Lychee genome tells a colorful story about a colorful tropical fruit


Date:
January 3, 2022
Source:
University at Buffalo
Summary:
Radiant and flavorful, lychees were so beloved that they were
domesticated not just once in ancient times, but independently in
two different regions of China, a study finds.



FULL STORY ========================================================================== They're prickly on the outside, sweet on the inside, and beloved for
their iconic pink shells and pearly, fragrant fruit. In the U.S., you
might encounter them as a flavorful ingredient in bubble tea, ice cream
or a cocktail. You can also peel them and eat them fresh.


========================================================================== Lychees have been grown in China since ancient times, with records of cultivation dating back about 2,000 years. Fresh lychees were an object
of such desire that in the Tang Dynasty, one emperor set up a dedicated
horse relay to deliver the fruits to the imperial court from harvests
made far to the south.

Now, scientists have used genomics to peer even deeper into the lychee's history. And in the process, they've uncovered insights that could help
shape the species' future, too.

"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," says Jianguo Li, PhD, professor in
the South China Agricultural University (SCAU) College of Horticulture
and a senior author of the study. "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," adds Rui Xia, PhD, professor in the same
college at SCAU and another senior author of the research.

"Like a puzzle, we're piecing together the history of what humans did
with lychee," says Victor Albert, PhD, University at Buffalo evolutionary biologist, also a senior author of the study. "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 study will be published on Jan. 3 in Nature Genetics. It was led
by SCAU in collaboration with a large international team from China,
the U.S., Singapore, France and Canada.



========================================================================== Senior authors 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.

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 Saloja"rvi from the Nanyang Technological University.

A fruit so beloved, it was domesticated more than once To conduct the
study, 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 the cultivars belong to the same species, Litchi chinensis).

The research shows that the lychee tree, Litchi chinensis, 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, the
analysis suggests.

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 L. chinensis 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.

When will this lychee tree flower? A simple genetic test could tell The
study not only adds new chapters to the history of the lychee; it also
provides an in-depth look at flowering time, a hugely important trait
in agriculture.

"Early-maturing lychees versus late-maturing lychees came from different
places and were domesticated independently," says Albert, PhD, Empire Innovation Professor of Biological Sciences in the UB College of Arts
and Sciences. "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?" By comparing the DNA of many
lychee varieties, the team identified a genetic variant that could be
used to create a simple test for identifying early- and late-blooming
lychee plants.

The variant is a deletion -- a chunk of missing DNA -- that lies near
two genes associated with flowering, and may help to control the activity
of one or both of them.

Yunnan cultivars that bloom very early have the deletion, inheriting it
from both parents. Hainan varieties that mature late do not have it at
all. And Feizixiao -- a hybrid with nearly equal amounts of DNA from each
of the two regional populations -- is "heterozygous" for the deletion,
meaning that it has only one copy inherited from one parent. This makes
sense, as Feizixiao flowers early, but not extremely early.

"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," Albert says.

Sequencing the lychee genome is only the start The team at SCAU initiated
the lychee genome study as part of a bigger project that hopes to greatly 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," Xia says. "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," Xia adds. "The main
research interests will be flowering, secondary metabolism leading
to flavors and fragrances, flower and fruit development, among others." ========================================================================== Story Source: Materials provided by University_at_Buffalo. Original
written by Charlotte Hsu.

Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Guibing Hu, Junting Feng, Xu Xiang, Jiabao Wang, Jarkko Saloja"rvi,
Chengming Liu, Zhenxian Wu, Jisen Zhang, Xinming Liang, Zide Jiang,
Wei Liu, Liangxi Ou, Jiawei Li, Guangyi Fan, Yingxiao Mai, Chengjie
Chen, Xingtan Zhang, Jiakun Zheng, Yanqing Zhang, Hongxiang Peng,
Lixian Yao, Ching Man Wai, Xinping Luo, Jiaxin Fu, Haibao Tang,
Tianying Lan, Biao Lai, Jinhua Sun, Yongzan Wei, Huanling Li,
Jiezhen Chen, Xuming Huang, Qian Yan, Xin Liu, Leah K. McHale,
William Rolling, Romain Guyot, David Sankoff, Chunfang Zheng,
Victor A. Albert, Ray Ming, Houbin Chen, Rui Xia, Jianguo Li. Two
divergent haplotypes from a highly heterozygous lychee genome
suggest independent domestication events for early and late-maturing
cultivars. Nature Genetics, 2022; DOI: 10.1038/s41588-021- 00971-3 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/01/220103121718.htm
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