Honeycrisp’s genome will help scientists grow better apples

(2022). DOI: 10.1101/2022.08.24.505160″ width=”800″ height=”530″/>

Physiology and physiological disorders of the “Honeycrisp” apple. (A) Healthy ‘Honeycrisp’ apples. (B) ‘Honeycrisp’ apples with leaf zonal chlorosis symptoms. ‘Honeycrisp’ apples with fungal disease symptoms (C) bitter rot pathogen complex (Colletotrichum gloeosporiodes and C. acutatum) and (D) black rot pathogen (Botryosphaeria obtuse). ‘Honeycrisp’ apples with postharvest storage disorders (E) bitter pit, (F) soft burn, and (G) wet decay. credit: (2022). DOI: 10.1101/2022.08.24.505160

A team of researchers at Cornell University has sequenced the genome of the Honeycrisp apple, a boon for scientists and breeders working with this popular and economically important variety.

Sequenced with state-of-the-art technology, the genome – available on an open-source basis for anyone to access – provides a valuable resource for understanding the genetic basis of important traits in apples and other tree fruit species that can be used to improve breeding efforts , according to the document.

U.S. apple production is worth $23 billion a year, and Honeycrisp is its most valuable variety, bringing growers roughly twice the value per pound of the second-most valuable Fuji variety. Thanks to its favorable characteristics, including crispness, flavor, cold hardiness and resistance to apple scab, breeders have used Honeycrisp as a parent in nine new cultivars on the market, including the Cornell University-developed Snapdragon.

At the same time, growing Honeycrisp can be challenging.

“Although it has many positive traits, it is one of the most difficult apple varieties to grow in an orchard production system; it suffers from a lot of physiological and postharvest problems,” said Awais Khan, associate professor in the School of Integrative Plant Science at Cornell AgriTech and first and co-corresponding author of the paper, “A Phased, Chromosome-Scale Genome of Honeycrisp Apple,” published last month in the magazine gigabyte.

For starters, Honeycrisp trees have a hard time getting enough nutrients on their own and require a specific nutrient management program for good yields and health, Hahn said. Without such management, trees commonly develop “zonal leaf chlorosis,” in which leaves turn yellow and curl due to an imbalance of carbohydrates and nutrients.

Honeycrisp apples are also susceptible to disorders such as bitter pit, due to a calcium imbalance, and bitter rot, a fungal infection. Such problems are fundamentally genetically controlled, although improper post-harvest handling and storage can exacerbate them.

“If we don’t know the genome and the genes in Honeycrisp, then we can’t specifically target and select for favorable traits and select for unfavorable traits through breeding,” Hahn said.

Advances in genetic sequencing technology made it possible to sequence, assemble and publish the Honeycrisp genome in a short time. Overall, the apple genome, first sequenced with the Golden Delicious cultivar in 2010, is complex, large and heterozygous, meaning that there are many versions of specific genes.

The apple genome also has many repetitive sequences. In 2010, when the first apple genome was published, technology could only read short fragments of DNA at a time, say 150 letters. Scientists would then overlap sequences of perhaps 50 letters and, like a puzzle, use computing programs and algorithms to match the end of one reading with the beginning of another. This allowed them to assemble longer strings of DNA to identify entire genes and eventually the genome. But one problem with this method is that repeating elements can mess up the process.

In this study, the researchers used a combination of current sequencing technologies—called PacBio HiFi, Omni-C, and Illumina—that translate long reads of genetic sequences.

“We can continuously sequence the entire larger fragment of the DNA sequence, so we don’t have these big challenges of computational biology or bioinformatics to assemble and find the overlapping sequences,” Hahn said.

Long-read sequencing also helped them crack the apple’s diploid genome; like humans, apples have two sets of chromosomes, one from each parent. New technologies allowed the researchers to sequence two single sets of chromosomes, which in future work could be used to distinguish between specific genetic contributions of each parent.

Using these advanced methods, the Honeycrisp genome covers 97% of all protein-coding genes. In comparison, the 2010 Golden Delicious genome assembly covered only 68% of the genes.

This research was a collaboration between Cornell University, Alex Harkes of the HudsonAlpha Biotechnology Institute and Auburn University, and Loren Honaas of the United States Department of Agriculture’s Agricultural Research Service (USDA-ARS) Tree Fruit Research Laboratory in Wenatchee, Washington.


Apple trees bear more fruit when they are surrounded by good neighbors


More info:
Awais Khan et al, A stepwise, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica), gigabyte (2022). DOI: 10.46471/gigabyte.69

Courtesy of Cornell University

Quote: Honeycrisp genome will help scientists grow better apples (2022, October 26) retrieved October 26, 2022 from https://phys.org/news/2022-10-honeycrisp-genome-scientists- apples.html

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