Sequencing of cacao genome to help chocolate industry, subsistence farmers

The effort is the result of a partnership between USDA's Agricultural Research Service (ARS); Mars, Inc., of McLean, Va., one of the world's largest manufacturers of chocolate-related products; scientists at IBM's Thomas J. Watson Research Center in Yorktown , N.Y.; and researchers from the Clemson University Genomics Institute, the HudsonAlpha Institute for Biotechnology, Washington State University, Indiana University, the National Center for Genome Resources, and PIPRA (Public Intellectual Property Resource for Agriculture) at the University of California-Davis.

Team leaders from USDA included molecular biologist David Kuhn and geneticist Raymond Schnell, both at the ARS Subtropical Horticulture Research Station in Miami, Fla., and ARS computational biologist Brian Scheffler at the Jamie Whitten Delta States Research Center in Stoneville, Miss. ARS is the principal intramural scientific research agency of USDA. This research supports the USDA priority of promoting international food security, and USDA's commitment to agricultural sustainability.

"Because of the talent and dedication brought together by this unique partnership, researchers and plant breeders will be able to accelerate the genetic improvement of the cacao crop now cultivated in tropical regions around the world," said Edward B. Knipling, ARS administrator. "This will benefit not only the chocolate industry, but also millions of small farmers who will be able to continue to make their living from cacao."

Cocoa comes from the cacao tree, Theobroma cacao. The tree seeds are processed into cocoa beans that are the source of cocoa, cocoa butter and chocolate. But fungal diseases can destroy seed-bearing pods and wipe out up to 80 percent of the crop, and cause an estimated $700 million in losses each year.

Worldwide demand for cacao now exceeds production, and hundreds of thousands of small farmers and landholders throughout the tropics depend on cacao for their livelihoods. An estimated 70 percent of the world's cocoa is produced in West Africa.

Scientists worldwide have been searching for years for ways to produce cacao trees that can resist evolving pests and diseases, tolerate droughts and produce higher yields. ARS researchers have been testing new cacao tree varieties developed with genetic markers. But having the genome sequenced is expected to speed up the process of identifying genetic markers for specific genes that confer beneficial traits, enabling breeders to produce superior new lines through traditional breeding techniques.

Sequencing cacao's genome also will help researchers develop an overall picture of the plant's genetic makeup, uncover the relationships between genes and traits, and broaden scientific understanding of how the interplay of genetics and the environment determines a plant's health and viability.

The research team will continue to improve the quality and analyze the properties of the cacao genome sequence in preparation for publication in a peer-reviewed journal.