Using genetic variation to improve plant growth

Genetic exchange in AMF

Most eukaryotes, like us and like most fungi, exhibit sexual reproduction. Sexual reproduction allows genetic recombination and a re-shuffling of genes among the offspring. There are claims that AMF have not undergone sexual reproduction for over 400 millions years. But there is little, or no, evidence to support this other than the fact that biologists have not observed sexual structures in AMF. Because of the dogma about the long-term absence of sex in AMF, no one had looked to see if AMF exchange DNA. Because we knew about genetic differences among AMF from one field in Switzerland, we could choose AMF that were either genetically near or genetically distant and see if they would fuse (anastomose) and exchange DNA. Prof. Manuela Giovannetti and colleagues at the University of Pisa, Italy showed that genetically near and genetically distant AMF would anastomose (when the hyphae fuse) and that rapid streaming of the cytoplasm occurs in both directions (see the video to the right). We then showed with molecular techniques that these fusing AMF produce new AMF that carry the DNA from both parents – in other words, genetic exchange takes place (Croll, et al. New Phytologist 2009). When we take two genetically different AMF and allow them to exchange DNA, we call this “crossing” and the genetically novel AMF we refer to as “crossed lines”.

After two AM fungi have fused and they produce new spores. The new spores develop into fungi that are not only genetically different from the parents, but often also have phenotypes that are different from the parents (Croll et al. New Phytologist, 2009). Even more importantly, we have shown in two studies that crossed AMF lines can either make plants grow worse or grow better than the non-crossed parental lines (Angelard et al. Current Biology 2010; Colard et al. Appl. Envrion. Microbiol. 2011). See the animation lower right.

A type of segregation in AMF

Genetic exchange between AMF produces genetically different offspring. We think that this is because the two fungi mix their nuclei. We hypothesized that when the fungus makes new spores, by chance one spore could receive a different complement of the genetically different nuclei. Firstly, this could be what we call complete segregation, where a newly developed spore does not receive all the different nuclei present in the mother fungus. This can be detected as qualitative differences in the presence or absence of alleles between the AMF lines. Secondly, after new spores are made there could be differences in the quantity of genetically different nuclei among the siblings – we call this partial segregation. We have shown using several molecular techniques that partial segregation occurs but we don’t know whether complete segregation occurs (Angelard et al. Current Biology 2010). We have also shown that following partial segregation, AMF lines have different effects on the growth of rice compared to their parental AMF lines. In some cases, segregation lead to poorer rice growth and in some cases very large increases in rice growth. This is a very exciting development. See the animation on the right ….

Using natural variation in AMF to improve growth of crops

For several thousand years farmers have used natural genetic variation in plants to breed new better varieties of crops. Of course, at first this was done with no knowledge of genetics. New crop varieties are made by crossing genetically different plants and then looking at the characters of the offspring after segregation and choosing the best new varieties. Now with marker-assisted breeding this is done in a more directed way to breed desirable traits into crops by looking at the genetic composition of plants after crossing and predicting which will be the best on the basis of their genetic composition. No one tried to do this with AMF because they thought it was impossible to cross AMF or that segregation occurs in AMF. However, as explained above, this is not the case. We have chosen genetically different AMF, crossed them and produced segregated AMF lines. We have shown that both crossed and segregated AMF lines have very different effects on the growth of rice compared to the effects of parental lines. On the basis of these results and others that we have have in the group, we propose that it should be possible to “breed” AMF to improve them and make them more effective with a given crop, especially in the tropics.

This is one of the goals in our group and we try and do this with globally important crops in the tropics. This is why we have an applied part of our research in parallel running in Colombia with cassava.

Our long term goal

Our long-term goals are to be able to do with AMF what plant breeders do using marker-assisted breeding. We want to understand how the genetic composition of AMF and how genetic variation in AMF alters how globally important crop plants grow. To do this we need to be able to study how the presence of given genetic markers affect what we call quantitative traits in the crop plants. At present, we can produce lots of genetically novel AMF and we can grow them up cheaply with a company called Mycovitro S.L. in amounts that are needed for large-scale use but we cannot predict which of the lines will be the best for a given crop until we have tried them in the field. We would like to be able to take new AMF lines from the lab, characterize them genetically and be able to better predict which of those lines will make a given crop plant grow better. This is not a trivial exercise. When plant breeders do this they look at the presence and absence of genetic markers and which markers are associated with given traits of the crop plant. However, because of changes in the frequency of different nuclei in AMF, we have to look at how quantitative changes in the different nuclei affect the effect of the fungus on plant traits. Unravelling this puzzle is a long-term project, requiring the development of new molecular genetics, analytical and bioinformatic tools. We ultimately hope to use this to have a targeted approach to developing novel AMF, that can be produced cheaply and that will be beneficial for globally important crops. See the page on our long-term goals.


Arbuscular mycorrhizal fungal (AMF) spores. Photo by M. Hijri (Warhol-like modification by Ian)


This video was made by Prof. Manuela Giovannetti (University of Pisa, Italy) and published in the New Phytologist (Croll et al. New Phytologist, 2009)