- Author: Vanessa Ashworth
- Author: Philippe Rolshausen
Department of Botany and Plant Sciences, UC Riverside
Advances in molecular tools already have led to the development of large numbers of genetic markers distributed across the avocado genome. These markers are being put to good use, many forming the basis for projects to inventory avocado germplasm repositories and, in our own case, to create a pathway toward marker-assisted selection. Most recently, the first avocado genome was sequenced, marking the beginning of a new era. Genome annotation entails adding functional information about genes and other compartments of the genome, aided by comparisons with model organisms. The challenge is that the avocado occupies a highly divergent position on the evolutionary tree of life, close to such plants as laurel and magnolia, near the base of the flowering plants lineage and far removed from convenient model organisms (such as Arabidopsis) for which annotations are most advanced and comprehensive. Therefore, genome annotation in avocado is likely to be slower. While there is great potential for exploring the genome for interesting gene regions, the procedures will not be insignificant and will require bioinformatics and experimental verification before breeding targets can be identified. Additionally, quantitative traits such as yield-related traits are not controlled by a single gene but, instead, by many genes of small effect distributed across the entire genome. Even when the genome becomes thoroughly annotated, it is still only one genome and will not include all the variation present in the large pool of avocado germplasm. In comparison, efforts are underway to sequence 1 million human genomes. Clearly, additional avocado genomes will allow broader comparisons and will lead to an acceleration and broadened scope of breeding efforts.
Figure 1: Diversity of shape, size, skin color and surface texture of fruit picked from trees sharing the same maternal parent. Some of these fruit were assayed in the QTL analysis for fruit nutrient content.
A major goal of molecular breeding is to pinpoint which genes are responsible for a trait of interest and to make this relationship accessible for experimental manipulation. In avocado, many genetic markers1 have been developed in recent years and used widely to characterize scion and rootstock germplasm collections. However, few studies have attempted to examine how genetic markers are related to specific traits and how they can be used to improve breeding material using marker-assisted selection. In a recent scientific article, we reported our findings from a genetic study to identify genes and markers controlling various yield-related and nutritional traits in avocado. It centered on a procedure called Quantitative Trait Locus (QTL) analysis2 and presents a high-density linkage map3 for avocado useful for molecular breeding. Our study included quantitative traits (tree height, canopy diameter, and trunk diameter, and contents of vitamin E, beta-sitosterol and carotenoids in the fruit flesh) and a qualitative trait (flowering type) (Figure 1 and 2). Here are some of the major findings of our research.
Flowering type: Avocado flowers exhibit either A- or B-type flowering, a mechanism designed to prevent self-pollination and that increases fruit set. We found that a tight cluster of markers on chromosome 10 showed a very strong signal for flowering type. It appeared that a single gene on that chromosome is likely responsible for controlling which flowering type a tree will have when it reaches maturity. In orchards devoted to ‘Hass', with A-type flowering, inter-planting with B-type pollinizer cultivars is the norm to boost pollination and fruit set. Currently, most pollinizers are green-skin cultivars (especially ‘Bacon', ‘Fuerte', and ‘Zutano') whose fruit do not fetch a good price compared to ‘Hass', reducing overall market value of the orchard yield. Therefore, when breeding new cultivars for ‘Hass'-like taste and appearance, it would be advantageous to be able to include an early screen for B-type flowering: this would ensure that any promising breeding material with ‘Hass'-like attributes would also be usable as B-type pollinizers that produce marketable fruit. The screen would involve a routine lab procedure performed on DNA extracted from young leaves of the seedlings in a breeding program: the strategy would be to only keep those seedlings that have the particular marker that coincides with B-type flowering and to discard the rest. All seedlings progressing through subsequent tiers of the breeding program would have B-type flowering and there would be no wastage of time and resources by having to cull mature trees once they have been revealed as A-type flowerers.
Nutrient content of the fruit flesh: We also found that the content of alpha-tocopherol, a form of vitamin E, is strongly associated with a group of markers on chromosome 3. This finding opens up the possibility of breeding avocado for enhanced vitamin E concentrations and to further elevate its status as a nutritious fruit. Selection for a suitable marker in young seedlings would avoid the long wait until the seedlings have produced fruit, which can take many years. Though weaker, a signal for marker association with beta-sitosterol was also detected on a short section on chromosome 1. This plant sterol has been shown to have anti-oxidative properties and to reduce blood cholesterol levels in humans. The fact that vitamin E and beta-sitosterol are controlled by genes on different chromosomes is a practical advantage because it means that breeding for one nutrient can be performed independently of the other nutrient. It is noteworthy that both vitamin E and beta-sitosterol have been cited as targets for biofortification in other crops.
Avocado production in California, the main avocado-producing state in the US, cannot keep pace with consumption, and the market is supplemented by imports from Mexico and many other countries. For now, almost all fruits imported are of ‘Hass' or “Hass-like” cultivars, yet taste panels at UC Riverside suggest that consumers are open to new tastes and visuals. Supermarket offerings in the form of a startling abundance of different apple and pear cultivars are in stark contrast to those for avocado, which is essentially synonymous with ‘Hass' alone. The time for customized breeding may be ripe. As a nutritious and tasty fruit crop, avocado has acquired a strong culinary following and is prized for its healthy attributes. Having shown that vitamin E content is amenable to marker-assisted selection, future breeding could focus on generating nutrient-enriched cultivars, and future elucidation of similar trait-marker associations could create opportunities to generate high-value avocados that would coexist alongside the mainstream crop. Currently, health-conscious consumers and avocado fans are being short-changed, and molecular breeding can play a role in developing new and interesting material.
Figure 2: Tree height—a quantitative trait—at different locations in identical genotypes (clonally replicated). The white stick in each photo measures 1 m in length.
Definitions
1 Genetic markers: specific locations on the DNA sequence that can be readily identified by molecular methods. They are also known as molecular markers.
2 QTL analysis: infers which markers on a linkage map influence a trait of interest. Results are shown in a chart with all markers on the map plotted against their (statistical) contribution to the trait.
3 Linkage map: a map showing the order of markers and genes along each of an organism's chromosomes (i.e., how they are linked). It is also called a genetic map.
- Author: Ben Faber
In any single location, there are typically more earthworms and more earthworm species found in temperate regions than in the tropics. Global climate change could lead to significant shifts in earthworm communities worldwide, threatening the many functions they provide. These are the two main results of a new study published in Science. The research was led by scientists from the German Centre for Integrative Biodiversity Research (iDiv) and Leipzig University. They brought together 140 researchers from across the globe to compile the largest earthworm dataset worldwide, encompassing 6928 sites in 57 countries.
Earthworms can be found in many ecosystems worldwide. Where the soil is not frozen (permafrost), too wet, acidic, or completely dry (deserts), earthworms substantially shape the way ecosystems function. They dig holes, mix soil components and eat organic debris. By doing so, they drive a wide range of ecosystem services, such as nutrient provision, freshwater supply, carbon storage, climate mitigation or seed dispersal. It is for these reasons that earthworms are considered highly important "ecosystem engineers". This importance is also reflected by the large amount of biomass that accumulates in earthworms: in fact, the total earthworm biomass is often larger than that of all mammals living in the same area.
Although the great impact of earthworms on ecosystems and the services they provide to people are well known, little is known about how they are distributed on a global scale. "Researchers have known for decades that for any given area in the tropics we would usually expect more species than in the same sized area in temperate regions," says first author Dr Helen Phillips, researcher at the German Centre for Integrative Biodiversity Research (iDiv) and Leipzig University (UL). "But until now, we had been unable to quantitatively investigate the same global patterns for earthworms, as there was no global earthworm dataset."
Phillips and her colleagues aimed to create a global map using as much data on earthworm diversity, abundance and biomass as possible. Working as part of an international sDiv (iDiv's synthesis centre) working group, Phillips, senior authors Nico Eisenhauer (iDiv, UL) and Erin Cameron (Saint Mary's University), as well as members of the working group contacted earthworm researchers from around the world and asked them to provide their data for compiling a whole new global earthworm dataset with open access for everyone. "Initially, we thought this is a crazy idea. But then, we were impressed how many colleagues were highly motivated to share their data for this exciting endeavour," says senior author Prof Nico Eisenhauer, research group head at iDiv and Leipzig University. "We basically started from scratch in 2016 - only a couple of years later we could publish one of the largest datasets on soil biodiversity. This is an amazing achievement of the lead author Helen Phillips and the many scientists that trusted in us."
The results of this huge effort show that patterns of belowground biodiversity do not match those observed for organisms living aboveground. Plant, insect or bird diversity (number of species within any given area) typically increases from high to low latitudes, meaning that the number of species is highest in the tropics. For earthworms, however, the researchers found the opposite pattern. In fact, highest local earthworm diversity was found in Europe, northeastern USA and New Zealand. Similar patterns were found for earthworm abundance (number of individuals per area) and earthworm biomass (mass per area) - also showing highest values in temperate regions.
At the same time, earthworm species in the tropics seem to have smaller distribution ranges. "In the tropics, if you drive just a few kilometres, you may find a whole new set of earthworm species, while in the colder regions they remain more or less the same," says Helen Phillips. "This could mean that while there are few species found in a single location in the tropics, the total number of species across the whole region may in fact be extremely high. But we don't know yet." The main reason for this uncertainty is that many tropical earthworm species have not yet been described. Thus, earthworms identified at different locations could belong to the same species or not - a question to be resolved.
The researchers also assessed which environmental factors drive the number of earthworm species, as well as their abundance and biomass. They found that factors related to precipitation and temperature had the largest effects. "Based on these strong climate effects, we conclude that climate change could cause shifts in earthworm communities and change the functions and services ecosystems provide," says Nico Eisenhauer. "Given their role as ecosystem engineers, we are concerned about potential cascading effects on other organisms like microbes, soil insects and plants."
The results of the study have implications for conservation priorities: Biodiversity is usually an important criterion for the selection of protected areas. However, focusing only on aboveground diversity may result in insufficient protection of earthworms. Thus, belowground biodiversity needs to be included for a complete assessment - enabling conservationists to identify the planet's true biodiversity hotspots. "It's time for a paradigm shift in the conservation of biological diversity - because they are mostly dwelling in the soil, we easily forget about the amazing creatures under our feet," says Nico Eisenhauer. "Earthworms may be cryptic and may not have the charisma of a panda bear, but they are extremely important for other organisms and the functioning of our ecosystems."
Higher local earthworm diversity in temperate regions than in the tropics
Image: Infographic depicting main results of new Science publication. (Picture: Fuse Consulting)
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