The tea plant contains three billion base pairs of DNA, four times more than coffee or cacao. It took five years to unravel but the first high-quality map of the genome was published in May. Now it’s time to get to work coming up with practical applications of the tea genome for commercial tea production.
By Dan Bolton
Ten commercial tree crop genomes have been published since 2000. Apples, apricots, pears, grape, papaya, and peach trees were the easy ones — and they took years. Cacao was sequenced in 2013 and robusta coffee in 2014. The pace has since quickened. The first public genome sequence for Coffea arabica, the species responsible for more than 70% of global coffee production, was released in January by researchers at the University of California, Davis.
It was high time for tea.
In May a team of 29 Chinese scientists from 12 research institutes in China, South Korea, and the United States, published their findings in the journal Molecular Plant. They describe a remarkably complex DNA that at one point during the plant’s long evolution doubled in size.
Researchers selected the Yunkang 10 cultivar to study, it is an assamica cultivar growing in Yunnan. The task was made difficult because tea over eons has learned to duplicate beneficial sequences. The plant experienced two “whole genome duplication” events in the past 50 million years equipping it with greater disease resistance, the ability to cope with stress brought by drought, tolerance to heat, and the ability to identify and deal with pathogens within itself.
ALSO:
DNA Mapping of Tea Could Stave off a Pending Crisis
What Knowing the Tea Tree Genome Means to the Flavors in Our Cup
Professor Zeno Apostolides in the department of biology at the University of Pretoria, South Africa, expressed delight at the news. “I expect that a flurry of scientific publications will follow, in the next 15 years, describing cultivars of tea with improved yield, increased tolerance to insect pests, fungal and bacterial diseases and drought,” he said.
“The tea genome will also allow breeding of new cultivars with unique flavours, e.g. low or high caffeine for different market segments, slow fermenters for green tea, fast fermenters for black tea, high theanine for the umami taste or high catechins for health properties. The achievements will be made possible by classical breeding and selection, without any genetic modification of the tea plant,” he said.
Unraveling the Tea Genome
This diagram shows how the tea tree genome evolved in relation to similar plants.
The process
“Sequencing capabilities have exploded in the last decade making it much cheaper and faster to generate genetic sequences,” writes Professor Shaun R. Broderick, assistant research/extension professor of ornamental horticulture in the department of plant and soil sciences at Mississippi State University.
“Most sequencing technologies require that DNA be fragmented into small pieces before sequencing,” Broderick said. “These short sequences are then strung back together using computer software. The tea genome is about the same size as the human genome, but tea DNA doubled at one point during its evolutionary past, meaning that there are at least two copies of every gene. It’s like trying to put together a puzzle where every piece has a nearly identical matching piece. On top of that, the puzzle has hundreds of millions of pieces. It is exciting to see this technology develop to the point that researchers can now solve puzzles that are this complicated.
“Sequencing the tea genome will allow researchers to more easily answer questions about where tea plants originated and their breeding pedigrees. We can use it to help us identify the genes that control heat tolerance, cold tolerance, disease resistance, flavor compounds, secondary metabolites and yield. Almost all genetic research in tea will be made easier and faster. In many ways, we can use it to direct breeding and genome editing efforts to produce improved cultivars that don’t require as much water, fertilizer, or pesticides while still maintaining high-quality flavor profiles.”
Unraveling the Tea Genome
Phylogenetic analysis of the retrotransportation sequence in the tea genome.
Inside the gene
The lead researcher in the sequencing is Professor Lizhi Gao, a botanist at the Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming.
“Our lab has successfully sequenced and assembled more than 20 plant genomes,” Prof. Gao told the BBC, “But this genome, the tea tree genome, was tough.” The genome contained 3 billion base pairs.
The Camellia genus is largely ornamental with more than 100 species. But only Camellia sinensis is grown commercially for making tea, according to professor Gao. This is because researchers found that the leaves of the tea plant contain high levels of chemicals that give tea its distinctive flavor. They include flavonoids and caffeine.
Gao found the biochemical pathways involved in the synthesis of the compounds important in the taste of tea are also present in some of the ancestors of tea and have been conserved for about 6.3 million years. There are even hints some modification may be related to human cultivation.
Coffea arabica is complex too, according to researchers at UC Davis. In a release, the university described “C. arabica is a hybrid cross derived from two other plant species: C. canephora (robusta coffee), and the closely related C. eugenioides. As a result of that hybrid crossing, C. arabica’s complex genome has four sets of chromosomes — unlike many other plants and humans, which have only two chromosome sets.”
UC Davis researchers estimated that UCG-17 Geisha has a genome made up of 1.19 billion base pairs — about one-third that of the human genome.
Unraveling the Tea Genome
Evolutionary differences of three important metabolic pathways(caffeine, flavenols, and theanine) associated with tea-processing suitability and quality among the 25 Camellia species.
Work continues
The next step will be finding DNA markers that are closely associated with desirable traits, explains professor Apostolides. “In tea, there are some known physical markers that are closely, but not perfectly, associated with some desirable traits, e.g. leaf pubescence with tea aroma, yellow leaf color with good quality, small leaf size for drought tolerance, and horizontal leaf poise for mechanical harvesting,” Gao explains. “Earlier work in my laboratory has enabled us to identify 10 RAPD markers (each only 10 base pairs long) associated with desirable tea traits, e.g. black tea quality, high yield, drought, cold, fungal, and insect.1
“We are currently busy with the bioinformatics analysis of 12,000 DNA markers (each only 69 base pairs long) that we hope will associate, to some degree, with desirable tea traits. The publication of the tea genome will enable us to determine which of our markers occur in genes that form parts of proteins, and the biochemical pathways in which these proteins operate that could be associated with the desirable tea traits. Once we know which of our markers are closely associated with the desirable traits, we will be able to score potential parent trees for these markers and select very good parents for breeding the next generation of tea trees. By careful selection of tea parents, we will be able to breed new tea cultivars with the desirable traits. It will probably still take 15 years to breed and select the new cultivars, but we will be able to breed designer-cultivars for e.g. high or low caffeine or any other trait. This information will also enable us to breed new cultivars with combinations of more than one traits, e.g. fast fermenters for black tea, that are high in health promoting antioxidants (catechins), that have high yield and are drought and cold tolerant, with good aroma and horizontal leaf poise,” he writes.
In the US Dr. Guihong Bi, a colleague of Prof. Broderick at Mississippi State University, along with several collaborators is working to develop tea as a specialty crop on the US mainland.
“We have submitted a grant to further develop growing methods for tea and to measure the diversity of our collection, which includes cultivars from many regions,” said Broderick.
“Once we know that we have a good collection and know a little bit about their performance, we can start to make mapping populations and identify accessions that perform well under specific climates. We can sequence these accessions and compare those sequences to those from accessions that perform poorly and identify regions of the genome that are correlated with improved performance. Having a genome gives us a framework to which we can align all of our sequencing data, making this process much more straight forward and faster,” he said.
It will probably take 15 years to breed and select new cultivars, according to Apostolides.
“We will be able to breed designer-cultivars for e.g. high or low caffeine or any other trait. This information will also enable us to breed new cultivars with combinations of more than one traits, e.g. fast fermenters for black tea, that are high in health promoting antioxidants (catechins), that have high yield and are drought and cold tolerant, with good aroma and horizontal leaf poise,” he predicts.
New cultivars have been developed by classical breeding and selection in other annual and tree crops, based on knowledge of their genome sequences, he said.
“I am confident that new tea cultivars will be developed for tea now that the tea genome has been published,” he said. “Scientists in all tea producing countries will be able to use the tea genome sequence to develop new cultivars, suited to their climates.
“This will require, however, that tea breeders improve their bioinformatics skills to be able to use the information of the tea genome sequence to their full advantage,” he concludes.