Improvement of genomics-assisted selection tools, gain of users and uses

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Texas A&M AgriLife Research rose breeder and geneticist David Byrne is director of a game-changing grant-funded project for polyploid plant breeding.


Sam Craft/Texas A&M AgriLife Communications

Thanks to the development and adoption of specialized computer tools, recent years have seen major advances in the breeding of “polyploid plants” – plants with more than two sets of chromosomes in their cells.

Polyploid specialty crops, which include roses, many lawns, and food crops such as blackberries, potatoes, and sweet potatoes, are worth more than $9 billion annually in the United States and several times that value in the world.

David Byrne, a Texas A&M AgriLife Research rose breeder and geneticist who is also a professor in the Department of Horticultural Sciences, is the director of a four-year grant-funded project to create and improve polyploid genetic analysis software. .

Byrne and his colleague Oscar Riera-Lizarazu, a plant geneticist at AgriLife Research and an associate professor of horticultural sciences, received $4.3 million from the National Institute of Food and Agriculture at the U.S. Department of agriculture in 2020 to develop tools for genomics-assisted selection in polyploids.

Polyploid tools are a game-changer for plant breeders

One of the objectives of the project is to develop computational tools for quantitative trait analysis, genomic selection and haplotype analysis in polyploid crops. Another objective is to train breeders and geneticists to use the tools in public breeding programs for a wide range of ornamental and food crops.

This USDA-NIFA-Specialty Crop Research Initiative grant project includes national and international collaborators from academia from Arkansas, Maine, New York, North Carolina, Oregon, Pennsylvania, Texas , Washington and Wisconsin as well as the Netherlands and New Zealand.

The team has hosted conferences over the past two years aimed at introducing the tools to new users, measuring the usefulness of the tools, and guiding their evolution.

“We had 300 people in 2021 and were only expecting about 75,” Byrne said. “There were 300 more this year, and more are expected in future programs. This is a fairly specialized but very important public given the diversity of food and ornamental plants with which these professionals work. What’s exciting is how many new faces we see every time.

Excitement, adoption among participants

Byrne said the conferences have attracted a wide range of industry experts, including plant breeders, molecular and computational geneticists, plant pathologists and physiologists, and entomologists.

About 30% of the participants work with fruit plants, 28% with roots or tubers, 16% with grasses and the remaining 26% with ornamental plants, vegetables or cereals.

Plants that will be affected by polyploid genetic advances include forage grasses and turfs, fruits such as kiwi, strawberries and blackberries, ornamentals ranging from chrysanthemums to roses, and roots and tubers such as potatoes and Sweet potatoes.

One exciting thing beyond the diversity of attendees’ fields, Byrne said, is that most attendees were in their 20s and 30s, with nearly equal numbers of men and women. Most of the trainees also participated in public plant breeding programs or were students. This group will shape the breeding programs of the future, he said.

Byrne added that the project is truly an international endeavor with about half of the conference attendees coming from organizations outside of the United States.

In 2021, 45% of attendees were international and the remaining 55% were from North America, he said. But this year, 55% of attendees came from outside North America, with Europe, Africa and South America coming out on top.

Byrne said the breakout sessions and subsequent feedback on the tools at conferences has been invaluable to advancing the technology. This ongoing development is also facilitated by inviting software users to attend the annual workshop and present their research.

“There’s a lot of brainstorming and networking going on, and bringing users together,” Byrne said. “The interactions have led to collaborations on similar projects and the use of the tools in actual research.”

Practicality and versatility

The overall project aims to coordinate research around the development of computer tools, increase training and improve ease of use, Byrne said. The Polyploid Breeding Community Resource website serves as a repository for computational toolsets, genomic information, training datasets, and other materials. An associated YouTube channel contains recordings of all training presentations given at the workshops.

Despite the importance of polyploid cultures, major barriers to the use of genomic tools in the past have included a shortage of appropriate software and technical expertise. Before the development of polyploid tools, genomic information was readily used only for diploid crops – plants with only two sets of chromosomes like corn, rice, soybeans and tomatoes.

Byrne said these computational tools enable the use of genomic information to accelerate the rate of genetic gain in a wide range of polyploid breeding programs, which will lead to faster development of higher quality, more productive, and higher quality cultivars. resistant.

The software maps polyploid genes, essentially locating phenotypic traits of interest and linking these traits to associated DNA. The software works with a range of polyploid crops: tetraploids, such as roses, potatoes and blackberries; hexaploids, such as sweet potatoes; octoploids, such as strawberries; decaploids, such as sugar cane; and more.

The software also works well with diploids, and the researchers modify it to deal with odd ploidy levels such as triploids, which include bananas, hops and seedless watermelons.

There is growing interest in the range of apps, which has spurred new collaborations and enhancements, Byrne said.

“These breeders and programs were all doing similar things but separately,” he said. “There is benefit in standardizing information and sharing ideas and methods, and there is enthusiasm in solving problems.”

Expand technology, training, application

Byrne said the project expands the training and accessibility of the tools and expands their application in the field of plant breeding. The software developed is open-source, so collaborators can tinker with it and improve it.

Reducing the software’s computational requirements is a challenge the team hopes to overcome, Byrne said.

There are also plans to make the tools more visual, allowing users to see markers in a visual context and allowing for gene sequence overlays. For example, contextual and visualized overlay would allow users to see where genes are located on chromosomes and identify connections to traits of interest.

Byrne said he’s pleased with the advancements in technology, and he’s delighted that literature continues to be released on the software and that more people are using it more often – clear signs that the app and user interface are going in the right direction.

“The enthusiasm around the tools is far beyond my expectations,” Byrne said. “It’s exciting to see the excitement surrounding it.”

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