Dongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

Advances in sequencing technologies have made it possible to analyse large amounts of germplasm against low production costs, which has opened the door to screen genebank collections more efficiently for DNA sequence variation. The present study explores how these developments may affect the operations of genebanks and, consequently, how genebank agendas may change. It is argued that the new developments are more likely to have an impact on the user-oriented activities than the housekeeping operations of genebanks. To better facilitate the user community, genebanks may have to strengthen their core business, in particular, by improving quality management procedures and by providing access to a wider diversity of a crop's gene pool. In addition, genebanks may have to provide novel services, such as the introduction of specific user-oriented collection types, including research populations and genetically purified lines, and the development of novel information services, including plant genetic resources portals that should guide users to the information and materials of specific interest. To improve their user-oriented services, genebanks need to increase their communication and collaboration with the user community and to develop strategic alliances with this sector.

The primary mission of germplasm collections is to preserve genetic diversity, but germplasm is preserved so that it can be used. Historically, the standard practice is that all germplasm accessions should be maintained as collected, so that even self-pollinated accessions are maintained as heterogeneous seed lots. In theory, this seems like an ideal strategy for preserving genetic diversity, but in practice, it is simply not workable. Heterogeneous accessions are in constant risk of change and loss. It is possible to mitigate the risk factors, but they can only be lessened and not eliminated. Maintaining pure-lined accessions for self-pollinated species not only eliminates the problems associated with genetic drift and natural selection, but also enhances the accuracy of the evaluations and fosters effective germplasm utilization. Neither the current potential to characterize entire germplasm collections with tens of thousands of DNA markers nor the future potential of whole genome sequencing to completely characterize the diversity of all accessions in collections can be fully realized for self-pollinated species unless accessions are homogeneous and homozygous. In this manuscript, the case is made for pure-lining self-pollinated germplasm accessions using the USDA Soybean Germplasm Collection, which has maintained pure-lined accessions for over 50 years, as an example. There is also an analysis of the extensive seed distribution from this collection to indicate the value of a diverse collection of genotypes.