Plant breeding sees cloning breakthrough

Scientists in California have discovered how to replicate seeds that are clones of a parent hybrid rice plant

What if crops could be cloned? What if there was no need to buy hybrid seed every year but, instead, we could take advantage of the cloned seeds from the parent plants of last year’s crop? And what if those designer seeds were all high yielding as well as climate tolerant and disease resistant?

Scientists at the University of California, Davis, have made a breakthrough toward meeting those goals by discovering how to replicate seeds that are clones of the parent hybrid rice plant.

Cloning crop plants has been a goal of plant breeders and geneticists for decades, but finding the molecular pathways that trigger the onset of a flowering plant embryo after fertilization and prevent its occurrence without fertilization is not well understood.

As well, it is all the more challenging given that seeds from hybrid plants are not always of the same quality as the originals.

“Hybrids have specific combinations of genes that make them superior,” said Venkatesan Sundaresan, a professor of plant biology and plant sciences at the university.

“(But) because genes and chromosomes are shuffled when gametes (eggs and sperm cells) are formed, the progeny gets combinations of genes that are different from the parents.”

Those differences may mean the progeny is inferior to the hybrid original. In addition, commercial crop species cannot produce seeds without fertilization, despite the fact that 400 wild plant species are able to do so.

“The requirement for fertilization to make seeds is the norm among flowering plants,” said Sundaresan.

“Only a small number of plant species have evolved away from this requirement. They are called apomicts and there are about 400 species out of a total 400,000 species of flowering plants.”

The focus of the research team’s work on cloning a rice plant is centred on the BBM1 gene, which Sundaresan described as a master regulator of many other genes. It belongs to a family of plant genes known as BBM, or “Baby Boom,” and is found in sperm cells but not in eggs.

Only after an egg is fertilized does the BBM1 gene, coming from the male contribution to the genome, switch on the ability of the fertilized egg to form an embryo. It actually turns on a whole suite of genes that transform the egg cell into a zygote, which is a cell that is able to regenerate an entire organism.

However, there is a reason why the BBM1 is confined to its male quarters.

“If it is also expressed in egg cells, the egg cell would go on to make an embryo,” said Sundaresan.

“This embryo would be haploid, i.e., containing only half the chromosomes and resulting in a weak and sterile plant. So, plants evolved a mechanism to keep the BBM1 gene silenced in the egg cell.”

Under normal circumstances, after fertilization, the egg and sperm go through a process of cell division in which half of the parental chromosomes are randomly lost, a process known as meiosis. It was at this point that the researchers blocked the process to explore their cloning hypothesis.

“We blocked this process by mutating three genes using a technique called genome editing,” he said.

“So instead of this specialized cell division process, we have a regular cell division that retains all the parental chromosomes (a process of mitosis), resulting in a diploid egg cell that is clonal. We also engineered the BBM1 gene so that it is switched on in the egg cell. Now the diploid egg cell goes on to form a diploid embryo without fertilization. This embryo will also contain all the parental chromosomes without gene shuffling, so it is clonal.”

According to the researchers’ report published in December 2018 in Nature, the clonal trait can be inherited through multiple generations of clones. With the research establishing the much-desired feasibility of reproduction cloning in crops, it would be possible to maintain quality hybrids from one generation to the next.

With this development, the research team plans to further the study to make the system more efficient, identify additional genes that would help the process and find additional ways to switch on BBM1 more efficiently.

Sundaresan said all flowering plants appear to have BBM1-like genes, and the closest related genes to BBM1 are found in other cereal crops, so the cloning process should work with them, too.

“Currently, the high costs of producing hybrid seeds is a major barrier to farmers in developing countries, especially South Asia and Africa,” said Sundaresan.

“Hybrid rice can increase yields by 50 percent or more, but it is only 10 percent of the rice in India and almost none in Africa compared to 30 percent in China. If this method can be efficiently deployed, it could potentially be a game-changer for poorer farmers who would only need to purchase the hybrid seeds once and plant the progeny seeds in subsequent seasons.”

Sundaresan worked on the project with UC Davis postdoctoral researcher Imtiyaz Khanday and colleagues at Iowa State University and the French National Institute for Agricultural Research.

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