Barley, switchgrass and millet
INCORPORATING PANGENOMICS INTO CROP BREEDING PROGRAMS HudsonAlpha Faculty Investigator Josh Clevenger, PhD , is helping crop and animal breeding programs worldwide incorporate pangenomics into their breeding strategies. When breeding a new variety of plants or a new breed of livestock, breeders often begin with a small group of individuals selected to serve as the genetic basis for the new varieties, called a founder population. Pangenomes are especially helpful in breed- ing programs based on founder populations. They can reveal genes that are present in some founders but absent in the reference genome. These accessory genes might be crucial for adaptation or specific traits, and a pangenome ensures they are not overlooked. Pangenomes also help capture larger-scale genetic differenc- es, such as insertions, deletions, and rearrange- ments of DNA. These structural variations can have significant effects on traits and are often missed by traditional methods. Using their proprietary data analysis plat- form Khufu ® , the Clevenger team generates custom genomic tools for breeding programs, including pangenome graphs (KhufuPAN™). With the pangenome graph, breeders can make more informed decisions about the selection, breeding or mating, and management of their founder populations, leading to more rapid genetic gain and the development of superior cultivars or livestock breeds. The KhufuPAN technology allows for a more comprehensive and accurate analysis of genetic variation, which can benefit breeding programs. Clevenger and his team offer pangenome
analysis, helping to reveal novel genetic markers that may be associated with important traits and identify and correctly call genetic variants, even in complex regions of the genome. So far, Clevenger and his lab have built pangenome graphs for collaborators for chicken, grape, hemp, pumpkin, watermelon, blueberry, oak, and peanut breeding programs. Through a collaboration with the Groundnut Improvement Network of Africa , Clevenger and his lab are also creating pangenomic resources for peanut breeders across the continent of Africa. WIREGRASS PEANUT PROJECT Dr. Clevenger doesn’t just offer pangenom- ic services to collaborators, he is also using pangenomics as the basis for a peanut breeding program he leads in Dothan, Alabama. The Wiregrass Peanut Project (see p. 54 for more details) is one of the first known breeding programs in the world to base breeding decisions on founder pangenomics. A diverse set of peanut individuals was used to start the Wiregrass Peanut Project breeding population. Clevenger and his team created a pangenome for this founder popula- tion. Now, when the students participating in the project sequence their individual peanut plant, they can compare the genomics back to the pangenome instead of a standard reference genome. This higher-resolution comparison allows the students and the Clevenger lab to identify useful genomic variants that could confer benefits to peanut plants specific to the Wiregrass region, such as drought tolerance and disease resistance. ■
RESEARCH REPORT 2023-2024
45
Made with FlippingBook - Online magazine maker