Apomixis, the Holy Grail is at hand

For a long time, it was no more than a botanical curiosity, of interest to a few scholars with a passion for taxonomy and evolution. Today, it has become the Holy Grail of agricultural genetics. We are talking about apomixis, i.e. the ability to produce viable seeds that are completely identical to the mother plant, bypassing the need for fertilisation. “Research has been going in waves, now we are on the crest,” says Emidio Albertini, an apomixis expert at the University of Perugia and the organiser of a recent workshop on the subject at the Plant & Animal Genome Conference (San Diego, 13 January 2023).

The mood among experts is high and the goal has never seemed so close, especially thanks to the brilliant results announced in Nature Communications on 27 December 2022 by a French-US team. With the help of CRISPR, Venkatesan Sundaresan of the University of California at Davis and his colleagues have achieved a very high level of efficiency in engineering apomixis in rice. How did they do it and what hurdles are left? What will be the next species? We asked the Italian geneticist many questions, but it is worth starting with the most important – how big are the stakes? 

“Apomixis is a character present in around 400 wild species and its evolution is still debated. It is not clear what came first: reproduction by seed with or without sex?”, Albertini says. Reproducing this natural phenomenon in agronomically important plants, however, would have potentially revolutionary consequences. “When we succeed, it will be easier for breeders to fix superior genetic combinations and adapt them to different contexts. Furthermore, breeders will be able to save hybrid seeds for the following crop, getting plants that are uniform in quality and yield, generation after generation’. The economic gains could run into billions of euros, and the first to benefit could be small farmers in developing countries who today cannot afford to buy seed every year.

“Not everyone knows that many varieties are marketed in the form of hybrids, which perform best in the first generation but then produce highly variable progeny due to the mixing of genes occurring in sexual reproduction,” explains Albertini. Apomixis is used to generate plants that are clones of the mother plant, so it would magically solve the problem, lowering seed production costs and allowing the crop to be reseeded. How did this idea come about?

The history of apomixis studies begins in 1829 in London’s Kew Gardens, the same place where Peter Pringle’s techno-thriller on apomixis is set (the original title is ‘Day of the Dandelion’, because dandelions are an apomictic plant). The first curator of the prestigious English botanical gardens noticed that three female specimens of an Australian hollyhock-like shrub (Alchornea ilicifolia) produced seed in the absence of pollen.

‘In 1869, Mendel also stumbled upon the phenomenon without knowing so, by making crosses with the species Hieracium pilosella, but explaining the results of those experiments took another 40 years,’ Albertini says. Subsequently, the character was found in many other plants, both mono- and dicotyledons, and a handful of geneticists tried to transfer it to the species of interest through crosses, but this path proved to be a dead end. More fruitful, by comparison, was the work of mapping the molecular pathways of apomixis, looking for the genetic buttons to switch from one reproduction mode to another. Once the key genes were found, scientists started the experiments to transfer them, first with genetic engineering and then with genome editing. 

Emidio Albertini works, together with Lucia Colombo of the University of Milan, with the Apostart gene. ‘We have studied it in the model plant Arabidopsis and in the future we plan to try with rice,’ he tells us. The Dutch company Keygene focuses on the Par gene. France’s jewel is MiMe, which consists of three genes (the acronym means that mitosis takes the place of meiosis, so the egg cell retains the entire chromosome set instead of halving it as is usually the case in sex cells). These groups and others are participating in two large EU-funded projects, called MAD and Polyploid respectively, which focus precisely on apomictic plants.  

A decisive leap forward was made by the US group led by Sundaresan in 2019, with the description in Nature of the development of apomictic rice lines with a success rate of around 40%. The recipe involved two steps: first the rice was engineered with a gene that allows embryos to develop without fertilisation (Baby Boom1), then CRISPR was used to introduce the MiMe system eliminating meiosis. The good news is that the effect has been maintained for at least eight generations, so the DNA keeps working properly even without the paternal contribution. The latest exciting development is that the success rate of apomixis was raised to 95% by synchronising the two in a single move. In practice, CRISPR made it possible to simultaneously transfer the four genes (BabyBoom plus the three from MiMe) into the same package.

The goal is close but not yet fully achieved, Albertini points out: ‘Before thinking about commercialisation, the problem of grain-filling needs to be solved. Indeed, the apomictic rice described in Nature Communications, when grown in a greenhouse, tends to produce a certain number of ‘deflated’ seeds in which the formation of the endosperm is not properly initiated. It remains to be seen whether the fault lies with the starting hybrid line or the low penetrance of the gene package.

Meanwhile, the University of Davis has started the first field trials with apomictic rice and researchers are testing a similar system on two other species. ‘Sundaresan told me that they have chosen sorghum and cowpea, two plants important for developing countries and for which producing hybrids is complex,’ the geneticist explains, recalling that the project is funded by the Gates Foundation.

My final question concerns the timeframe for the market debut: will our generation, which lived through the GMO controversy and then saw the birth of CRISPR, be able to eat apomictic risotto? Albertini is cautiously optimistic: ‘Before the latest exploit I would have said no, but now I’m starting to believe it. Maybe we will have to go and eat it in the United States, where they have advanced technologies, generous funds and favourable regulations’.

This article was published in Agriscienza

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