• Fri. Aug 12th, 2022

Lychee genome tells colorful story about colorful tropical fruit – sciencedaily

They’re tangy on the outside, sweet on the inside, and loved for their signature pink hulls and pearly, fragrant fruit. In the United States, you might meet them as a tasty ingredient in bubble tea, ice cream, or cocktail. You can also peel them and eat them fresh.

Lychees have been cultivated in China since ancient times, with traces of cultivation dating back around 2,000 years. Fresh lychees were so desired that in the Tang Dynasty an emperor set up a dedicated horse relay to deliver the fruits to the imperial court from crops made far to the south.

Now, scientists have used genomics to delve deeper into the history of lychee. And in the process, they uncovered information that could also help shape the future of the species.

“Lychee is an important tropical agricultural crop in the Sapindaceae (maple and horse chestnut), and it is one of the most economically important fruit crops grown in East Asia, especially for the annual income of farmers in southern China, ”said said Jianguo Li, PhD, professor at South China Agricultural University. (SCAU) College of Horticulture and lead author of the study. “By sequencing and analyzing wild and cultivated lychee varieties, we were able to trace the origin and history of lychee domestication. We demonstrated that extremely early and late maturing cultivars were derived from domestication events. independent human rights in Yunnan and Hainan, respectively. ”

In addition, “we have identified a specific genetic variant, a deleted expanse of genetic material, which can be developed as a simple biological marker for the screening of lychee varieties with different flowering times, thus contributing significantly to future programs. selection, ”adds Rui Xia, PhD, a professor at the same college at SCAU and another senior research author.

“Like a puzzle, we piece together the story of what humans did with lychee,” says Victor Albert, PhD, evolutionary biologist at the University of Buffalo, also lead author of the study. “Here are the main stories told by our research: the origins of lychee, the idea that there were two separate domestications and the discovery of a genetic deletion that we believe causes different varieties to fruit and flower at different times. . “

The study will be published January 3 in Nature Genetics. It was led by SCAU in collaboration with a large international team from China, the United States, Singapore, France and Canada.

The main authors are Rui Xia, Jianguo Li and Houbin Chen from SCAU; Ray Ming of the University of Illinois at Urbana-Champaign; and Victor Albert from UB. The first authors are Guibing Hu, Junting Feng, Chengming Liu and Zhenxian Wu from SCAU; Xu Xiang from the Guangdong Academy of Agricultural Sciences; Jiabao Wang of the Chinese Academy of Tropical Agricultural Sciences; and Jarkko Salojärvi from Nanyang Technological University.

A beloved fruit, it has been domesticated more than once

To conduct the study, the scientists produced a high-quality “reference genome” for a popular lychee cultivar called “Feizixiao” and compared its DNA to that of other wild and farmed varieties. (All cultivars belong to the same species, Lychee chinensis).

Research shows that lychee, Lychee chinensis, was probably domesticated more than once: wild lychees originated in Yunnan in southwest China, spread to the east and south of Hainan Island, then were domesticated independently in each of these two places, suggests the analysis.

In Yunnan, people have started cultivating very early flowering varieties, and in Hainan, late flowering varieties which bear fruit later in the year. Eventually, the crossing between cultivars from these two regions led to hybrids, including varieties, like ‘Feizixiao’, which remain extremely popular today.

The exact timing of these events is uncertain. For example, the study suggests that a milestone, the evolutionary division between L. chinensis the populations of Yunnan and Hainan, which occurred before domestication, may have occurred around 18,000 years ago. But this is only an estimate; other solutions are possible. Yet the analysis offers a fascinating look at the evolutionary history of lychees and their connection to humans.

When will this lychee bloom? A simple genetic test could tell

The study not only adds new chapters to the history of lychee; it also provides an in-depth look at the flowering time, an extremely important characteristic in agriculture.

“Early maturing lychees compared to late maturing lychees came from different places and were domesticated independently,” says Albert, PhD, Empire Innovation Professor of Biological Sciences at UB College of Arts and Sciences. “This in itself is an interesting story, but we also wanted to know what causes these differences: why do these varieties fruit and flower at different times? “

By comparing the DNA of many lychee varieties, the team identified a genetic variant that could be used to create a simple test to identify early and late flowering lychee plants.

The variant is a deletion – a piece of missing DNA – that is found near two genes associated with flowering, and can help control the activity of one or both.

Yunnan cultivars that flower very early have the deletion, inheriting it from both parents. Late ripening Hainan varieties do not have any at all. And Feizixiao – a hybrid with almost equal amounts of DNA from each of the two regional populations – is “heterozygous” for the deletion, meaning it has only one copy inherited from a parent. This makes sense, as Feizixiao flowers early, but not very early.

“This is very useful for breeders. Because lychee is perishable, the flowering periods have been important in extending the season for which lychee is available in the markets,” explains Albert.

Lychee genome sequencing is just the start

The SCAU team has launched the lychee genome study as part of a larger project that hopes to significantly expand what we know about the DNA of important flowering plants within the same family, Sapindaceae.

Sapindaceae is a large family that includes many economically important plants, “says Xia.” So far only a few of them, including lychee, longan, rambutan, yellow horn and maple, have had their entire genome sequenced. “

“We, the SCAU Horticultural College, are working on a large collaborative sequencing project more Sapindaceae species native to China and of economic importance, such as rambutan, sapindus (honey) and balloon grapevine, aiming for broad and in-depth comparative genomic studies for Sapindaceae genomics, ”adds Xia. “The main research interests will be flowering, secondary metabolism leading to flavors and fragrances, flower and fruit development, among others. “