Genetic integrity

Contact person for Genetic integrity: Jessica Rey, IRRI, Philippines

Contributors to this page: IRRI, Los Baños, Philippines (Jessica Rey, Kenneth McNally, Ruaraidh Sackville Hamilton); Bioversity International, Montpellier (Elizabeth Arnaud); CIMMYT, Mexico (Suketoshi Taba); CIP, Peru (David Tay); ICARDA, Syria (Kenneth Street); ICRISAT, Patancheru, India (Hari D Upadhyaya).


The magnitude of genetic differences between supposedly duplicate samples is disturbingly high, even unacceptably high. All causes of genetic change are significant contributing factors – genetic drift, unintentional selection, pollen contamination, seed contamination, and mislabelling. In particular, analysis has demonstrated an unexpectedly high rate of mislabelling, a risk that existing “best practices” for genebank management have failed to manage. Similarly, existing best practices to not address the loss of diversity of genes for flowering date noted in the maize dataset.

The greatest changes in genetic composition are apparent between duplicates maintained at different genebanks; the differences are such that “duplicates” at different genebanks should perhaps be described as “equivalents” rather than “duplicates”. Significant changes also occur during management within a genebank.

Thus it is important and urgent to improve both the handling of accessions within genebanks and the transfer of accessions between genebanks, and to develop a strategy and protocols to do so.

General recommendations

Recommendations for clonal crops

Model: Musa

For misclassification

For mislabelling

For off-types

Thus during management of Musa, there is a need for more regular, specific morphological and molecular characterization to ensure adequate quality control.

Recommendations for seed crops

Existing FAO/IPGRI (1994) recommended standards for genebank management include these recommendations for seed increase:

These standards are supported, but should be more rigorously enforced and operationalized. It is recommended that the following elements of best practices be added:

The maize data demonstrate a loss of diversity following regeneration, particularly in genes controlling flowering date; but they revealed no relation between the number of ears saved in the regenerated cycle and loss of genetic integrity among the accessions studied. This suggests that gene-specific selection is more important and random drift less important, (but it exists with inbreeding of the population, and should be preferably known with respect to the numbers of ears saved. However, it is usually assumed that outbreeding maize populations has a minimum level of inbreeding. Thus, a theoretical sampling strategy can still be employed to ensure conservation of the diversity present in the population. Inbred lines may need another study at SNP diversity level at various inbreeding cycles (as maize inbred can diverge in seed stocks maintained at the different seed genebanks and breeding stations) than has previously been supposed. It is concluded that the maize regeneration protocol should be modified to maintain the diversity of flowering dates unchanged.

In chickpea and rice, increases in average heterozygosity, as measured with Arlequin 3.0, were observed following regeneration. The results indicate that the consequences of cross-pollination and seed contamination are greater than have previously been supposed. It is common practice to ignore both factors, for example growing adjacent plots of self-pollinating crops with no control over cross-pollination. The results show this is inappropriate.

In rice it is known that almost all of the limited cross-pollination occurs over very short distances, between adjacent plots. Since 2007, the extent of cross-pollination between rice regeneration plots has been reduced in IRRI by sowing adjacent plots to varieties differing by more than two weeks in flowering date, so that a plot is never releasing pollen at the moment its neighbours have receptive stigmata: it has not been possible to evaluate the consequence of this management change during the current activity. Other methods need to be designed and introduced to reduce seed contamination.


A range of innovations is urgently needed to prevent the rapid losses of genetic integrity noted here. These include the introduction of new technologies such as barcoding, “DNA barcoding” with SNP chips and high-precision GPS. Morphological verification remains essential, both for somaclonal variants or other mutants that are difficult to identify with molecular methods, and for efficiently screening out obvious errors. In addition, we need a thorough re-evaluation of genebank management standards.

References and further reading

FAO/IPGRI. 1994. Genebank standards. Food and Agriculture Organization of the United Nations, Rome and International Plant Genetic Resources Institute, Rome. Available in English, Spanish, French and Arabic.

Hirano R, Jatoi SA, Kawase M, Kikuchi A, Watanabe N. 2009. Consequences of ex situ Conservation on the Genetic Integrity of Germplasm Held at Different Gene Banks: A Case Study of Bread Wheat Collected in Pakistan. Crop Science 49:2160-2166.

The Genebanks

The 11 CGIAR genebanks currently conserve 730,000 of cereals and grain legumes, forage crops, tree species, root and tuber crops, bananas and crop wild relatives.