Posts Tagged: DNA

Polyphagous Shot Hole Borer: San Diego Population Now Known as Kuroshio Shot Hole Borer

Through DNA sequencing, UCR entomologist have determined that we have two separate invasions of the Polyphagous Shot Hole Borer (PSHB) here in southern California attacking avocados. One invasion in San Diego County and the second in Los Angeles County. UCR entomologist, Richard Stouthamer states the two are different species genetically, but morphologically they are indistinguishable, luckily they both respond to the same lure. They do however carry different fungal symbionts with them.

The species that has invaded San Diego, is now known as the Kuroshio shot hole borer, and is originally found only in two places in the presumed native range: highlands of Taiwan and in Okinawa. The species of beetle that has invaded Los Angeles County will now be known solely as the Polyphagous, its native range is in Vietnam, South China, North Thailand, low lands of Taiwan and Okinawa, this species has also invaded Israel and South Africa.

These Shot Hole Bores are Ambrosia beetles, a specialized group belonging to the family Scolytidae. The shot hole borer was first found in Whittier Narrows in Los Angeles County in 2003. From 2003-2010 the beetle was found on a few ornamental trees, then in 2010 it was the presumptive cause of the death of a large number of box elder street trees in Long Beach. In 2012 the beetle was collected from a backyard avocado tree in South Gate, and from several tree species at local botanical gardens, since then it has been causing havoc in the avocado industry. It now appears to be established in Los Angeles, Orange, San Bernardino and Riverside Counties, and is expanding its range in San Diego County. A single beetle was caught in Santa Cruz County in 2014 and has now been found less than 2 miles from Ventura County line.

 The beetle is dark brown to black and tiny, with females between 0.07 and 0.1 inches long, and males even smaller, usually about 0.05 inches long. They differ from the bark beetles in this family in several ways. While bark beetles burrow in the phloem layer or at the juncture of the bark and sapwood, ambrosia beetles bore through the bark and into the sapwood. The shot hole bores are highly specialized and feed on fungi that they cultivate on the walls of the tunnels. In the case of the shot hole bores, they transport the pathogenic fungus, Fusarium euwallacea and both the adults and larvae feed on the fungus.

Shot hole borers attacks hundreds of tree species, but it can only successfully lay its eggs and/or grow the fungi in certain hosts. These include: Avocado, Box elder, California sycamore, Coast live oak, White alder, Japanese maple, and Red willow. Visit http://eskalenlab.ucr.edu/ for the full list. Infection with the fungus can cause a dry or wet and oily dark stain surrounding the entry holes, discolored wood, leaf discoloration and wilting, and dieback of entire branches. In box elders and avocados, a while crusty ring of sugar, also called a “sugar volcano” can be produced. Frass (wood dust left behind from boring) may be produced, but because this can quickly dissolve if it rains it can be missed sometimes. If the barked is scraped away, dark dead tissue may be found around the galleries.

 

Currently there is no cure for the fungus once the tree has become infected. Chipping and solarizing/tarping infested wood can help to limit the spread of the beetle/fungus. Wood should be chipped to pieces smaller than 1". Don't forget to sterilize pruning tools between uses to avoid spreading the fungus.

 

If you suspect you may have the shot hole bore in your grove please feel free to contact your local CE Farm Advisor/Specialist.

The Clegg Collection: A Valuable Resource

Department of Botany and Plant Sciences, University of California, Riverside

 

An unusual population of avocado trees may soon suffer the same fate as many commercial orchards elsewhere in California: its water supply will be cut off and the trees fed to a wood chipper.  And yet these trees (Fig. 1) potentially hold a key to the avocado's future:  they are the cornerstone of scientific research at the University of California, Riverside, aimed at unravelling the genetic underpinnings of agricultural traits and at placing avocado breeding on a molecular footing. 

It is well known to plant breeders that the traits observed in a promising selection are rarely transmitted to its offspring.  This is because the so called phenotype (what you see or measure) is a poor predictor of the genotype (the underlying genetic machinery). Unfortunately, for breeding to make any progress, phenotypic traits need to have a genetic basis. Traditional breeding, which cannot distinguish between phenotype and genotype—only works because it starts our with a large pool of trees and, by chance, ends up with a few selections that show promise as future cultivars.  In avocado, the selection efficiency of traditional breeding is in the order of 0.1-0.2%; in other words, only 1–2 promising selections are recovered for every 1000 trees that have been laboriously (and expensively) screened over the course of a minimum of 5–10 years. Clearly, a better understanding of the relationship between phenotype and genotype  would make the breeding process more efficient.

Recognizing this need, Professor Michael Clegg of (then) UC Riverside established a carefully designed experimental population of avocado trees, later known as the Clegg Collection. It consisted of over 200 progeny from a single cultivar Gwen mother tree, and each progeny tree was clonally propagated four-fold, taking the total number of trees to ca. 800.  The seedlings were grafted to a uniform Duke 7 rootstock to further reduce the impact of non-genetic variability. Between the fall of 2001 and spring of 2003 half of the trees (two clonal replicates of each unique genotype) were planted out at UC Riverside and the other half at South Coast Research and Extension Center, Irvine.

In this experimental design, every tree genotype is represented twice at each of two locations. Any variation between the clonal replicates at the same location sheds light on how much of a trait is environmental and how much of it is genetic. Only the genetic component is useful for breeding purposes. The environmental component is the “noise” that misleads breeders and, regrettably, often has a large influence on agriculturally relevant traits.

Since 2003 the Clegg trees have been put to good use. First, a quantitative genetic study was initiated to address the mismatch between genotype and phenotype and, specifically, to determine whether certain vegetative growth characteristics are amenable to breeding. This work (Chen et al. 2007) revealed that about 30% of the total phenotypic variation in growth rate and flowering was genetic in origin and thus amenable to breeding.

While the initial value of the Clegg experimental population arose from its utility in teasing apart genetic and environmental effects on a phenotype, the trees soon acquired additional roles. Genetic markers offer the opportunity of placing phenotypic measurements in a molecular framework. Microsatellite markers were used to determine the pollen parent of each ‘Gwen' progeny tree, revealing that approximately three quarters of the genotypes had been pollinated in roughly equal proportions by ‘Bacon', ‘Fuerte', and ‘Zutano', with the remaining quarter sired by miscellaneous cultivars or rogue pollen sources. What better opportunity than to examine genetic variation of traits in the context of the pollen parent. An interesting finding from this line of study was that ‘Gwen' ´ ‘Fuerte' progeny had significantly wider canopies and shorter stature than their half-sibs sired by ‘Bacon' or ‘Zutano' (Fig. 2). The fact that tree width and height is amenable to breeding is an encouraging result in the context of high-density planting such as that commonly practiced in apple.

At a time when avocado was gaining cudos as a healthy fruit with excellent nutritional qualities and beneficial effects in the treatment of high cholesterol and cancer, the Clegg Collection was next harnessed in a study on fruit nutritional composition. Data was gathered on fruit nutrient content in each genotype. Again, taking advantage of the experimental setup, the environmental “noise” associated with each measurement was stripped away to extract the

genetic portion that proved to be appreciable (Calderón-Vázquez et al. 2013).

The next step was to connect this data with a new type of molecular marker. These markers—so called SNP markers (Single Nucleotide Polymorphisms)—were developed using gene sequences from a subset of the Clegg trees. They were designed to reside in genes known to control the accumulation of particular fruit nutrients. Statistical analyses revealed that beta-sitosterol contents were being tracked by one of the SNP markers: in other words, the presence of this marker in an individual was indicative of high beta-sitosterol levels in its fruit.

Markers that are highly predictive of desirable traits and are relatively easy to measure in young seedlings are the nuts-and-bolts of marker-assisted selection, a breeding method that draws on molecular tools. Consequently, a third project was initiated that harnessed the SNP marker that predicted high fruit beta-sitosterol contents. Progeny from trees of the Clegg population were screened using the marker. Out of an initial pool of over 600 seedlings 73 seedlings (12%) were identified that had the desirable form (allele) of the marker, and 12 seedlings (2%) were eventually planted out. The selection intensity of marker-assisted selection therefore is at least 10-fold higher than under traditional breeding.

A loss of the Clegg Collection would surely represent an opportunity lost. Many more projects could be envisaged that address the genetic determination of a trait, its association with SNP markers, the influence of the pollen donor, or the utility of a marker for marker-assisted selection. The Collection has also been the nucleus of a genetic mapping project. Significantly, the SNP markers developed for these trees are also relevant for studies beyond fruit nutrient content because their biosynthetic pathways intersect with those underlying plant stress and disease responses. This property makes the candidate genes equally relevant for studies on pathogen or salinity tolerance and a key resource that could help secure the future of avocado production in California during turbulent times.

Literature Cited

Chen, H., V. E. T. M. Ashworth, S. Xu, and M. T. Clegg. 2007. Quantitative genetic analysis of growth rate in avocado.  J. Amer. Soc. Hort. Sci. 132 (5): 691–696.

Calderón-Vázquez, C., M. L. Durbin, V. E. T. M. Ashworth, L. Tommasini, K. K. T. Meyer, M. T. Clegg. 2013. Quantitative genetic analysis of three important nutritive traits in the fruit of avocado. J. Amer. Soc. Hort. Sci. 138 (4): 283–289

 

The Clegg Collection: the trees shown here are growing at UC Riverside

Clegg collection

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