- Author: Ben Faber
BUFFALO, N.Y. -- We now know the DNA of guacamole. A repost from: https://www.eurekalert.org/pub_releases/2019-08/uab-glr080619.php
Scientists have sequenced the avocado genome, shedding light on the ancient origins of this buttery fruit and laying the groundwork for future improvements to farming.
With regard to modern affairs, the study reveals for the first time that the popular Hass avocado inherited about 61 percent of its DNA from Mexican varieties and about 39 percent from Guatemalan ones. (Avocados come in many types, but Hass -- first planted in the 1920s -- comprises the bulk of avocados grown around the world.)
The research also provides vital reference material for learning about the function of individual avocado genes, and for using genetic engineering to boost productivity of avocado trees, improve disease resistance and create fruit with new tastes and textures.
The study is important for agriculture. The growing global market for avocados was worth about $13 billion in 2017, with Mexico, the largest producer, exporting some $2.5 billion worth of the fruit that year, according to Statista, a provider of market and consumer data. Around the world, avocados are spread on tortillas, mashed up to flavor toast, rolled into sushi and blended into milkshakes (a popular treat in parts of Southeast Asia).
Scientists sequenced not only the Hass avocado, but also avocados from Mexico, Guatemala and the West Indies, which are each home to genetically distinct, native cultivars of the fruit.
The project was led by the National Laboratory of Genomics for Biodiversity (LANGEBIO) in Mexico, Texas Tech University, and the University at Buffalo. The research was published on Aug. 6 in the Proceedings of the National Academy of Sciences.
"Avocado is a crop of enormous importance globally, but particularly to Mexico. Although most people will have only tasted Hass or a couple of other types, there are a huge number of great avocado varieties in the species' Mexican center of diversity, but few people will have tried them unless they travel south of the U.S. border. These varieties are genetic resources for avocado's future. We needed to sequence the avocado genome to make the species accessible to modern genomic-assisted breeding efforts," says Luis Herrera-Estrella, PhD, President's Distinguished Professor of Plant Genomics at Texas Tech University, who conceived of the study and completed much of the work at LANGEBIO, where he is Emeritus Professor, prior to joining Texas Tech University.
"Our study sets the stage for understanding disease resistance for all avocados," says Victor Albert, PhD, Empire Innovation Professor of Biological Sciences in the UB College of Arts and Sciences and a Visiting Professor at Nanyang Technological University, Singapore (NTU Singapore). Albert was another leader of the study with Herrera-Estrella. "If you have an interesting tree that looks like it's good at resisting fungus, you can go in and look for genes that are particularly active in this avocado. If you can identify the genes that control resistance, and if you know where they are in the genome, you can try to change their regulation. There's major interest in developing disease-resistant rootstock on which elite cultivars are grafted."
The family history of an eccentric, big-pitted fruit
While the avocado rose to international popularity only in the 20th century, it has a storied history as a source of sustenance in Central America and South America, where it has long been a feature of local cuisines. Hundreds of years ago, for example, Aztecs mashed up avocados to make a sauce called āhuacamolli.
Before that, in prehistoric times, avocados, with their megapits, may have been eaten by megafauna like giant sloths. (It's thought that these animals could have helped to disperse avocados by pooping out the seeds in distant locations, Albert says.)
The new study peers even further back into time. It uses genomics to investigate the family history of the avocado, known to scientists as Persea americana. "We study the genomic past of avocado to design the future of this strategic crop for Mexico," Herrera-Estrella said. "The long life cycle of avocado makes breeding programs difficult, so genomic tools will make it possible to create faster and more effective breeding programs for the improvement of this increasingly popular fruit."
The avocado belongs to a relatively small group of plants called magnoliids, which diverged from other flowering plant species about 150 million years ago. The new research supports -- but does not prove -- the hypothesis that magnoliids, as a group, predate the two dominant lineages of flowering plants alive today, the eudicots and monocots. (If this is right, it would not mean that avocados themselves are older than eudicots and monocots, but that avocados belong to a hereditary line that split off from other flowering plants before the eudicots and monocots did.)
"One of the things that we did in the paper was try to solve the issue of what is the relationship of avocados to other major flowering plants? And this turned out to be a tough question," Albert says. "Because magnoliids diverged from other major flowering plant groups so rapidly and so early on, at a time when other major groups were also diverging, the whole thing is totally damn mysterious. We made contributions toward finding an answer by comparing the avocado genome to the genomes of other plant species, but we did not arrive at a firm conclusion."
Magnoliids were estimated by a 2016 research paper to encompass about 11,000 known living species on Earth, including avocados, magnolias and cinnamon. In comparison, some 285,000 known species were counted as eudicots and monocots.
The avocado as a chemist, and the heritage of the hybrid Hass
Scientists don't know how old the avocado is, and the new study doesn't address this question. But the research does explore how the avocado has changed -- genetically -- since it became its own species, branching off from other magnoliids.
The paper shows that the avocado experienced two ancient "polyploidy" events, in which the organism's entire genome got copied. Many of the duplicated genes were eventually deleted. But some went on to develop new and useful functions, and these genes are still found in the avocado today. Among them, genes involved in regulating DNA transcription, a process critical to regulating other genes, are overrepresented.
The research also finds that avocados have leveraged a second class of copied genes -- tandem duplicates -- for purposes that may include manufacturing chemicals to ward off fungal attacks. (Tandem duplicates are the product of isolated events in which an individual gene gets replicated by mistake during reproduction.)
"In the avocado, we see a common story: Two methods of gene duplication resulting in very different functional results over deep time," Albert says.
"In plants, genes retained from polyploidy events often have to do with big regulatory things. And genes kept from the more limited one-off duplication events often have to do with biosynthetic pathways where you're making these chemicals -- flavors, chemicals that attract insects, chemicals that fight off fungi. Plants are excellent chemists," Herrera-Estrella says.
Having addressed some ancient mysteries of the avocado, the new study also moves forward in time to explore a modern chapter in the story of this beloved fruit: how humans have altered the species' DNA.
Because commercial growers typically cultivate avocados by grafting branches of existing trees onto new rootstocks, today's Hass avocados are genetically the same as the first Hass avocado planted in the 1920s. These modern-day Hass avocados are grown on Hass branches grafted onto various rootstock that are well adapted for particular geographic regions.
While the Hass avocado was long thought to be a hybrid, the details of its provenance -- 61 percent Mexican, 39 percent Guatemalan -- were not previously known. The scientists' new map of the Hass avocado genome reveals huge chunks of contiguous DNA from each parental type, reflecting the cultivar's recent origin.
"Immediately after hybridization, you get these giant blocks of DNA from the parent plants," Herrera-Estrella says. "These blocks break up over many generations as you have more reproductive events that scramble the chromosomes. But we don't see this scrambling in the Hass avocado. On chromosome 4, one whole arm appears to be Guatemalan, while the other is Mexican. We see big chunks of DNA in the Hass avocado that reflect its heritage."
"We hope that the Mexican Government keeps supporting these types of ambitious projects that use state-of-the-art technology to provide a deep understanding of the genetics and genomics of native Mexican plants," Herrera-Estrella said.
In addition to LANGEBIO, UB and Texas Tech University, the avocado genome sequencing team included scientists from the Swedish University of Agricultural Sciences; Instituto de Ecología, A.C.; Universidad Nacional Autónoma de México; Nanyang Technological University; University of Ottawa; VIB-UGent Center for Plant Systems Biology; Universidad de Guanajuato; University of Florida; University of Nevada, Reno; Queensland Alliance for Agriculture and Food Innovation; Universitat de Barcelona; USDA-ARS Subtropical Horticulture Research Station; Universidad Autónoma Chapingo; Natural History Museum of Denmark; and Université Paul Sabatier.
The research was funded by SAGARPA/CONACYT, the Governors University Research Initiative of the State of Texas, the U.S. National Science Foundation, Horticulture Innovation Australia Ltd. and the Australian Bureau of Agricultural and Resource Economics and Sciences.
- Author: Vanessa Ashworth
- Author: Mary Lu Arpaia
- Author: Philippe Rolshausen
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.
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