Researchers Sequence Genome of Lychee

An international team of scientists from the United States, China, Singapore, France and Canada has decoded the genome of the lychee (Litchi chinensis), an exotic tropical fruit with a distinct flavor. Their results will improve understanding of the lychee genome, accelerating genetic improvement of the fruit and its relatives in the family Sapindaceae (maple and horse chestnut).

The lychee (Litchi chinensis). Image credit: Xuan Duong.

The lychee (Litchi chinensis). Image credit: Xuan Duong.

Lychee is an important tropical fruit tree species worldwide, and a valuable fruit for which the edible portion is an aril. It is cultivated in over 20 countries, where it is an integral part of local economies.

Its desirable characteristics include outstanding nutritional profile, exotic flavor and an appealing fruit color, making it one of the most attractive tropical or subtropical fruits on the international market.

Lychee has been cultivated in southern China for millennia. The earliest record of lychee cultivation traces back to the second century BCE.

In the ancient Tang Dynasty, roughly 1,300-1,100 years ago, the emperor set up a courier service with fast horse relays to transport fresh lychee from southern China to the imperial court because of the prodigious flavor of this spoilable fruit.

Lychee trees have the longest productive lifespans among tropical and subtropical fruit trees. The oldest lychee tree, Songxiang, from Fujian, China, is over 1,250 years old, and is still fruiting today.

Lychee originated in broad, yet isolated and distant, regions of southern China, where numerous wild lychees exist in the Hainan and Yunnan rainforests, and hilly areas of western Guangdong and eastern Guangxi.

However, the exact center of origin and the history of lychee domestication remains unknown.

To address these questions and provide a genome-enabled breeding platform, South China Agricultural University’s Professor Jianguo Li and colleagues generated a high-quality reference genome of a popular lychee cultivar called Feizixiao.

“Lychee is an important tropical agricultural crop in the Sapindaceae 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,” Professor Li said.

“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.”

“Additionally, 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,” said Professor Rui Xia, also from the South China Agricultural University.

“Like a puzzle, we’re piecing together the history of what humans did with lychee,” said Dr. Victor Albert, an evolutionary biologist at the University at Buffalo.

“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 shows that the lychee tree was likely domesticated more than once: wild lychees originated in Yunnan in southwestern China, spread east and south to Hainan Island, and then were domesticated independently in each of these two locations.

In Yunnan, people began cultivating very early-flowering varieties, and in Hainan, late-blooming varieties that bear fruit later in the year.

Eventually, interbreeding between cultivars from these two regions led to hybrids, including varieties, like Feizixiao, that remain extremely popular today.

The exact timing of these events is uncertain. For instance, the study suggests that one milestone, the evolutionary split between lychee populations in Yunnan and Hainan, which took place before domestication, could have occurred around 18,000 years ago.

But that is only an estimate; other solutions are possible. Still, the analysis provides a fascinating look at the evolutionary history of lychees and their link with humans.

“Sapindaceae is a large family that includes many economically important plants,” Professor Xia said.

“So far, only a few of them, including lychee, longan, rambutan, yellowhorn and maple, have had their full genomes sequenced.”

The findings were published in the journal Nature Genetics.

_____

G. Hu et al. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nat Genet, published online January 3, 2022; doi: 10.1038/s41588-021-00971-3

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