Huanglongbing (HLB) or citrus greening is a bacterial disease spread by the Asian citrus psyllid, and poses a serious threat to the citrus industry. In infected trees, the bacteria kill citrus by disrupting the trees’ food transportation systems.

To address exotic diseases like HLB, breeders need sophisticated tools that rapidly characterize citrus varieties and hybrids and locate genes for disease resistance, fruit quality, and other essential traits.

Two plant geneticists at the University of California, Riverside have received a $450,000 grant from the National Institute of Food and Agriculture (NIFA) of the U.S. Department of Agriculture to develop a genetic tool that citrus breeders can use to improve the efficiency with which citrus varieties are bred.

Mikeal Roose and Timothy Close, both professors of genetics and the principal investigator and co-principal investigator, respectively, of the two-year grant, will lead the project on developing a “high-density SNP genotyping array” for citrus — an important tool that geneticists and molecular breeders use to do genetic analyses of animals and plants.

Single nucleotide polymorphism (SNP) refers to a genetic variation at a single position in a DNA sequence among individuals. As is now commonly known, a DNA sequence is formed from a chain of four nucleotide bases: A, C, G, and T. When more than one percent of a population does not carry the same nucleotide at a specific position in the DNA sequence, SNP is said to have occurred.

Given the large amounts of citrus genomic data that are possible to generate today as well as the availability of technologies for detecting SNPs accurately, it is possible now to design high-density SNP arrays for citrus.

When developed, the array will allow investigators to rapidly determine the particular SNPs present in a citrus variety or hybrid. The thousands of SNPs detected with this array will then be related to the traits displayed by the various individuals studied.

“We will use this tool to study essentially all trees in our Citrus Variety Collection and several large citrus families in which individuals vary for traits of economic importance,” said Roose, the chair of the Department of Botany and Plant Sciences. “We will then correlate the particular SNPs carried by an individual to measured traits such as disease resistance and fruit quality.”

Specifically, the team of researchers, including graduate students and postdoctoral scholars, will first develop sequences for a large and diverse set of citrus varieties. They will then analyze all available sequence data to identify SNPs and select a subset of SNPs to be used on the array. The SNP array will be manufactured by a commercial company. Next, they will apply the assay to the Citrus Variety Collection, breeding populations used for mapping disease resistance and tolerance, and populations already selected for fruit quality traits.

“A valuable outcome of this project will be a comprehensive understanding of relationships among citrus varieties and how these relate to economically valuable characters,” Roose said.

UC Riverside has a long tradition in citrus research, with citrus production and development of new varieties being a major focus.  Used extensively to solve citrus disease problems and improve commercial varieties, the university’s Citrus Variety Collection is one of the world’s most diverse living collections of citrus and related types with approximately 1,000 different varieties (including mandarins, blood oranges, navel oranges, citrons, clementines, tangors, grapefruit, Valencia oranges, and pummelos).

In total, NIFA announced nearly $9 million in grants for research into issues affecting plant breeding and production, leading to improvements in plants that are critical to the sustainability and competitiveness of American agriculture.  A list of research institutions receiving the grants can be found here. Details of the funded research projects can be found here.

The awards were made under the Agriculture and Food Research Initiative Foundational Program priority area of plant breeding for agricultural production.