This special issue focuses on how genomics of plant genetic resources (PGRs) provides key information and materials to meet the challenges that agriculture will face in the next few decades to meet the fast-growing demand for plant-derived products. Sessions at the 3rd International Symposium on Genomics of Plant Genetic Resources (GPGR3; www.GPGR3.com) held in Jeju, Korea, from 16 to 19 April 2013 covered topics including basic plant genome diversity and its applications. This meeting followed on the successful previous two editions in Beijing, China (2005), and in Bologna, Italy (2010). In this special issue, a total of 35 short review and research articles have been selected from the 312 oral and poster presentations during GPGR3.

The overall objective of GPGR3 was to present and discuss state-of-the-art genomics research and how to best use it to harness PGR diversity for global food security. In view of the recent food crises, PGRs are critical for fulfilling the future food, feed, fibre and fuel needs of an expanding population, as well as for addressing the challenges posed by climate change and depletion of natural resources, water, in particular. This collection of articles and the references cited therein highlight the increasing strategic role of plant genomics in the interrogation of germplasm collections to discover agronomically beneficial superior alleles for use in conventional breeding and, subsequently, to determine gene function. Below, we present a brief introduction on the impact of emerging next-generation sequencing (NGS) technologies applied to diversity studies of PGRs and the importance of public–private partnerships (PPPs) for more effective management of PGRs and the release of improved cultivars.

Although various biotechnologies have been developed and/or applied to crop improvement, the supply of plant-derived products is still insufficient to meet the needs of a rapidly increasing population. Therefore, global food demand is projected to increase steadily until 2050, while crop productivity will be negatively affected because of the growing competition for land, water, fertilizers and energy and the negative effects of climate change, which will inevitably result in higher food prices (Godfray et al., Reference Godfray, Beddubgton, Crute, Haddad, Lawrence, Muir, Pretty, Robinson, Thomas and Toulmin2010; Chang and Hsu, Reference Chang and Hsu2011). The increasing demand for not only food but also for biofuels as renewable sources of energy has resulted in competition for crop resources of energy (Fargione et al., Reference Fargione, Hill, Tilman, Polasky and Hawthorne2008). Food security must be solved and is one of the urgent challenges, e.g. feeding the projected nine billion people (Gregory and George, Reference Gregory and George2011).

In view of the growing concern for food security and preservation of biodiversity, the concept of PGRs was first developed in 1993, and since then, PGRs have been considered to be important for gene discovery and cultivar release and for developing more sustainable agricultural practices (Hammer, Reference Hammer2003). Both domestication and modern plant breeding have greatly reduced the genetic diversity in major crops (Tanksley and McCouch, Reference Tanksley and McCouch1997; Hyten et al., Reference Hyten, Smith, Frederick, Tucker, Song and Cregan2009). Thus, many efforts have been taken to preserve ex situ and in situ PGRs (Gepts, Reference Gepts2006; van Zonneveld et al., Reference van Zonneveld, Dawson, Thomas, Scheldeman, van Etten, Loo, Hormaza, Tuberosa, Graner and Frison2014). In early studies, genetic diversity was investigated based on the characterization of plant morphology, yield, quality and other simple phenotypic features (Gilbert et al., Reference Gilbert, Lewis, Wilkinson and Caligari1999; Hoisington et al., Reference Hoisington, Khairallah, Reeves, Ribaut, Skovmand, Taba and Warburton1999). More recently, the development of NGS technologies has allowed for the massive production of whole-genome/transcriptome sequence data, which in turn enables a more in-depth exploration of PGR diversity while allowing to develop novel molecular markers and identify agronomically important loci (Edwards and Batley, Reference Edwards and Batley2010; Tuberosa et al., Reference Tuberosa, Graner and Frison2014).

Recently, several NGS platforms including GS-FLX and Illumina HiSeq have been developed using which large amounts of sequence data can be produced in a relatively short period of time for either de novo assembly or resequencing (Van et al., Reference Van, Kim, Shin, Kim, Lee, Lee, Tuberosa, Graner and Frison2014). Whole-genome sequencing has been widely used in plant and animal species for the characterization of DNA sequence variations including the detection of single-nucleotide polymorphisms (SNPs). Genome-wide SNP genotyping can be implemented for association mapping and evolutionary analyses (Akhunov et al., Reference Akhunov, Nicolet and Dvorak2009; Varshney et al., Reference Varshney, Nayak, May and Jackson2009; Waugh et al., Reference Waugh, Jannink, Muehlbauer and Ramsay2009). Evolutionary studies in wild species when compared with those in modern cultivars will be helpful in terms of crop improvement. e.g. to determine structural variations in chromosomes as such variation can be a driving force in plant evolution, thus allowing for the discovery of new genes and valuable traits (Barabaschi et al., Reference Barabaschi, Guerra, Lacrima, Laino, Michelotti, Urso, Vale and Cattivelli2012). As we approach third-generation sequencing (Rusk, Reference Rusk2009), NGS technologies are powerful tools that can be used to conduct multiplexed genotyping and to develop genome-wide markers. These applications of NGS provide an important vehicle to the gateway to the new era of global food security (Gupta et al., Reference Gupta, Rustgi and Mir2008).

Another major issue with regard to the more effective utilization of PGRs to meet the challenges posed by food security is related to our capacity to forge strong PPPs to create additional research opportunities, particularly in the area of translational genomics aiming to release improved cultivars (Varshney and Tuberosa, Reference Varshney and Tuberosa2013; Baenziger et al., Reference Baenziger, Bakhsh, Lorenz, Walia, Tuberosa, Graner and Frison2014), including interactive forums and international research projects. Along this line, the purpose of the wrap-up session of GPGR3 was to inform on the opportunities offered by PPPs and discuss strategies on how to strengthen them and make them more effective.

The presentations addressing the first topic provided evidence that each PPP research project has its own peculiarities and can offer new and exciting opportunities to achieve win–win outcomes. To deal with global challenges, innovation is essential, especially through outward collaboration to develop new ways of thinking and seek better solutions. Valuable information, new platforms and strategies, and creative out-of-the-box ideas can be generated by properly putting together the puzzle pieces contributed by the different stakeholders from academia, governmental research centres, germplasm banks and seed companies. Notably, it has been reported that spontaneous collaborations outside of established grant schemes are often successful. More in general, it has been observed that successful PPPs require that all partners be on the same level and provide complementary skills and expertise.

As to the second topic, i.e. international collaboration and sharing of PGRs and databases, international collaborations between the International Atomic Energy Agency (IAEA), Leibniz Institute of Plant Genetics and Crop Plant Research, and Federal University of Pelotas in Brazil were discussed. The IAEA is currently expanding collaboration in science, research and innovation for food security, food safety and sustainable agriculture. The intention is to conduct joint research projects, share knowledge and encourage staff to increase food system resilience, to promote the improved and sustainable utilization of agricultural and natural resources, and to enhance member states' capabilities in the application of nuclear techniques. Furthermore, international collaboration in terms of information sharing in support of scientific research is very important. Currently, genomic information on biological species is publicly available through genebanks (1750 genebanks worldwide including an estimated 7.4 million accessions). Therefore, within the PGR framework, extensive international collaboration is needed for sharing and characterizing mapping populations, core collections, TILLING populations and introgression libraries (Bovina et al., Reference Bovina, Talamè, Ferri, Tuberosa, Chmielewska, Szarejko and Sanguineti2011; Frison and Demers, Reference Frison, Demers, Tuberosa, Graner and Frison2014; Grandillo, Reference Grandillo, Tuberosa, Graner and Frison2014).

With the availability of whole-genome sequences in many crop species including, among others, rice (Goff et al., Reference Goff, Ricke, Lan, Presting, Wang, Dunn, Glazebrook, Sessions, Oeller, Varma, Hadley, Hutchison, Martin, Katagiri, Lange, Moughamer, Xia, Budworth, Zhong, Miguel, Paszkowski, Zhang, Colbert, Sun, Chen, Cooper, Park, Wood, Mao, Quail, Wing, Dean, Yu, Zharkikh, Shen, Sahasrabudhe, Thomas, Cannings, Gutin, Pruss, Reid, Tavtigian, Mitchell, Eldredge, Scholl, Miller, Bhatnagar, Adey, Rubano, Tusneem, Robinson, Feldhaus, Macalma, Oliphant and Briggs2002; Yu et al., Reference Yu, Hu, Wang, Wong, Li, Liu, Deng, Dai, Zhou, Zhang, Cao, Liu, Sun, Tang, Chen, Huang, Lin, Ye, Tong, Cong, Geng, Han, Li, Li, Hu, Huang, Li, Li, Liu, Li, Liu, Qi, Liu, Li, Li, Wang, Lu, Wu, Zhu, Ni, Han, Dong, Ren, Feng, Cui, Li, Wang, Xu, Zhai, Xu, Zhang, He, Zhang, Xu, Zhang, Zheng, Dong, Zeng, Tao, Ye, Tan, Ren, Chen, He, Liu, Tian, Tian, Xia, Bao, Li, Gao, Cao, Wang, Zhao, Li, Chen, Wang, Zhang, Hu, Wang, Liu, Yang, Zhang, Xiong, Li, Mao, Zhou, Zhu, Chen, Hao, Zheng, Chen, Guo, Li, Liu, Tao, Wang, Zhu, Yuan and Yang2002), soybean (Schmutz et al., Reference Schmutz, Cannon, Schlueter, Ma, Mitros, Nelson, Hyten, Song, Thelen, Cheng, Xu, Hellsten, May, Yu, Sakurai, Umezawa, Bhattacharyya, Sandhu, Valliyodan, Lindquist, Peto, Grant, Shu, Goodstein, Barry, Futrell-Griggs, Abernathy, Du, Tian, Zhu, Gill, Joshi, Libault, Sethuraman, Zhang, Shinozaki, Nguyen, Wing, Cregan, Specht, Grimwood, Rokhsar, Stacey, Shoemaker and Jackson2010), pigeonpea (Varshney et al., Reference Varshney, Chen, Li, Bharti, Saxena, Schlueter, Donoghue, Azam, Fan, Whaley, Farmer, Sheridan, Iwata, Tuteja, Penmetsa, Wu, Upadhyaya, Yang, Shah, Saxena and Michael2011), corn (Schnable et al., Reference Schnable, Ware, Fulton, Stein, Wei, Pasternak, Liang, Zhang, Fulton, Graves, Minx, Reily, Courtney, Kruchowski, Tomlinson, Strong, Delehaunty, Fronick, Courtney, Rock, Belter, Du, Kim, Abbott, Cotton, Levy, Marchetto, Ochoa, Jackson, Gillam, Chen, Yan, Higginbotham, Cardenas, Waligorski, Applebaum, Phelps, Falcone, Kanchi, Thane, Scimone, Thane, Henke, Wang, Ruppert, Shah, Rotter, Hodges, Ingenthron, Cordes, Kohlberg, Sgro, Delgado, Mead, Chinwalla, Leonard, Crouse, Collura, Kudrna, Currie, He, Angelova, Rajasekar, Mueller, Lomeli, Scara, Ko, Delaney, Wissotski, Lopez, Campos, Braidotti, Ashley, Golser, Kim, Lee, Lin, Dujmic, Kim, Talag, Zuccolo, Fan, Sebastian, Kramer, Spiegel, Nascimento, Zutavern, Miller, Ambroise, Muller, Spooner, Narechania, Ren, Wei, Kumari, Faga, Levy, McMahan, Van Buren, Vaughn, Ying, Yeh, Emrich, Jia, Kalyanaraman, Hsia, Barbazuk, Baucom, Brutnell, Carpita, Chaparro, Chia, Deragon, Estill, Fu, Jeddeloh, Han, Lee, Li, Lisch, Liu, Liu, Nagel, McCann, SanMiguel, Myers, Nettleton, Nguyen, Penning, Ponnala, Schneider, Schwartz, Sharma, Soderlund, Springer, Sun, Wang, Waterman, Westerman, Wolfgruber, Yang, Yu, Zhang, Zhou, Zhu, Bennetzen, Dawe, Jiang, Jiang, Presting, Wessler, Aluru, Martienssen, Clifton, McCombie, Wing and Wilson2009) and, hopefully soon, also wheat (Choulet et al., Reference Choulet, Caccamo, Wright, Alaux, Simková, Safár, Leroy, Doležel, Rogers, Eversole, Feuillet, Tuberosa, Graner and Frison2014), crop improvement will be accelerated by means of genomics-assisted strategies aimed at more effectively harnessing allelic diversity based on sequence information (Moose and Mumm, Reference Moose and Mumm2008) and a better understanding of gene function (Harrison, Reference Harrison2012). This special issue offers a glimpse on how genomics can assist in the characterization of PGRs to (1) identify beneficial alleles the manipulation of which through marker-assisted selection and/or genetic engineering will be crucial for helping secure the future well-being of mankind while reducing the impact of agricultural practices on the environment and (2) optimize the collection, management and conservation of natural and artificially induced plant biodiversity.