Silk road contains genomic resources for improving apples

Date:
November 2, 2020
Source:
Boyce Thompson Institute
Summary:
The fabled Silk Road is responsible for one of our favorite and
most valuable fruits: the domesticated apple. Researchers have now
assembled complete reference genomes and pan-genomes for apple and
its two main wild progenitors, providing detailed genetic insights
into apple domestication and important fruit traits that could help
plant breeders improve the crop's flavor, texture, and resistance
to stress and disease.



FULL STORY ==========================================================================
The fabled Silk Road -- the 4,000-mile stretch between China and Western
Europe where trade flourished from the second century B.C. to the 14th
century A.D. - - is responsible for one of our favorite and most valuable fruits: the domesticated apple (Malus domestica).


========================================================================== Snack-packing travelers would pick apples at one spot, eat them and
toss their cores many miles away. The seeds grew into trees in their
new locations, cross- bred with the wild species, and created more than
7,000 varieties of apples that exist today.

Hybridizations with wild species have made the apple genome very complex
and difficult to study. A global team of multi-disciplinary researchers
-- co-led by Zhangjun Fei, faculty member at Boyce Thompson Institute
(BTI), and Gan-Yuan Zhong, scientist with the USDA-Agricultural Research Service (ARS) in Geneva, New York -- tackled this problem by applying cutting-edge sequencing technologies and bioinformatics algorithms to
assemble complete sets of both chromosomes for the domesticated apple
and its two main wild progenitors.

The researchers discovered that the apple's unique domestication
history has led to untapped sources of genes that could be used for crop improvement, such as improving size, flavor, sweetness and texture.

"Plant breeders could use this detailed information to improve upon
traits that matter most to consumers, which today is primarily flavor,"
says Fei, also an adjunct associate professor in Cornell University's
School of Integrative Plant Science (SIPS).

"Perhaps more importantly," he added, "the information will help
breeders produce apples that are more resistant to stress and disease."
The research is described in a paper published in Nature Genetics on
November 2, with authors from BTI, Cornell University, Cornell AgriTech,
the U.S.

Department of Agriculture (USDA) and Shandong Academy of Agricultural
Sciences.



==========================================================================
From the Silk Road to Geneva, N.Y.

According to Fei, the new study was the outgrowth of an earlier
collaboration, published in Nature Communications in 2017, which traced
the history of apple domestication and evolution along the Silk Road.

Follow-up discussions among Fei, Zhong and other colleagues at Cornell, inspired them to build better and new apple reference genomes by applying
new sequencing and assembly technologies to material in USDA's Geneva
Clonal Repository. The repository, which is housed at Cornell AgriTech,
holds the largest collection of apple accessions in the world. Many of
these accessions can be traced back to the Silk Road.

In the current work, the researchers sequenced, assembled and compared
the full reference genomes for three species: Gala, a top commercial
cultivar of M.

domestica; and apple's two main wild progenitors, the European crabapple
(M.

sylvestris) and the central Asian wild apple (M. sieversii), which
together account for about 90% of the domesticated apple's genome.

The results provide apple breeders with detailed genomic roadmaps that
could help them build a better apple.



==========================================================================
"We wanted to develop new genomes, especially the wild progenitors,
because of the tremendous impact they could have on understanding
apple's genetic diversity and identifying useful traits for breeding
new cultivars," said Zhong, who is also an adjunct associate professor
in SIPS.

By comparing the three genomes, the researchers were able to identify
which progenitor species contributed the genes responsible for many
traits in the domesticated apple. For example, the team found that the
gene giving apple its crunchy texture is located near the gene that
makes it susceptible to blue mold.

"Now that we know exactly where those two genome regions are," Fei said, "breeders could figure out a way to keep the texture gene and breed out or
edit out the blue mold gene to produce a more disease-resistant cultivar." Discovering what's missing The team also assembled pan-genomes for the
three species. A pan-genome captures all of the genetic information
in a species, unlike a reference genome that captures one individual
organism. Pan-genomes are especially important for a very diverse species
like apple.

The team identified about 50,000 genes in the pan-genome of the
domesticated apple, including about 2,000 that were not present
in previously published reference genomes for apple species. "These
'missing genes' turn out to be really important, because many of them
determine the traits of greatest interest to apple breeders," Fei said.

Using RNA extracted from different stages of Gala fruits, they also
identified genes linked to texture, aroma and other fruit characteristics
that were preferentially expressed between the two copies of the genes.

"That provides us and breeders with an even deeper understanding of
the genetic diversity underlying a particular trait," Zhong said. "The
findings will help our group better manage and curate more than 6,000
apple accessions in the USDA Geneva Clonal Repository," Zhong adds, "as
well as enable us to provide critical genetic and genomic information associated with the accessions to breeders and other researchers."
The team is planning on sequencing other wild apple species, which Fei
says may have valuable traits that could improve stress-resistance and resilience in the domesticated apple.

The research was supported by a Non-Assistance Cooperative Agreement
between USDA-ARS and BTI (No. 58-8060-5-015), and by grants from the
U.S. National Science Foundation (IOS-1855585 and IOS-1339287).


========================================================================== Story Source: Materials provided by Boyce_Thompson_Institute. Original
written by Aaron J.

Bouchie. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Xuepeng Sun, Chen Jiao, Heidi Schwaninger, C. Thomas Chao, Yumin Ma,
Naibin Duan, Awais Khan, Seunghyun Ban, Kenong Xu, Lailiang Cheng,
Gan- Yuan Zhong & Zhangjun Fei. Phased diploid genome assemblies
and pan- genomes provide insights into the genetic history of
apple domestication.

Nature Genetics, 2020 DOI: 10.1038/s41588-020-00723-9 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/11/201102120046.htm

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