Sequencing of Citrus Genomes Points to Need For More Genetic Diversity

11 Jun 2014 --- Sequencing the genomes of domesticated citrus revealed a very limited genetic diversity that could threaten the crop’s survival prospects, according to an international research team.

In a study published in the June issue of Nature Biotechnology, the international consortium of researchers from the United States, France, Italy, Spain and Brazil analyzed and compared the genome sequences of 10 diverse citrus varieties, including sweet and sour orange along with several important mandarin and pummelo cultivars. The findings provide the clearest insight to date of how citrus has been cultivated and point to how modern genomics-guided development could help produce crops that better resist environmental stresses and pests.

The team, led by Fred Gmitter of the University of Florida Citrus Research and Education Center, included the U.S. Department of Energy’s Joint Genome Institute (JGI) and the HudsonAlpha Institute for Biotechnology Genome Sequencing Center. To discover how various types of citrus have been cultivated, the team compared the genetic sequences of several species of citrus.

The HudsonAlpha Genome Sequencing Center (GSC), led by Jeremy Schmutz and Jane Grimwood, contributed sequence and assembled the genome of the Clementine variety, creating its first “reference genome” for comparative analysis. The GSC is one of the few centers in the world performing de novo sequencing of plants and specializing in applying genomic techniques to understand how plants function in response to environmental stimuli. Schumtz leads the plant program in the JGI.

“Citrus is a major US crop, and in Florida, the country’s major producer, citrus is being killed now by greening and other diseases,” said Schmutz. “What we’ve found is that we’re planting very similar trees to what were planted 4,000 years ago. These same genotypes do not provide much diversity to resist diseases, and there is very little wild citrus that can be used to easily add diversity to modern citrus. This study shows how understanding the genomics of these plants can help identify sources of diversity, whether from introducing genes from wild species or selecting for desired traits using genetic techniques.”

Citrus is the world’s most widely cultivated fruit crop. In the U.S. alone, the citrus crop was valued at more than $3.1 billion in 2013. Originally domesticated in Southeast Asia thousands of years ago before spreading throughout Asia, Europe and the Americas via trade, citrus is now under attack from citrus greening, an insidious emerging infectious disease that is destroying entire orchards. Citrus greening is one of the most serious citrus plant diseases in the world, and once a tree is infected there is no cure.

To help defend citrus against this disease and other threats, researchers worldwide are mobilizing to apply genomic tools and approaches to understand how citrus varieties arose and how they respond to disease and other stresses. By understanding the relationships between various cultivated species with what they describe as “very narrow genetic diversity,” researchers hope to enable sequence-directed improvement, which could lead to crops that are more resistant to disease and stresses such as environmental changes.

The consortium found that diverse varieties are derived from two wild citrus species that diverged in Southeast Asia more than five million years ago. The team also found that pummelos indeed are a distinct citrus species, but mandarin oranges are not. Sequences of traditional mandarins like Ponkan and Willowleaf — believed to have grown without contact with other species — as well as known hybrid mandarins, all contain parts of the pummelo sequence, meaning that their genomes are not as distinct as originally believed.

As citrus varieties are reproduced asexually by vegetative propagation, trees producing a specific type of fruit are typically genetically identical. This growing strategy produces a uniform, high-quality fruit, but has the drawback that if one tree is susceptible to disease, they all are. By inferring the past hybridization events that gave rise to these common citrus varieties — either in the wild populations before domestication or in early undocumented human-directed breeding efforts —the team hopes to enable strategies for improving citrus, including resistance to greening and other diseases.

The study highlights how understanding genetics can help introduce (or in this case, restore) diversity to citrus and other crops to aid growth rates and resistance to environmental stresses like disease and drought. It also shows how modern agricultural systems need to adapt to maintain healthy, valuable crops. “Traditionally, agriculture has selected for robust, high yield cultivars and ignored much of the available wild diversity after initial domestication,” said Schmutz. “This study shows that you need to continue to introduce genetic diversity into the crop development process.” The discovery of a genetically unique Mangshan variety also shows that wild, unrelated versions of citrus may still exist, and could be used to provide more robust, diverse plants in the mix of citrus crops.