Asia (71%), followed by Europe (16%). The top ten countries with the most requests for rice germplasm are presented in Table 3. After the Philippines, China and India made the most requests. China and India are also the top rice-producing countries in the world, with about 203 and 164 million tons of paddy rice harvested, respectively, in 2018 (World Rice Statistics, IRRI, www.ricestat.irri.org).
While there were only 2174 requests, the total number of accessions requested between 2012 and 2018 was 230,136. This is because each requestor could request multiple number of accessions. On average, a request include 106 accessions, but the distribution was highly skewed. The mode was 1, and 81% of requests made between 2012 and 2018 include less than 100 accessions (Fig. 3).
Responses to the 2019 survey were received from users in 48 countries (out of 63), representing all geographical regions. The majority were from countries in Asia (69%), followed by Europe (17%). About two-thirds of survey respondents (66%) had requested germplasm more than once in the previous 7 years. Forty percent of the respondents had requested germplasm in the previous year, indicating that it was easier to get responses from recent users and demonstrating the importance of regularly seeking feedback.
Why do users want germplasm?
The IRRI genebank distributes different rice genetic materials for different purposes and asks requestors to specify their intended purpose in a request form. Providing rice genetic materials for basic research and evaluation for traits are important functions of the genebank. IRRI identifies ten purposes for requesting germplasm in the request form:
2. Crop improvement
6. Other purposes
8. Rejuvenation with characterization
9. For further distribution
10. Direct use by farmers
Figure 4 illustrates the intended uses of germplasm requests as indicated in the request forms. On average, two-thirds of requests for rice germplasm were intended for research (51%) and evaluation (25%). Both activities are indicative of active rice improvement programs worldwide.
Survey respondents confirmed the usefulness of IRRI germplasm for various purposes. More than 80% of respondents found the germplasm to be useful for their research, breeding, characterization, and evaluation work, and some materials were still being evaluated at the time of the survey (Fig. 5). The 2019 survey confirmed that rice germplasm received from IRRI was less frequently used for direct planting or educational purposes.
What kind of germplasm is used?
The IRRI genebank conserves different germplasm types to serve different research and breeding objectives. Demand for advanced breeding materials and genetic stocks implies an active breeding program. Landraces and wild relatives are often used for resistance traits, as well as for basic research. According to the data in Genesys, 37% of accessions conserved at IRRI are landraces, 9% are breeding or research materials, and 8% are genetic stock (Fig. 6).
The 2019 user survey confirmed that most respondents in the past seven years had requested landraces or traditional cultivars (62%), followed by breeding or research materials (41%), advanced or improved cultivars (29%), and wild species (27%) (Fig. 7). Genetic stocks were also requested by around 22% of the respondents. Because some respondents (29%) requested germplasm samples multiple times, and each sample could be intended for multiple purposes, the percentages across purposes sometimes sum up to more than 100%. These data confirmed that the IRRI collection is an important source of traditional rice cultivars and landraces.
What characteristics are users seeking?
The types of traits sought by the recipients provide insight into the demand for germplasm held at genebanks. IRRI identifies eight traits in its current germplasm request form:
Environmental and abiotic stresses
Rice Tungro Disease (RTD)
Rice Grassy Stunt Virus (RGSV)
Rice Ragged Stunt Virus (RRSV)
Bacterial Blight (BB)
Out of 368 requests that specified desired traits in the request form, 55% of requestors sought accessions with tolerance to environmental stresses, followed by tolerance to diseases (29%) other than RTD, RGSV, RRSV, and BB. The 1995 IRRI user survey had a higher proportion of respondents seeking certain morpho-agronomic traits, but most of the samples were used to evaluate for tolerance to environmental stresses, such as shade, cold, drought, and salinity. Tolerance to RRSV and RGSV was also important. RRSV and RGSV, transmitted between plants by insect vectors, have resulted in severe yield losses in several tropical Asian countries (Morales 2008).Footnote 5
Survey respondents in 2019 were asked to classify the traits they were looking for and the relevance of the rice germplasm received for their purposes. Several traits were identified: tolerance to abiotic stresses, tolerance or resistance to biotic stresses, yield, crop quality/nutrition, or ‘other’. Abiotic stresses include heat, flooding, and salinity. Biotic stresses comprise pests and diseases that negatively affect plants’ health and growth. Yield is the level of productivity per area planted. Quality refers to a particular characteristic of the harvested crop, including nutrient content.
Eighty-four percent of respondents confirmed they used IRRI rice germplasm for improving yield (Fig. 8). Many germplasm samples were also intended for improvements in nutrition and/or quality. Other important traits were resistance to drought and salinity. The total percentage of respondents and samples exceeded 100% because germplasm are often evaluated for multiple traits.
The findings were slightly different from the US NPGS survey, which reported a lower proportion of germplasm samples intended for improving yield (12%), while biotic resistance or tolerance was the most frequently cited desirable trait (Smale and Day-Rubenstein 2002). Tolerance to insects, other pests, and diseases was also more important to respondents from the 1995 IRRI survey than those from our 2019 survey.
More respondents to the 2019 survey used IRRI materials to improve rice quality, nutrition, and tolerance to drought and salinity. This result indicates a shift of interest from biotic to abiotic stress tolerance in the past two decades. The global discourse on climate change, the United Nations Sustainable Development Goals, and the impact of increased occurrences of extreme weather events have likely contributed to this shift.
What are the contributions of the genebank to rice science?
The long-term nature of agricultural research and crop breeding suggests that we almost certainly underestimated the actual use and value of IRRI germplasm materials in the current survey. First, the option value from ensuring the long-term availability of rice diversity was not taken into account. Second, recent users were most likely to respond, meaning that we were unable to capture some future uses of the germplasm. Indeed, some respondents were still evaluating the germplasm materials received from IRRI. Received materials are perceived useful when incorporated into research activities many years later. Nevertheless, the survey confirmed the usefulness of the germplasm to respondents within the seven years covered.
We validated the usefulness of germplasm by asking respondents to confirm key outputs that resulted from the IRRI samples they received (Table 4). While many respondents were still evaluating the seeds for other possible uses, 95 respondents reported that they had published scientific publications using the IRRI materials as a basis for their research. Tracing this output could be easier in the future with the adoption of germplasm-level Digital Object Identifiers (DOIs). DOIs provide a globally unique and permanent mechanism for identifying germplasm (Alercia et al. 2018). Ninety-six percent of IRRI’s germplasm are registered with the Global Information System on plant genetic resources for food and agriculture, which is managed by the ITPGRFA (CGIAR Genebank Platform 2020).
Approximately 35% of the respondents had generated characterization and evaluation data, 23% produced genetic markers, and another 35% identified useful traits for potential incorporation in crop improvement programs. Additionally, 19% of respondents also recognized the importance of expanded germplasm options from the IRRI genebank as a key output.
What is the demand outlook for rice germplasm?
About half of the respondents (52%) expected an increase in their demand for IRRI rice germplasm in the next ten years (Fig. 9). A third (34%) anticipated about the same level of demand, and 4% expected a decrease in their demand for IRRI materials. When asked about the types of germplasm they are likely to request, respondents indicated that while there is increased interest in wild species and genetic stocks, most will continue to source traditional cultivars or landraces from IRRI (Fig. 10). Respondents anticipated greater demand for specific traits, such as drought tolerance and resistance to rice plant diseases, in the next ten years (Table 5).
What are alternate sources of rice germplasm?
Many respondents sourced rice genetic materials from IRRI exclusively or also from national genebanks (Table 6). Some others indicated that they had multiple sources of rice germplasm. We examined germplasm sources according to the institutional affiliation of the respondent and confirmed that respondents employed at CGIAR centers sourced more than 90% of rice seeds from the IRRI genebank (Fig. 11). Respondents from universities and other learning institutions also received more seed samples from IRRI than from other sources, confirming the important role of the IRRI genebank in rice research and breeding programs around the world.
Linking the demand for accessions to germplasm data
A total of 2174 requests for 24,792 unique accessions of rice germplasm were received from more than 1000 unique requestors between 2012 and 2018. Summary statistics for the variables included in the analysis are presented in Table 7. The first variable, the number of requests per accession, showed that each accession was requested three times, on average, between 2012 and 2018. The mean PDCI value across the requested accessions was 5.2199, with a standard deviation of 1.2327, a minimum value of 2.95, and a maximum of 8.1.Footnote 6
IRRI has regularly acquired new accessions for conservation since 1961. On average, requested accessions have been stored in the genebank for 30 years. The frequency distribution shows peaks in the years 1977/78 and 2010/11. Correspondingly, this indicates that accessions collected from over 40 years ago are still requested frequently. Twenty-five percent of the accessions requested are traditional cultivars/landraces, followed by genetic stocks (20%). Almost all accessions requested are available under the MLS.
Table 8 presents the most requested accessions in the past seven years. All were sourced in the Philippines, except for the two genetic stocks from China and India. The top requested rice accessions were Dinorado and Jasmine, acquired in the Philippines in 1962 and 1976, respectively. Between 2012 and 2018, 107 requests were made for the two accessions, about 15 requests per year.
We present the estimation results in Table 9 for the three regression models: OLS, Poisson, and Negative Binomial. The likelihood-ratio (LR) test of alpha (estimate of the dispersion parameter) in the Negative Binomial model indicated that the outcome variable was overdispersed, which was not sufficiently captured in the Poisson model.Footnote 7 We, therefore, focused on the results of the Negative Binomial model, but we present the others here for reference. Nevertheless, the sign of the coefficients and the statistical significance of estimates were consistent across models. To facilitate the interpretation of coefficients, we included the estimates for the incident rate ratios (IRR).
Conditional on being requested, the IRR for PDCI showed that the incident rate of number of requests for an accession increased by 8% for every unit increase in PDCI. We also observed an increase of 1% on the incident rate of number of requests for an accession for every year’s increase in storage. While the majority of materials from the IRRI genebank are available in the MLS, the estimate provided evidence that making genetic resources in the MLS indeed promotes the use and exchange of those materials. The results also showed positive effects from genetic stocks, wild relatives, and advance improved cultivars.
For robustness check, we ran the regression model on the full sample of accessions available at the IRRI genebank. However, as we noted earlier, this dataset has excess zeroes since only 24,792 (19%) unique accessions were requested between 2012 and 2018. We used Zero-Inflated Poisson and Negative Binomial models to account for the excess zeroes in the dependent variable, as recommended in Long and Freese (2006). The coefficients for our variables of interest remained consistent. The relationship between PDCI and the number of requests for that accession was positive and statistically significant (see Additional file 1: Table S1).
While there are recognizable limitations to our initial analyses, this study could motivate future work to explore the impact of different types of germplasm data on the demand for specific accessions. We focused on passport data, which are readily available in Genesys. There is, in addition, a wealth of accession-level information from phenotyping and genotyping activities that were not considered in our analyses. Users of the IRRI genebank could presumably select accessions more efficiently and effectively if they have better access to more information on certain morphological characteristics and genomic traits. The international resequencing effort of 3000 rice genomes, for example, offers opportunities for large-scale discovery of novel alleles for future rice improvement (The 3000 rice genomes project 2014). Key characteristics of genebank users could also be incorporated in future analyses to better capture the factors that could affect the demand for germplasm.
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