Researchers use genomics to dig deeper into lychee’s history

Lychees, prickly on the exterior but sweet inside are loved for their iconic pink shells and pearly, fragrance. In the United States Lychees are majorly seen as a flavorful ingredient in ice cream, bubble tea, or a cocktail. They can also be peeled and consumed fresh.


Image Credit: Thanphitcha Thana/

Lychees were also cultivated in China since ancient times. There are records of cultivation that date back around 2,000 years. The fresh lychees were desired heavily—an emperor from the Tang Dynasty set up a horse relay to supply the fruits to the imperial court from harvests made far to the south.

Recently researchers employed genomics to obtain a deeper insight into lychee’s history and they revealed insights that might also help shape the species’ future.

Lychee is an important tropical agricultural crop in the Sapindaceae (maple and horse chestnut) family, and it is one of the most economically significant fruit crops grown in eastern Asia, especially so to the yearly income of farmers in southern China.”

Jianguo Li PhD, Study Senior Author and Professor, College of Horticulture, South China Agricultural University

Jianguo Li adds, “By sequencing and analyzing wild and cultivated lychee varieties, we were able to trace the origin and domestication history of lychee. We demonstrated that extremely early- and late-maturing cultivars were derived from independent human domestication events in Yunnan and Hainan, respectively.”

We identified a specific genetic variant, a deleted stretch of genetic material, that can be developed as a simple biological marker for screening of lychee varieties with different flowering times, contributing importantly to future breeding programs.”

Rui Xia PhD, Study Senior Author and Professor, South China Agricultural University

Victor Albert PhD, also a senior author of the study and University at Buffalo evolutionary biologist states, “Like a puzzle, we’re piecing together the history of what humans did with lychee. These are the main stories our research tells: The origins of lychee, the idea that there were two separate domestications, and the discovery of a genetic deletion that we think causes different varieties to fruit and flower at different times.”

The research was headed by SCAU in association with a large international group from China, Singapore, the United States, France, and Canada. The study was published on January 3rd, 2022, in the Nature Genetics journal.

Senior authors of the study are Rui Xia, Jianguo Li, and Houbin Chen from SCAU; Ray Ming from 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 from the Chinese Academy of Tropical Agricultural Sciences; and Jarkko Salojärvi from the Nanyang Technological University.

A fruit so beloved, it was domesticated more than once

The researchers developed a high-quality “reference genome” for a well-known lychee cultivar known as “Feizixiao”, and matched its DNA to other farmed and wild varieties (The cultivars were from the same species, Litchi chinensis).

The study revealed that the lychee tree, Litchi chinensis, was possibly domesticated more than once. The investigation revealed that wild lychees originated in Yunnan in southwestern China, and spread east and south to Hainan Island. They were then domesticated independently in each of these two locations.

People in Yunnan cultivated very early-flowering varieties while people in Hainan cultivated late-blooming varieties that bear fruit later in the year. In due course, interbreeding between cultivars from these two regions resulted in hybrids, including varieties, such as “Feizixiao”, that are widely popular today.

However, uncertainty prevailed regarding the timing of these events. For example, the research suggests that a major milestone—the evolutionary split between L. chinensis populations in Hainan and Yunnan—which occurred before domestication, could have taken place around 18,000 years ago.

However, this is just an estimate; there might also be other possible solutions. Yet, the study offers an appealing look at the evolutionary history of lychees and their association with humans.

When will this lychee tree flower? A simple genetic test could tell

The research along with providing new insights on the history of the lychee also offers a deeper understanding of the flowering time, a major trait in agriculture.

Early-maturing lychees versus late-maturing lychees came from different places and were domesticated independently. This, by 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?”

Albert PhD, Empire Innovation Professor, Biological Sciences, College of Arts and Sciences, University at Buffalo

The researchers compared the DNA of numerous lychee varieties and recognized a genetic variant that can be employed to generate an easy test for the identification of early- and late-blooming lychee plants.

The variant is a deletion—a piece of missing DNA—that is seen close to the two genes linked to flowering and might aid regulate the activity of one or both of them.

Yunnan cultivars blooming very early contain the deletion which they inherited from both parents. However, Hainan varieties that mature late do not possess it. Feizixiao—a hybrid possessing nearly equal amounts of DNA from the two regional populations—is “heterozygous” for the deletion. This means that it possesses only a single copy inherited from one parent. Notably, Feizixiao flowers early, however not extremely early, evidencing the observation.

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

Sequencing the lychee genome is only the start

The group at SCAU started the lychee genome research as part of a bigger project that is anticipated to significantly expand the understanding of the DNA of important flowering plants belonging to the same family, Sapindaceae.

Xia adds, “Sapindaceae is a large family that includes many economically important plants. So far, only a few of them, including lychee, longan, rambutan, yellowhorn, and maple, have had their full genomes sequenced.”

“We, the College of Horticulture at SCAU, are working on a large collaborative project of sequencing more Sapindaceae species native to China and of economic importance, such as rambutan, sapindus (soapberries), and balloon vine, aiming at broad and thorough comparative genomics investigations for Sapindaceae genomics,” states Xia.

The main research interests will be flowering, secondary metabolism leading to flavors and fragrances, flower and fruit development, among others,” concludes Xia.

Journal reference:

Hu, G., et al., (2022) Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nature Genetics.


The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of AZoLifeSciences.
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