Lychee is a sweet and succulent tropical fruit that grows within prickly pink shells that can be peeled without much effort, much like a boiled egg, to reveal the translucent pearly white kernel within. Generally eaten fresh off the branches in countries where they grow such as China, Thailand, India—in the United States, you’re more likely to come across lychee in your flavored tea, ice cream, or cocktail.
“The main issue of lychee cultivation is its short maturation period, mostly May to July. The lychee fruit is really hard to store post-harvest. So, all the fresh harvested fruits need to be consumed within two months. This is a big shock to the fresh market, and affects the profit of farmers greatly, as high yield cannot guarantee good price—normally the reverse,” said Rui Xia, PhD, professor at the College of Horticulture in South China Agricultural University (SCAU) in Guangzhou, China. “So, it is really important to breed new cultivars to extend the fruit maturation time, especially those super-early or super-later varieties.”
An article published in the journal Nature Genetics on January 3 reports on the genomic analysis of this exotic fruit (“Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars”). The genome study revealed that the fruit was so cherished in ancient China that it was domesticated not once but twice. The study also provides insights on the evolutionary history of the fruit and its link with humans that may help predict flowering times of popular varieties, shaping the economic impact of this important crop.
“We found a really good marker which can be used for breeding. Using this molecular marker, we can quickly assess the fruit maturation time when the plants are very small, without waiting for the tree to grow to have flower and fruit,” said Xia, who is also a co-senior author of the study.
The study, led by scientists at SCAU and the University at Buffalo, showed that the highly heterozygous lychee genome represents two divergent lineages that suggest early- and late-maturing varieties of the fruit originated from independent domestication events.
“Lychee is an important tropical agricultural crop in the Sapindaceae (maple and horse chestnut) family. 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,” said Jianguo Li, PhD, professor at the SCAU College of Horticulture and a senior author of the study.
The earliest record of lychee cultivation can be traced back to Southern China in the second century BC. The oldest lychee tree, in Fujian, China, is over 1,250 years old, and is still bearing fruit today!
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.”
Xia added, “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.”
Victor Albert, PhD, professor of evolutionary biology at the University at Buffalo and another co-senior author of the paper said, “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.”
Any genomic study needs a reference sequence. So, the collaborative team first focused on producing a high-quality reference genome of Litchi chinensis from a popular variety of cultivated lychee called “Feizixiao.” They then compared this reference sequence to that of other wild and cultivated varieties of this species.
The results showed wild lychee trees originated in Yunnan in southwestern China and spread east and south to Hainan Island and were domesticated independently in the two regions. The findings suggest that the evolutionary split between Litchi chinensis populations in Yunnan and Hainan could have occurred around 18,000 years ago, although this is not certain.
The results showed early-flowering varieties were farmed in Yunnan whereas late-flowering varieties were grown in Hainan. Later, interbreeding between the two varieties formed hybrids, including varieties like Feizixiao that are popular today.
“Breeding lychees for year-round fruiting is an important commercial goal. To make genetic-assisted breeding practical, a genome sequence is absolutely required as well as detailed genomic research on multiple varieties with different fruiting times and other traits,” said Albert. “Hence, in addition to our reference genome of Feizixiao, we sequenced tens of additional varieties to discover that lychees were in fact domesticated twice, in Yunnan and Haianan respectively, and that Feizixiao is almost a primary, F1, hybrid of extremely early and late flowering/fruiting varieties.”
Albert said, in addition to the interesting story of their origin, the team wanted to understand the genetics causing different varieties of lychee to fruit and flower at different times.
“Using genome wide association studies and other approaches, we uncovered that variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes—involved in flowering time regulation in model plant systems such as Arabidopsis—probably regulate fruit maturation differences among lychee cultivars,” said Albert.
Yunnan varieties of lychee that bloom early inherit this 3.7kb deletion from both parents whereas Hainan varieties that flower late do not have it. The contemporary Feizixiao hybrid with nearly equal genetic contributions from Yunnan and Hainan varieties bears only one copy of the deletion (heterozygous) inherited from its Yunnan ancestry. As a result of its heterozygous state, Feizixiao varieties flower early, but not as early as varieties where both copies of the chromosome bear the deletion (homozygous).
The ability to predict flowering times has obvious agricultural and economic advantages. The team next used the genetic insight to create a simple genetic test to identify early- and late-blooming trees.
“We developed a simple PCR-based protocol to screen for the variable 3.7kb deletion linked to lychee flowering/fruiting time. This way, when making crosses, breeders can readily screen progeny even at embryonic stages to ascertain whether a seedling should be early or late maturing, permitting this knowledge to be obtained long before the first flowering/fruiting of a given offspring tree,” said Albert. “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.”
The authors also reported on another gene cluster (VRN1) present in all flowering plants that bear two seed leaves upon germination (eudicots) but is expanded specifically in Sapindeceae. The conservation of the gene cluster suggests a functional role and its expansion in Sapindeceae may be related to the adaptation in members of the family.
The current study is part of a bigger project that aims to better understand the genetics of important flowering plants in the Sapindaceae family. “Sapindaceae is a large family that includes many economically important plants,” Xia said. “So far, only a few of them, including lychee, longan, rambutan, yellowhorn, and maple, have had their full genomes sequenced.”
Xia added that the team at SCAU is 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.”
The project aims at extensive comparative genomics of the Sapindaceae family to better understand flowering and metabolic pathways important in the development of flavors, fragrances, and fruits.