Subtropical Fruit Crops Research & Education
University of California
Subtropical Fruit Crops Research & Education

Posts Tagged: breeding

Citrus Grower Meeting Coming Soon

Every year growers get together to learn what is being done in the citrus research world that could affect their operations. This June, University of California and the Citrus Research Board are bringing some good talks to three different growing areas. All growers are invited, but RSVPs are appreciated.


CRB-GrowerSeminar-Flyer 2017
CRB-GrowerSeminar-Flyer 2017

Posted on Friday, May 19, 2017 at 6:13 AM
Tags: ACP (86), alternate bearing (5), breeding (4), citrus (338), disease (57), fertilizers (6), grapefruit (27), huanglongbing (66), irrigation (79), irrigation (79), lemons (9), mandarins (5), nutrition (5), oranges (6), pests (25), tangerines (1)

New Rootstocks for the Little 'Pixie'

'Pixie' mandarin is a very vigorous, upright tree. Although the fruit is small, hence its name, it can produce fruit on the ends of long branches which deform the canopy structure, making it hard to pick. The sweet, seedless fruit is worth picking, though. The rootstock standards for this small industry are ‘Citrumelo' and ‘C-35' citrange. The industry is looking for alternatives to these choices, especially those that reduce the vigor of the trees.

There is no one ideal rootstock at this point and growers have the option of a wide range of choices. The search includes those that are resistant to Citrus Tristeza Virus (CTV), Phytophthora, calcareous soils and ideally one that is resistant to the bacteria that causes Huanglongbing.

In many California coastal growing areas, land is expensive, water scarce and costly and prone to calcareous soils that are derived from marine sediments which can bring on iron chlorosis. Growers are also looking for smaller trees that will give early economic returns, are easier to prune and pick, and may be more compatible with the economics driven by Huanglongbing.

‘Citrumelo' citrange yields a large tree with good quality and quantity of fruit. It is tolerant of CTV (Citrus tristeza virus) and Phytophthora spp, but is susceptible to iron chlorosis in high pH soils. ‘C-35' citrange is a smaller tree than Citrumelo, also has resistance to Phytophthora spp and CTV, and is more tolerant of high pH soils.

The USDA had a breeding program in California which was taken over by the University of California. Out of this breeding project, the university selected three rootstocks for release in 2009 because of their horticultural characteristics, such as dwarfing, although not as much as ‘Flying Dragon' trifoliate, resistance to CTV and tolerance of calcareous soils. These three rootstocks also show good tolerance to Phytophthora parasitica and nematodes.

Pixie growers have been looking for a more compact tree, easier to handle and not need so much pruning. They funded a long-term project to see how these newer selections of rootstock performed in their area which has a hot summer/cool winter. A 2014 planting of ‘Pixie' has been evaluating the size reducing effects of the relatively new rootstocks ‘Bitters' citrange, ‘Carpenter' citrange and ‘Furr' citrange. After two years, ‘Pixie' on ‘Citrumelo' is the largest tree. Of the new rootstocks, ‘Furr' is the largest and ‘Bitters' the smallest. The trial was replicated at two sites with two different pH soils. At one site with the highest soil pH, ‘Bitters' showed iron chlorosis.

Photo: long whip growth on 'Pixie'

pixie whips
pixie whips

Posted on Saturday, May 6, 2017 at 8:55 AM
Tags: avocado (289), breeding (4), citrus (338), irrigation (79), lemon (100), nutrients (21), orange (69), rootstocks (7), rootstocks (7), tangerine (3)

Avocado Cultivars, Botanical Races and Genetic Footprints

Vanessa Ashworth and Philippe Rolshausen, Department of Botany and Plant Sciences, University of California Riverside.

Have you ever wondered where your favorite avocado variety came from? Not the nursery where it was purchased but the long, tortuous path that led to its selection. How are different varieties related? Did the expert tell you that your avocado is a “Guatemalan x Mexican” but you were afraid to ask what that means? Has your carefully nurtured seedling raised from a ‘Hass' pit morphed into a tree bearing unconvincing fruit? If so, read on.

Avocado breeders refer to the different types of avocado as varieties or, more correctly, as cultivars. The ‘Hass' cultivar is by far the best known, but several hundreds of named avocado cultivars have been bred in the USA alone since avocado was first introduced here. None was developed by the big commercial seed companies; Instead, avocados were patiently selected, originally by indigenous cultures of Mesoamerica, much later by growers/enthusiasts, and fairly recently in avocado breeding programs. Almost never do we know the precise pedigree of a cultivar. We are sometimes told the maternal parent, but older cultivars (including ‘Hass') typically lack a record of parentage, and any thought of fitting today's cultivars into a concise family tree is hopelessly optimistic. In any case, prior to the mid-19th century very little is known about the plant material that was imported from abroad, with at best an indication of geographic provenance. And yet it would be far more efficient if we could arrange cultivars in a hierarchy or a series of related assemblages, instead of just looking at a random scatter.

In order to understand how today's cultivars are related we need to dig deeper. Going back in time, we know that indigenous civilizations in Mesoamerica recognized the value of the avocado's wild ancestor(s) and were actively selecting superior forms for thousands of years, which eventually led to a semi-domesticated avocado. Evidence of selection by human hand as far back as 8,000 years before present is preserved in archaeological sites in Puebla State, Mexico. At the time of European contact, written records indicate that there already existed three distinct types of avocado, each from a separate geographic center of origin. Today, we refer to them as botanical races, and they represent the “primeval soup” that gave rise to modern avocado cultivars.

Here is what we know about the three botanical races of avocado, respectively called (1) the West Indian (formerly known also as the South American), (2) the Guatemalan, and (3) the Mexican (also known as the “criollo”): Each exhibits a characteristic suite of traits that includes differences in leaf chemistry, peel texture and color, and sources of tolerance (diseases and salinity). The races were domesticated in separate geographic regions, the “West Indian” race in lowland coastal Mesoamerica (possibly Yucatán), the Guatemalan race in upland Guatemala, and the Mexican race in highland Mexico. The Guatemalan and Mexican races remained fairly local, so their names reflect their respective centers of domestication, but the “West Indian” race seems to have been spread far and wide by indigenous cultures in Meso- and South America and was, incorrectly, named for a much later destination. The explorations of the 15th and 16th centuries kicked off the worldwide distribution of (mostly West Indian race) avocados, reaching Spain in the early 17th century, Jamaica in the mid-17th century, and Indonesia by the mid-18th century. It wasn't until the mid- to late 19th century that the three races of avocado found their way to the United States, primarily Florida and California.

After the avocado was introduced to California and elsewhere, there followed countless rounds of selection, generally resulting in hybrids among the botanical races. The selection process consisted of growing out seedlings from the seeds of “good” cultivars and screening them for chance seedlings with promising characteristics. However, in the same way that children are not identical to their parents, seedlings grown from the pit of a fruit are not identical to the tree the fruit came from. Each seedling represents a reshuffled version of its parents' genomes. The only procedure that preserves an identical genome is clonal propagation. Budding and grafting techniques that, today, ensure clonal propagation and keep cultivars “true to type” were not used until the first half of the 20th century.

Contrary to many major crops, most avocado cultivars we have today are bursting with so much genetic diversity that breeding is actually rendered difficult. When we grow out seedlings we get a huge number that look (and taste) nothing like their parents and most are discarded. The poor selection efficiency (an estimated 0.2%) has to do with the large variability caused by multiple domestication centers and a long history of open-pollination. There is no immediate danger of a genetic bottleneck, but breeding is slow and outcomes are unpredictable.

In the absence of accurate breeding pedigrees, we have come to describe avocado cultivars in terms of their resemblance to one or several botanical races, based on their combination of traits. For example, ‘Hass' is considered to be a Guatemalan x Mexican (G x M) hybrid because it has the thick, rough skin of the Guatemalan race but the high oil content of the Mexican race. Cultivar ‘Gwen' is also called a G x M hybrid, but is possibly a little more Guatemalan than Mexican and certainly more Guatemalan than ‘Hass'. Cultivar ‘Fuerte' is often called a G x M hybrid or sometimes Mexican which makes it more Mexican than ‘Hass' and a lot more Mexican than ‘Gwen' but not as Mexican as ‘Mexicola'... What these examples show is that description of avocado cultivars in terms of botanical race composition has its limitations and we are most likely dealing with a continuum of blending among the three botanical races. Can we improve on this? ¡Sí, se puede!

Enter the modern tools of genomics: molecular markers and new analytical approaches are emerging that can peek inside ancestral genomes and discover hidden patterns within genetic information. The new approaches track the progress of tiny nuggets of genetic information (markers) by comparing their distribution across a large numbers of cultivars. Several studies have revealed that today's cultivars continue to harbor the genetic footprints of the three botanical races and a lot more besides. In this instance, having cultivars bursting with genetic diversity is a good thing. Eventually, given a large enough dataset (markers and cultivars), we will be able to place cultivars into assemblages that go beyond first-pass assignments to one or more botanical races.

A working framework of cultivar assemblages confers predictive information that helps guide cultivar choice and breeding decisions. In a slow-growing tree crop such as avocado where years elapse before many traits are available, a marker-guided, predictive framework represents huge savings in time and resources. A simple example illustrates this point: In the event of an epidemic there is no time to start breeding new cultivars from scratch. Instead, the first line of defense is to explore tolerance present in existing cultivars, and having access to a framework helps prioritize among hundreds of cultivars. Avocados of Mexican ancestry are known to exhibit better disease tolerance than Guatemalan and West Indian stock, so material that contains a Mexican-race footprint would be a good choice for early screenings for tolerance. Epidemics such as grape phylloxera or potato blight are well known examples where the mainstream cultivars shared too uniform a genetic base and where a cultivar monoculture permitted disease pressure to attain dangerous proportions. Consequently, today's dominance of ‘Hass' should be viewed with some trepidation.

In fact, it is possible that we are facing a new epidemic right now: Fusarium dieback (FD) has impacted many tree species, especially the avocado, in southern California since its introduction in 2013. The Fusarium fungus is transmitted by a beetle, the polyphagous shot hole borer (PSHB), and fungus and beetle act in partnership to breach the defenses of their plant host, leading to wilting, branch dieback, and fruit losses. Moreover, we know that ‘Hass' is highly susceptible to the disease. It is time to look for sources of tolerance and to revisit the cultivars that have lost ground to ‘Hass', such as ‘Bacon', ‘Fuerte', and ‘Reed', and to take advantage of germplasm collections that contain material of older vintage, often dating back to the start of the 20th century, if not before. A major germplasm collection is maintained at the University of California South Coast Research & Extension Center in Irvine, and additional material is grown at UC Riverside's Agricultural Operations. A good digital resource to study the diversity of cultivars available in California is the UC Riverside Avocado Information website

Is the consumer ready to embrace new cultivars? Preliminary evidence is promising. There are few opportunities today to come face-to-fruit with the more unusual cultivars because they have largely been banished to back yards or live sheltered lives in today's germplasm collections. A notable exception is the UC Riverside avocado breeding program. Headed by Dr. Mary Lu Arpaia, the program runs a monthly avocado tasting session where participants record their views on visual (external) fruit characteristics and on fruit sensory qualities (flavor). These tasting sessions have shown that participants are drawn to novel fruit shapes/sizes and value the taste of many cultivars, not just of ‘Hass'. There is also considerable interest in learning more about existing cultivars and about the history of avocado breeding and domestication.


Some of the avocado cultivars featured on the UC Riverside Avocado Information website

Clearly, to place avocado cultivars into a workable framework that reflects their interconnections as well as the footprint of the three botanical races will be a valuable addition to the tools available to breeders and will benefit our knowledge of avocado diversity. For now, however, we are unable to give concise answers to the questions of the introductory paragraph, but it is safe to say that your favorite cultivar is probably a hybrid between at least two botanical races of avocado, contains genetic footprints left by ancient Mesoamerican breeders, capriciously gives rise to highly promising seedlings, and has a murky pedigree yet to be laid bare.

Hassx Fuerte
Hassx Fuerte

Posted on Tuesday, May 24, 2016 at 3:57 AM
Tags: avocado (289), breeding (4), cultivars (2)

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
Clegg collection

Posted on Friday, January 16, 2015 at 7:40 AM
  • Author: Vanessa Ashworth
  • Author: Mary Lu Arpaia
  • Author: Philippe Rolshausen
Tags: avocado (289), breeding (4), Clegg (1), DNA (2)
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