Awais Khan at Cornell Orchards. Credit: Cornell University.
In 2010, the cost to sequence one’s personal genome was about $20,000 using the market-leading Illumina technology. By 2014, the cost was down to $1,000. By 2017, the cost was only $1,000.
This rapid development of DNA sequencing technology impacted not only human health and disease research, but many other areas of R&D as well, which now possessed the means to generate and study previously unavailable data.
For example, food scientists first sequenced the apple genome—the Golden Delicious—in 2010. At that time, the technology could read only short fragments of DNA at a time, about 150 letters. Scientists would then overlap sequences of about 50 letters and—like a puzzle—would use computational programs and algorithms to match the end of one reading with the start of another. This allowed them to piece together longer strings of DNA to identify entire genes and eventually the genome. But, the inherent shortcoming meant the method was vulnerable to errors. There are a lot of repeated sequences in the apple genome—and the repeated elements in the patchwork method confused the process.
Conversely, when researchers from Cornell University published the full genome of the Honeycrisp apple last month in the journal Gigabyte, they didn’t have quite the same problem. In fact, when they combined current sequencing technologies PacBio HiFi, Omni-C and Illumina, they were able to easily and quickly translate long reads of genetic sequences.
“We could sequence the whole larger fragment of the DNA sequence continuously, so we didn’t have these big challenges of computational biology or bioinformatics to assemble and find the overlapping sequences,” said Awais Khan, associate professor in the School of Integrative Plant Science at Cornell AgriTech and first author of the paper.
According to the study, the long-read sequencing helped the research team tease apart the apple’s diploid genome. Like humans, apples have two sets of chromosomes, one from each parent. The new technologies allowed the researchers to sequence two single sets of chromosomes, which in future work could be used to differentiate between specific genetic contributions of each parent.
Ultimately, the Honeycrisp genome covered 97% of all the protein-coding genes. By comparison, the 2010 Golden Delicious genome assembly only covered 68% of the genes.
The U.S. apple industry is worth $23 billion annually, and Honeycrisp is its most valuable cultivar, bringing growers roughly twice the value per pound than the second-most valuable cultivar, Fuji.
The sequencing provides a valuable resource for understanding the genetic basis of important traits in apples and other tree fruit species. It’s especially important for Honeycrisp, which boasts many favorable traits, including a resistance to apple scab fungal disease.
At the same time, Khan say it’s one of the most difficult apple cultivars to grow as it is susceptible to other disorders like bitter pit, due to calcium imbalances, and bitter rot, a fungal infection. Additionally, Honeycrisp trees have difficulty getting enough nutrients on their own and require a specific nutrient management program for good yields and health. Without precise management, the trees commonly develop “zonal leaf chlorosis,” where leaves yellow and curl due to carbohydrate and nutrient imbalances.
“If we don’t know the genome and the genes in Honeycrisp, then we cannot specifically target and select for favorable traits and select out unfavorable traits through breeding,” said Khan.
Even without the full genome available, breeders have already used Honeycrisp as a parent in nine cultivars on the market, including the Cornell-developed Snapdragon. Now, the researchers say the new data—which is open-access—will enable development of molecular markers linked to disease, pest resistance, abiotic stress tolerance and adaptation, as well as horticulturally relevant harvest and postharvest fruit quality traits for use in apple breeding programs.
“Ultimately, the addition of high-quality genomic resources for Honeycrisp can lead to enhanced orchard and supply chain management for many other apple cultivars, promoting future sustainability of the pome fruit industry,” conclude the researchers.