Genome sequencing of honey crispy apples promises to breed better apples

A team of researchers recently sequenced
the genome of a honey crispy apple.
Honey crisp apples are a popular and economically important variety, and their genome sequencing is a boon
for scientists and breeders.

The results were recently published in
the journal Gigabyte.
The use of advanced techniques to sequence genomes provides a valuable resource for understanding the genetic basis of important traits of apple and other fruit tree species, which can be used to enhance breeding efforts
.

The U.
S.
apple industry is worth $23 billion a year, and Honeycrisp is one of the most valuable varieties, costing growers about twice
as much per pound as Fuji.
Due to its crispy and sweet taste, cold tolerance and resistance to apple rust, breeders have adopted them as parents for 9 new varieties on the market
.

At the same time, the cultivation of honey brittle is also challenging
.

"Despite its many excellent traits, it is one of the most difficult apple varieties to grow in orchards; It faces some physiological and post-harvest problems," said Awais Khan, an associate professor in the College of Integrative Plant Sciences at Cornell University's College of Agriculture and Technology, who is the paper's first author and co-corresponding author
.

First, Khan, the Crispy Fruit Tree struggles to get enough nutrients on its own and requires a specific nutrient management plan to achieve good yields and health
.
Without such management, these fruit trees often experience "leaf yellowing", which is due to carbohydrate and nutrient imbalances, yellowing and curling
of leaves.

Honey crispy apples are also prone to diseases such as bitter pox due to calcium imbalance and bitter rot caused by fungal infections
.
These problems are fundamentally controlled by genes, but improper handling and post-harvest storage can make the problem worse
.

"If we don't understand the genome and genes of crispy apples, we can't breed to specifically select favorable traits and screen out unfavorable traits," Khan said
.

Advances in gene sequencing technology have made it possible to sequence, assemble, and publish
the honey crispy apple genome in a fraction of the time.
In 2010, the genome of the Golden Crown apple was sequenced
for the first time.
Overall, the apple genome is complex, large, and heterozygous, meaning there are multiple versions
of a particular gene.

Considering that there are also many repetitive sequences in the Apple genome, the researchers used a combination of sequencing technologies to sequence it, including PacBio HiFi sequencing, Omni-C (for chromosome fixation) and the Illumina sequencing platform
.

"We can sequence large pieces of DNA serially, so we don't have big computational biology or bioinformatics challenges in assembling and finding overlapping sequences," Khan said
.

Long-read sequencing also helped them tease out the diploid genome of apples; Like humans, apples have two sets of chromosomes, one from both
parents.
The new technique is able to sequence two sets of chromosomes, which in the future will hopefully distinguish the specific genetic contribution
of each parent.

By using these advanced methods, the honey crispy apple genome covers 97% of the protein-coding genes
.
By comparison, the 2010 Golden Crown apple genome covered only 68 percent of the genes
.

Original text search

Awais Khan, Sarah B.
Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas, A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica), Gigabyte, 2022 https://doi.
org/10.
46471/gigabyte.
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