- Author: Kathy Keatley Garvey
Danchin will speak on "Parasitic Success in the Absence of Sex: What Have We Learned from Nematode Genomes?" at 4:10 p.m., Monday, Nov. 20 in Room 122 of Briggs Hall. It also will be on Zoom. The Zoom link:
https://ucdavis.zoom.us/j/95882849672
Danchin, who specializes in genomics and adaptive molecular evolution, is with INRAE (French National Research Institute for Agriculture, Food and Environment) and is a senior scientist and scientific leader of the GAME team (Genomics and Adaptive Molecular Evolution) at ISA (Institut Sophia Agrobiotech), in Sophia-Antipolis, on the French Riviera.
"Root-knot nematodes are devastating plant parasites of worldwide importance. Interestingly, species that cause most damages reproduce entirely asexually," he writes in his abstract. "These nematodes are extremely polyphagous and have a wide geographic range. Theoretically, in the absence of sexual recombination animal species have lower adaptive potential and are predicted to undergo genome decay. To investigate how these species can be successful parasites on many hosts and in many places around the world, we have sequenced and analyzed their genomes. Out analysis confirmed these species are polyploid hybrids and the combination of several genotypes from different species might provide them with a general-purpose genotype. However, this does not explain how with a theoretically fixed genotype these species are able to overcome resistance genes or adapt to a new host. Therefore, we analyzed genomic variability across different populations and the possible mechanisms underlying genomic variations. In this presentation, I will provide an overview of our findings."
Etienne holds a doctorate in reproductive biology from the University of Paris (1980). He says on his website: "I am an evolutionary biologist working with genomes. I try to make biological sense of genomic singularities observed through comparative genomics. I have a special interest in plant parasites and I use bioinformatics as a tool to perform this research."
He lists his main research interests as:
- The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology
- Evolution and adaptation of animals in the absence of sexual reproduction and the underlying mechanisms
- Genomic signatures of adaptation to a parasitic life-style
Seminar coordinator is Brian Johnson, associate professor, UC Davis Department of Entomology and Nematology. For Zoom technical issues, he may be reached at brnjohnson@ucdavis.edu. The list of seminars is posted here.
- Author: Kathy Keatley Garvey
The next UC Davis Department of Entomology and Nematology seminar will focus on just that.
Brock Harpur, assistant professor, Department of Entomology, Purdue University, will speak on "Beekeeping in the 21st Century: Can We Incorporate Genomics into Beekeeping?" at 4:10 p.m., Wednesday, Nov. 6 in 122 Briggs Hall.
Host is Santiago Ramirez, associate professor, UC Davis Department of Evolution and Ecology, College of Biological Sciences.
"Humans and honey bees (Apis mellifera) have a long history of interaction one that today has culminated in the multibillion dollar beekeeping industry," Harpur says in this abstract. "Our history with honey bees is signposted by innovation driven by beekeepers. Innovations such as moveable frames and instrumental insemination have transformed how beekeepers manage their colonies. The modern beekeeper is likely to find that the innovations of today will become industry-standard in the not-so-distant future."
In his seminar Harpur will demonstrate "how the study and application of genomics provide new tools to understand honey bees and new means to manage and conserve them. I will present two direct uses of genomic information in modern apiculture: stock identification and genetic association. First I will demonstrate that genomic information can be used to quantify the ancestry of honey bee populations around the world. I will demonstrate how genomic information can be used to robustly discriminate among genotypes and how this can be incorporated into management practices. Second, I demonstrate how genomic approaches can identify loci associated with industry-relevant traits and how these associations can be used in an industry context. These discoveries represent the first steps that the beekeeping industry has taken into the modern age of genomics."
Harpur joined Purdue University faculty in January 2019 after completing a National Science and Engineering Research Council Postdoctoral Fellow at the Donnelley Centre, University of Toronto. He focuses his research on the evolution and genetics of honey bees.
"Brock has always been interested in insects and genetics, but after his first foray into beekeeping, he was hooked (stung, if you will)," according to the Purdue News Service. "Brock completed his Ph.D. on population genomics of honey bees at York University. He has established beekeeping programs in Northern Canada, worked with the City of Toronto to establish goals for pollinator health, and given public talks to dozens of local organizations. Brock was awarded the prestigious Julie Payette Research Scholarship from the National Science and Engineering Research Council of Canada, an Ontario Graduate Scholarship, the Entomological Society of Canada's President's Prize, and was an Elia Research Scholar during his time at York University. Brock and his wife Katey are new to the United States from Canada."
- Author: Elizabeth Fichtner
Recent advances in understanding the history of olive domestication
Elizabeth Fichtner, Farm Advisor, UCCE Tulare and Kings Counties
Olives are thought to have first been domesticated in the northeastern Levant, an area near the border of present-day Turkey and Syria. Map captured from Google Maps. |
With the emergence of the California olive oil industry, the state has witnessed a dramatic diversification in the olive cultivars grown commercially. Our mainstay black ripe olive industry, dominated by the ‘Manzanillo' olive, is now combined with increasing acreage of Spanish, Greek, and Italian cultivars used to create high quality, extra virgin oil. The historic table olive industry of California still represents around 18,000 acres of olives in the state, while approximately 40,000 acres are currently devoted to oil production.
Although olive cultivation in California is relatively new (dating back to the historic Spanish Missions established by Franciscan priests), olives are of key importance in the history and culture of the Mediterranean basin. A recent publication by a group of European, American, and North African scientists has re-evaluated the location of the domestication of the olive, providing genetic evidence that domestication occurred in the northeastern Levant, close to the present-day border of Syria and Turkey.
To complete the study, researchers collected plant material from nearly 2000 trees, sampling both wild oleaster populations and domesticated cultivars of olive. World Olive Germplasm Banks in Córdoba (Spain) and Marrakech (Morocco) served as sources of the majority of cultivars included in the study. Researchers utilized the genetic sequences of plastids (ie. chloroplasts) to discern differences between cultivars and wild oleaster populations. Plastids are organelles (structures inside cells) that contain their own DNA. Since plastids are generally inherited from one parent (similar to mitochondria), their genetic sequences are more conserved then that of nuclear DNA, which is contributed by both parents. Since olive is a wind-pollinated crop, nuclear DNA may be disseminated over large distances.
The genetic analysis of wild populations indicates three distinct lineages of olive: the Near East (including Cyprus), the Agean area, and the Straight of Gibralter. These three wild populations are likely linked to refuge areas where populations persisted through historic glaciation events. Interestingly, the geographic distribution of these three populations also corresponds to the subdivisions of the olive fruit fly, suggesting that these regions offered shared refuge habitat for both the host and the pest. The wild oleaster population in the eastern Mediterranean was found to be more diverse than previously thought and ninety percent of the present-day cultivars analyzed in the study matched this group. Common olive cultivars grown in California, including, Sevillano, Arbosana, Arbequina, and Koroneiki, all belong to this group originating in the eastern Mediterranean.
As a result of this study, it is proposed that the initial domestication of olive took place in the northeastern Levant; subsequently, plant material was disseminated to the whole Levant and Cyprus before being spread to the western Mediterranean. After these initial domesticated trees spread throughout the Mediterranean basin, they likely underwent subsequent domestication events by crossing with wild oleasters, thus introducing genetic material from the other two ancient western Mediterranean lineages.
Such studies may appear purely academic; however, they can also address more timely questions and assist in characterizing cultivars. For example, a 2010 study in California made genotypic comparisons between historic olive plantings in Santa Barbara, CA and at Santa Cruz Island, CA. The study elucidated that the olives on Santa Cruz Island, planted in the late 19th century are different than other historic olive plantings in Santa Barbara, CA. Olives planted at the Santa Barbara Mission in the late 18th century are the ‘Mission' cultivar, whereas those on Santa Cruz Island (Figure 3) are generally ‘Redding Picholine.' Interestingly, the olives on Santa Cruz Island are thought to have been planted for oil production, but there are no historic reports of harvest or sale of a crop. Additionally, the Santa Cruz Island olives have become somewhat invasive on the island due to their propensity to establish from seed. As a result of genotypic analysis of these populations and the fact that ‘Picholine' makes an excellent rootstock due to its ease of propagation from seed, it is hypothesized that the ‘Picholine' variety was intended as a rootstock, but the grafts never took. Consequently, maturation of a ‘Picholine' orchard may have just been an accident, a mistake, or simply bad luck. The completion of this local population genetics study may have helped explain the unsolved mystery of the historically unharvested trees on Santa Cruz Island.
Find Santa Cruz Island.
Besnard, G., Khadari, B., Navascués, M., Fernández-Mazuecos, El Bakkali, A., Arrigo, N., Baali-Cherif, D., Brunini-Bronzini de Caraffa, V., Santoni, S., Vargas, P., Savolainen, V. 2013. The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant. Proc R Soc B. 280: 20122833.
Soleri, D., Koehmstedt, A., Aradhya, M.K., Polito, V., Pinney, K. 2010. Comparing the historic olive trees (Olea europaea L.) of Santa Cruz Island with contemporaneous trees in the Santa Barbara, CA area: a case study of diversity and structure in an introduced agricultural species conserved in situ. Genet Resour Crop Evol 57:973-984.
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- Author: Jeannette E. Warnert
McClurg spoke to Alison Van Eenennaam, a UC Agriculture and Natural Resources Cooperative Extension specialist. Van Eenannaam is an animal geneticist based at UC Davis.
"We used to have somewhere roundabouts 25 million dairy cows in the United States, and we're down to nine million now,” says Van Eenennaam. "It [has] actually reduced the environmental footprint of a glass of milk by two-thirds relative to the 1950's."
Van Eenennaam is currently studying cattle genomics to understand the animals susceptibility to respiratory disease. Her research is funded by the USDA Agriculture and Food Research Initiative.
Read more about the benefits of genomics to the dairy industry and the environment in the UC Green Blog.
- Author: Jeannette E. Warnert
For the most part, dairy operators select cattle for breeding that have the highest genetic potential for milk production, health, structural soundness and fertility. The introduction in the 1940s of artificial insemination from bulls that were proven to father productive daughters resulted in dramatic changes to the industry, according to geneticist Alison Van Eenennaam, UC Cooperative Extension specialist with UC Agriculture and Natural Resources.
“In the U.S., we used to milk 26 million cattle, now there are 9 million, and despite that reduction we produce one and a half times more milk for American consumers,” said Van Eenennaam, who is based in the Department of Animal Science at UC Davis. “The carbon footprint of a glass of milk today is about one-third of what it was in the 1950s.”
Genomics does not involve genetically modified organisms (GMOs). It involves the sequencing and analysis of the cow genome. Mapping of the cow genome, completed in 2009, has provided scientists with information on the 3 billion base pairs on cattle DNA from which they can conduct research trials to tease out which pairs are responsible for which traits. The process is so complex that research will continue for decades, but progress is already reaping rewards for the dairy industry.
“There's almost always an inverse correlation between production and reproduction,” said Van Eenennaam. “If you don't include fertility in your breeding program, it will decline as you select for more productive cows. Genomics allows us to make selection more balanced and include all of the traits that are of importance to dairy production.”
Scientists are looking for bulls with the genetic markers for fertility combined with the markers for high milk yield. The combination of markers are genotypes.
Identifying bulls with the optimal genotypes is the first step. Next, the producers must decide how to use the information, according to Joe Dalton, a geneticist at the Center for Reproduction Biology at the University of Idaho. Dalton is a member of a team that received a grant from USDA to spread the word about dairy genomics to producers around the U.S.
Dalton suggested four potential ways dairy operators can use information about dairy cattle genotypes to optimally manage the genetics of their herds:
- To sell the animals
- To make breeding decisions
- To identify an animal's parentage
- To make informed purchasing decisions
Van Eenennaam is working with cattle genomics to address the animals' susceptibility to respiratory disease. When cows catch cold, the viruses can weaken the immune system. Opportunistic bacterial infections can settle in the lungs and result in pneumonia, which requires expensive treatment with antibiotics and can even cause premature death.
“We will need to prevent these diseases in the future,” Van Eenennaam said. “Cattle that are sick with pneumonia are frequently treated with antibiotics. Breeding in resistance to respiratory disease will reduce that.”
Van Eenennaam and her collaborators took DNA samples from 1,000 California dairy calves suffering from respiratory disease and their immediate neighbors who remained healthy. They compared the DNA profiles of sick calves with healthy calves to identify regions in the genome that differed between the groups.
Her research has shown that 21 percent of susceptibility to respiratory illness can be attributed to the genetics of the calves.
“More than 100 genomic regions were significantly associated with respiratory disease,” Van Eenennaam said. “That supports the idea that many genes are associated with susceptibility to the disease.”
In time, respiratory disease susceptibility can be included in the index that producers consider when selecting the genetics of the cows they milk on their farms.
This research project is being funded by the USDA Agriculture and Food Research Initiative.
An initiative to enhance competitive and sustainable food systems is part of UC Agriculture and Natural Resources Strategic Vision 2025.