Cotton Genome Sequence Could Boost Global Agriculture

Out of the 50 recognized species of cotton, just 4 are useful for the textile industry. A new study led by an informatics team at DePaul University has mapped out the genome of one of these vital cotton species - Gossypium herbaceum cultivar Wagad – to give a full account of how wild cotton was domesticated.

The study, say the authors, will hopefully give agricultural scientists a better sense of how to further enhance the crop’s use in the U.S. and around the world.

The study is published in the journal G3: Genes, Genomes, Genetics.

A genetic map of cotton

The study’s lead author is Thiru Ramaraj, an assistant professor of computer science at DePaul’s Jarvis College of Computing and Digital Media. His lab has been able to analyze the genome thanks to technological progress made over the past decade.

“The power of this technology is it allows us to create high-quality genomes that supply a level of detail that simply wasn’t possible before,” says bioinformatics expert Ramaraj. “This opens up the possibility for more researchers to sequence many crops that are important to the global economy and to feeding the population.”

Also involved in the project is Joshua Udall, the research leader for the Crop Germplasm Research Unit at the U.S. Department of Agriculture’s Agricultural Research Service. Udall suggests the research could offer a genetic map to improved cotton production, particularly for Wagad cotton – a diploid strain predominantly cultivated in African nations.

Future-proofing crops

The scientists’ first step was the reconstruction of the Wagad genome using high-quality, long DNA sequence data. The team used a selection of genomic tools to order and orient the gene data and then structure it over chromosomes.

Ramaraj then recruited Azalea Mendoza, a biologist and computer science graduate student who added context to the findings. Mendoza started her research with an overview of cotton's history. She explored variations in cotton using comparative genomics, focusing on annotated genes and their functions. “As we were studying the regions of the genome, we found many genes that were related to the content of fiber,” says Mendoza. “It was incredible to see the real-life application of the work.”

According to Udall, who has been collaborating with Ramaraj since 2015, the significance of cotton genomics for domestic agriculture is undeniable. The Crop Germplasm Research Unit holds approximately 10,000 accessions of various species in a repository, with the aim to safeguard the nation’s genetic resources for food and livestock.

That includes future-proofing crops against potential new threats. “When new diseases come to the U.S., or there's new invasive pests, one of the first things we do is screen the genetic diversity of cotton to see if any of the previous varieties are resistant to it,” Udall says. This gives farmers the chance to quickly develop resistant strains and avoid devastating crop loss.

While the cost of sequencing genomes has reduced over time, Udall and Ramaraj's study required almost two years of interdisciplinary work. Udall regards it as a positive step towards identifying other cotton genomes to sequence. For Mendoza, the work has wider impacts that could one day be felt globally. “This is the kind of work that is going to affect humans and sustainability into the future,” she concludes.

Reference: Ramaraj T, Grover CE, Mendoza AC, et al. The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. G3 Genes|Genomes|Genetics. 2023;13(2):jkac308. doi: 10.1093/g3journal/jkac308

This article is a rework of a press release issued by DePaul University. Material has been edited for length and content.