Open Access to Genetic Sequence Data Maximizes Value to Scientists, Farmers, and Society

October 10, 2020

Author

Jim Gaffney, Corteva Agriscience 

Redeat Tibebu, University of Minnesota

Abstract

Over the last 20 years, genome sequencing has become increasingly faster and  affordable, with genome sequences of thousands of species – plants, animals,  insects, bacteria, viruses – now curated in multiple, open access databases  available to all scientists worldwide with internet access. The open access database  system, as it stands today, offers fair and equitable sharing of GSD, promotes  sustainable use of biodiversity, while also contributing to conservation of biological  diversity. Yet this free and unencumbered access to GSD may now be threatened by policy-makers looking to regulate and monetize GSD in the hopes of creating more  “fair and equitable sharing of benefits from the use of genetic resources”.  Unencumbered, open access to GSD contributes directly to improved breeding  programs, more vibrant seed systems, greater agricultural productivity, and greater resilience of crops and farmers in the face of changing environmental conditions.  We ask that policy makers and politicians move with great care and caution when  considering regulation and monetization of GSD, beyond what currently exists for  international sharing and partnering of GSD. Public research and emerging  economies have the most to lose if GSD is further controlled, especially if the global  scientific community is not consulted.

Introduction

Combinations of the mononucleotides cytosine (C), guanine (G), adenine (A), and  thymine (T) are the building blocks of life, lining up in unique orders, or sequences,  thereby forming the genome, or genetic sequence data (GSD), specific to each  organism. Over the last 20 years, genome sequencing has become increasingly faster  and affordable, with genome sequences of thousands of species – plants, animals,  insects, bacteria, viruses – now curated in multiple, open access databases available to  all scientists worldwide with internet access. For example, just three of these plant focused databases, Legume Information System, SoyBase, and Maize GDB, serve 2300  to over 5200 users each month, accessed from nearly every country. (Figure 1). In a  paper recently published in the journal Global Food Security, a group of international  authors explain the value of GSD, and why the current system of open access to GSD is  critical to discovery, innovation, and more sustainable global agriculture and food  systems.1

Figure 1. Users by country and by month of select crop genomics databases.  Figure compliments of Carson Andorf and Lisa Hartman, USDA/ARS. 

Genomic sequence data, and broad, open, and unencumbered access to it, allows  scientists all over the world the freedom to leverage the vast genetic diversity of crop  varieties and their wild and weedy relatives, to enable a more thorough, precise, and  rapid breeding process. The combination of GSD and new breeding technologies  under development will continue to create opportunities for achieving greater food  security, a balanced diet and more climate-resilient crops. The open access database  system, as it stands today, offers fair and equitable sharing of GSD, promotes  sustainable use of biodiversity, while also contributing to conservation of biological diversity – the three objectives of the Conventions on Biodiversity (CBD).2 

Yet this free and unencumbered access to GSD may now be threatened by policy makers looking to regulate and monetize GSD in the hopes of creating more “fair and  equitable sharing of benefits from the use of genetic resources.”3,4,5 Negotiations  under the CBD, Nagoya Protocol, and International Treaty have reached a stalemate  and policy makers may use GSD as a bargaining chip or compromise. In so doing, they  may further threaten achieving the objectives of the CBD and limit the value of GSD. Funded by governments and philanthropic donor agencies, the open access databases  have grown in size and sophistication. Curators, most often in public research and  academia, have developed training tools and easy-to-use search applications to make  the sequence data widely available. Scientists from both the public and private  sectors have been the contributors of sequence data. The value of GSD, resides not in  the raw nucleotide sequences provided in the databases, but in the evaluation,  interpretation, and application of these data to generate information which is then  applied to develop improved crops, vibrant seed systems, and greater food security.  Developing this value requires creativity, resources, ingenuity, and importantly,  collaboration amongst scientists. Value is created when more productive and resilient  varieties of crops are integrated into a breeding pipeline and subsequently delivered  to farmers. More rapid delivery of improved crops and cropping systems is one of our  best opportunities to mitigate and adapt to climate change and help farmers become  more resilient in the face of ever-changing cropping environments.

The value created through a paid access and benefit sharing scheme for GSD, however  well-meaning, would pale in comparison to the monetary and non-monetary value  created when GSD is unencumbered by regulation and broadly available for innovation  and discovery. 

Examples of Value

Numerous examples exist of how GSD is being utilized in crops important to Africa and  Asia and serve to reinforce our points made above. Cassava, with 60 percent of global  production occurring in Sub-Saharan Africa (SSA), is threatened by viral and bacterial  disease and has numerous “anti-quality” traits, storage and nutritional problems.6,7,8 The availability of sequence data for this crop combined with other plant breeding  innovations has resulted in improved starch quality, higher levels of vitamin A in the  roots, iron and zinc biofortification, and brown streak disease resistance.9,10,11,12 Work  continues on other diseases and to improve storage of cassava roots. 

Sorghum is likewise an important food security crop, feeding around half a billion  people in SSA and Asia alone. Sorghum has amongst the largest libraries of GSD  available of any African indigenous crop.13,14,15,16,17,18,19 These data have been used to  evaluate numerous agronomic and quality traits, including grain size, heat tolerance,  starch content, nitrogen use efficiency, and anthracnose resistance.20,21,22,23,24,25,26 

Pearl millet, like sorghum, is indigenous to Africa and a resilient crop in the face of  high heat and drought conditions. The reference genome of pearl millet was published  with 38,579 genes and made available to plant scientists anywhere.27 The information  extracted from this database has been used to establish marker assisted breeding.  Marker-trait associations have been linked to root traits, plant height, yield, grain  quality, tolerance to water deficit and heat, and resistance to an ever-changing  disease and insect pest spectrum.28 

A final example is provided by how GSD could transform breeding efforts in Ethiopia’s  national crop, Eragrostis tef. When considering area under cultivation, the number of  farmers growing tef, and its importance to the diet, tef is far and away the most  important crop in Ethiopia.29 Yet it lags behind most other cereals in Ethiopia in terms  of productivity and yield and has numerous constraining agronomic  characteristics.30,31,32 Until very recently, a draft or completely sequenced genome  (GSD) was unavailable for tef, and tef improvement programs had to rely on direct  phenotypic selection and conventional breeding, which is slow and cumbersome. The  valuable genetic diversity of tef has therefore remained relatively hidden and  unknown, and while helpful, the sequenced variety “Dabbi” is one of hundreds of  farmer-used varieties sown in Ethiopia.33 The availability of openly accessible GSD on  greater numbers of farmer-preferred tef varieties would revolutionize tef  improvement by allowing application of molecular breeding and advanced plant  breeding approaches for achieving enhanced yield potential and beneficial agronomic  characteristics. Ultimately, millions of farmers would achieve greater productivity and  sustainability, over 100 million Ethiopians would have a more reliable and lower cost  supply of tef, and pressure on land resources would be reduced.

Vision for the Future 

Unencumbered, open access to GSD contributes directly to improved breeding  programs, more vibrant seed systems, greater agricultural productivity, and greater  resilience of crops and farmers in the face of changing environmental conditions. 

We ask that policy makers and politicians move with great care and caution when  considering regulation and monetization of GSD, beyond what currently exists for  international sharing and partnering of GSD. Public research and emerging economies  have the most to lose if GSD is further controlled, especially if the global scientific  community is not consulted. Administrative, financial, and legal barriers will quickly  weigh down research organizations making determinations as to GSD value, point of  origin, accessibility and with whom negotiations for access must be conducted. Many  of these tasks would take time and be difficult, if not impossible. It is imperative to  find ways to help scientists innovate while lowering legal and financial barriers to  innovation, which will contribute to the most productive path forward to equitable use  of genetic resources and GSD. 

While we have focused this discussion on plants and agriculture, human health and  public safety is also directly impacted by open access to GSD. In the early days of the  current coronavirus pandemic, scientists quickly and easily submitted and accessed  viral GSD to multiple open access databases, with freedom to operate and limited  legal implications.34 This access allowed scientists to rapidly gain a better  understanding of the virus, develop diagnostic tests, and envision a path on how best  to develop vaccines and other preventive measures.  

Maintaining open access and the use of GSD will serve to enable research  collaborations, maximize returns on investments and ensure creation of value to  scientists, farmers, and society. This also allows for greater scientific collaboration,  enabling and strengthening a global network of scientists. Crops like tef, sorghum,  cassava, and pearl millet will become more productive in regions where food security is  most at risk. The opportunity exists to create a new era of discovery and investment with GSD. 

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