Featured Research

from universities, journals, and other organizations

Retracing early cultivation steps: Lessons from comparing citrus genomes

Date:
June 8, 2014
Source:
DOE/Joint Genome Institute
Summary:
Citrus is the world's most widely cultivated fruit crop but it is now under attack from citrus greening, an insidious emerging infectious disease destroying entire orchards. 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. An international consortium of researchers analyzed and compared the genome sequences of ten diverse citrus varieties.

Citrus is the world’s most widely cultivated fruit crop but it is under attack from citrus greening, a disease that is destroying entire orchards.
Credit: Roy Kaltschmidt, LBNL

Citrus is the world's most widely cultivated fruit crop. In the U.S. alone, the citrus crop was valued at over $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. 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.

Related Articles


In a study published in the June 2014 edition of Nature Biotechnology, an international consortium of researchers from the United States, France, Italy, Spain, and Brazil analyzed and compared the genome sequences of ten diverse citrus varieties, including sweet and sour orange along with several important mandarin and pummelo cultivars. The consortium, led by Fred Gmitter of the University of Florida Citrus Research and Education Center, found that these diverse varieties are derived from two wild citrus species that diverged in Southeast Asia over five million years ago.

The U.S. Department of Energy Joint Genome Institute (DOE JGI) contributed to the citrus pilot project, Gmitter said, harnessing their expertise in plant genomics and capacity for high throughput sequencing. Initial support for the citrus effort arose 10 years ago under the auspices of the inaugural round of the Community Science Program (CSP -- formerly the Community Sequencing Program), which seeks to build scientific communities around cornerstone species of relevance to DOE missions in bioenergy, carbon cycling and biogeochemistry. There is a fledgling industrial effort underway in Florida to redirect the five million tons of annual citrus waste generated there from low-value cattle feed to produce ethanol for fuel. The research team's citrus trait analysis will inform breeding strategies beyond important agronomic traits.

One of these wild species gave rise to cultivated pummelo, the largest citrus fruit that can often range from two to four pounds. Surprisingly, the small, easily peeled mandarins were, in contrast, found to be genetic mixtures of a second species and pummelo. Sweet orange, the most widely grown citrus variety worldwide, was found to be a complex genetic hybrid of mandarin and pummelo, presumably accounting for its unique qualities. Seville or sour orange, commonly used in marmalade, was found to be an unrelated interspecific hybrid.

Since 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. "Now that we understand the genetic structure of sweet orange, for example, we can imagine reproducing the unknown early stages of citrus domestication using modern breeding techniques that could draw from a broader pool of natural variation and resistance," Gmitter said.

The genomes presented in the published study included pummelos, oranges and mandarins. One of the sequences was the high-quality reference genome of Clementine mandarin sequenced by an international consortium including Genoscope in France, the Institute for Genomic Applications in Italy, the DOE JGI, and the HudsonAlpha Institute for Biotechnology, with contributions from researchers in Spain and Brazil. Another was the sweet orange genome, produced jointly by researchers at the DOE JGI, the University of Florida, and 454 Life Sciences, a Roche company. By understanding the relationships between the various cultivated species with what they describe as "very narrow genetic diversity," the 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 analyses revealed that while pummelos represent a single citrus species (Citrus maxima), the same cannot be said of cultivated mandarins, even those long held as not having intermixed with other varieties. Comparing sequences of so-called "traditional" mandarins such as the Asian cultivar Ponkan and the Mediterranean cultivar Willowleaf with mandarins known to be developed hybrids indicated that all contain segments of the pummelo genome. The "wild" Mangshan mandarin from China is an exception to the rule, as its genome revealed it was in fact a separate species from other cultivated mandarins.

The findings echo Gmitter's quip when he spoke at the DOE JGI's 7th Annual Genomics of Energy & Environment Meeting in March 2012. "Citrus has incestuous genes," he told the audience. "Nothing is pure."


Story Source:

The above story is based on materials provided by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.


Journal Reference:

  1. G Albert Wu, Simon Prochnik, Jerry Jenkins, Jerome Salse, Uffe Hellsten, Florent Murat, Xavier Perrier, Manuel Ruiz, Simone Scalabrin, Javier Terol, Marco Aurélio Takita, Karine Labadie, Julie Poulain, Arnaud Couloux, Kamel Jabbari, Federica Cattonaro, Cristian Del Fabbro, Sara Pinosio, Andrea Zuccolo, Jarrod Chapman, Jane Grimwood, Francisco R Tadeo, Leandro H Estornell, Juan V Muñoz-Sanz, Victoria Ibanez, Amparo Herrero-Ortega, Pablo Aleza, Julián Pérez-Pérez, Daniel Ramón, Dominique Brunel, François Luro, Chunxian Chen, William G Farmerie, Brian Desany, Chinnappa Kodira, Mohammed Mohiuddin, Tim Harkins, Karin Fredrikson, Paul Burns, Alexandre Lomsadze, Mark Borodovsky, Giuseppe Reforgiato, Juliana Freitas-Astúa, Francis Quetier, Luis Navarro, Mikeal Roose, Patrick Wincker, Jeremy Schmutz, Michele Morgante, Marcos Antonio Machado, Manuel Talon, Olivier Jaillon, Patrick Ollitrault, Frederick Gmitter, Daniel Rokhsar. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology, 2014; DOI: 10.1038/nbt.2906

Cite This Page:

DOE/Joint Genome Institute. "Retracing early cultivation steps: Lessons from comparing citrus genomes." ScienceDaily. ScienceDaily, 8 June 2014. <www.sciencedaily.com/releases/2014/06/140608152724.htm>.
DOE/Joint Genome Institute. (2014, June 8). Retracing early cultivation steps: Lessons from comparing citrus genomes. ScienceDaily. Retrieved November 26, 2014 from www.sciencedaily.com/releases/2014/06/140608152724.htm
DOE/Joint Genome Institute. "Retracing early cultivation steps: Lessons from comparing citrus genomes." ScienceDaily. www.sciencedaily.com/releases/2014/06/140608152724.htm (accessed November 26, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Wednesday, November 26, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Classic Hollywood Memorabilia Goes Under the Hammer

Classic Hollywood Memorabilia Goes Under the Hammer

Reuters - Entertainment Video Online (Nov. 26, 2014) — The iconic piano from "Casablanca" and the Cowardly Lion suit from "The Wizard of Oz" fetch millions at auction. Sara Hemrajani reports. Video provided by Reuters
Powered by NewsLook.com
Pet Dogs to Be Used in Anti-Ageing Trial

Pet Dogs to Be Used in Anti-Ageing Trial

Reuters - Innovations Video Online (Nov. 26, 2014) — Researchers in the United States are preparing to discover whether a drug commonly used in human organ transplants can extend the lifespan and health quality of pet dogs. Video provided by Reuters
Powered by NewsLook.com
From Popcorn To Vending Snacks: FDA Ups Calorie Count Rules

From Popcorn To Vending Snacks: FDA Ups Calorie Count Rules

Newsy (Nov. 25, 2014) — The US FDA is announcing new calorie rules on Tuesday that will require everywhere from theaters to vending machines to include calorie counts. Video provided by Newsy
Powered by NewsLook.com
Feast Your Eyes: Lamb Chop Sent Into Space from UK

Feast Your Eyes: Lamb Chop Sent Into Space from UK

Reuters - Light News Video Online (Nov. 25, 2014) — Take a stab at this -- stunt video shows a lamb chop's journey from an east London restaurant over 30 kilometers into space. Rough Cut (no reporter narration). Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:

Strange & Offbeat Stories

 

Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:  

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile iPhone Android Web
Follow Facebook Twitter Google+
Subscribe RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins