The missing link between modern tomatoes and their wild ancestors

The tomato’s path from wild plant to household staple is much more complex than researchers have long thought. For many years, scientists believed that humans domesticated the tomato in two major phases. First, native people in South America cultivated blueberry-sized wild tomatoes about 7,000 years ago to breed a plant with a cherry-sized fruit. Later, people in Mesoamerica bred this intermediate group further to form the large cultivated tomatoes that we eat today.
But in a recent study, scientists showed that the cherry-sized tomato likely originated in Ecuador around 80,000 years ago. No human groups were domesticating plants that long ago, so this implies that it started as a wild species, although people in Peru and Ecuador probably cultivated it later.

Researchers also found that two subgroups from this intermediate group spread northward to Central America and Mexico, possibly as weedy companions to other crops. As this happened, their fruit traits changed radically. They came to look more like wild plants, with smaller fruits than their South American counterparts and higher levels of citric acid and beta carotene.
Geneticists were surprised to find that modern cultivated tomatoes seem most closely related to this wild-like tomato group, which is still found in Mexico, although farmers don’t deliberately cultivate it. 

What still isn’t known is how the intermediate group of tomatoes spread from South America to Central America and Mexico. Birds may have eaten the fruits and excreted the seeds elsewhere, or humans may have cultivated or traded them.
Another question is why this intermediate group “regressed” and lost so many domestication traits once it spread north. Natural selection in new northern habitats may have actively favored tomatoes with more wild-like traits. It also could be that humans weren’t breeding these plants and selecting for domestication traits, such as large fruits, which may require plants to use more energy than they would put into fruiting naturally.

Researchers reconstruct tomato history by sequencing the genomes of wild, intermediate and domesticated tomato varieties. They also carry out population genomic analyses, in which they use models and statistics to deduce the changes that have occurred to tomatoes over time. This work involves writing a lot of computer codes to analyze large amounts of data and look at patterns of variation in DNA sequences. They also work with other scientists to grow tomato samples and record data on many traits, such as fruit size, sugar content, acid content and flavor compounds.

Gene editing yields tomatoes that flower and ripen weeks earlier
Feeding a growing human population will require improving crop yields and quality. To do this, scientists need to know more about plant genes that are involved in phenomena such as fruit development and flavor and disease resistance. 
For example, research led by Zachary Lippman at the Cold Spring Harbor Laboratory in New York is using genome editing to manipulate traits that can help improve tomato yield. By tweaking genes native to two popular varieties of tomato plants, they have devised a rapid method to make the plants flower and produce ripe fruit more quickly. This means more plantings per growing season, which increases yield. It also means that the plant can be grown in latitudes more northerly than currently possible – an important attribute as the Earth’s climate warms. 
 

“Research in my lab over many years has been focused on identifying genes that are responsible for producing flowers in plants. In particular we work on tomato and flower production on tomato like on many crops is critical for making fruits and seeds, which is of course very important for agriculture. So in our most recent research, we have identified a new gene that is critical for tomato to be cultivated in northern latitudes such as the Mediterranean Basin where it was first introduced over 500 years ago, as well as the northern latitudes of California and even further north in Canada.   Now, it turns out that this gene is actually responsible for preventing flowering when the days are very long. In order for tomato to now be grown in northern latitudes, we had to have a change in the function, in the activity of this gene, so that it was not active as much as in the wild. In particular what we found is that when the activity of this gene was suppressed, tomato could now be cultivated in northern latitudes where the day lengths are longer but the growing season is shorter. We then went a step further and asked, “well, if we could completely eliminate the activity of this gene – mutate the gene entirely so that it no longer functions at all – then perhaps we could get even earlier flowering tomato varieties.” And we in fact did this using a new and very powerful gene editing technology known as CRISPR (Regulatory Interfaced Short Palindromic Repeats). By using this technology, we could pinpoint mutations directly in the genes; and when we generated these mutations, we then created plants that flowered two or three weeks earlier than most varieties. This may sound like a very subtle change but when you are talking to farmers you understand that having the ability to generate fruits at an earlier point in the season growing is not only important for production in order to get to market faster but also now opens the door to expanding the geographical range of where the tomato crop can be grown. For example in even higher northern latitudes of Canada where tomato season is very short. So our hope is that from the discovery of this gene in the lab that we can now implement this in other varieties of tomato and even other crops in order to achieve the same outcome of early yielding crops.” (Zachary Lippman, Professor, Ph.D., Cold Spring Harbor Laboratory)

Research provides an atlas of candidates for future tomato gene function studies. Scientists now can identify which genes were important at each stage of domestication history, and discover what they do. They also can search for beneficial alleles, or variants of specific genes, that may have been lost or diminished as the tomato was domesticated. They want to find out whether some of those lost variants could be used to improve growth and desirable traits in cultivated tomatoes.

Some complementary data
Authors: Hamid Razifard (Postdoctoral Researcher in Biology), Ana Caicedo (Associate Professor of Biology), University of Massachusetts Amherst

Video available at:
https://www.youtube.com/watch?v=Jem3hP734uA&feature=emb_logo

Source: theconversation.com