UC Davis researchers successfully produced the most highly extensive DNA sequencing of pistachios, alongside an in-depth characterization of the pistachio development stages
By MADELINE HASS — science@theaggie.org
Until recently, relatively little research has been conducted on pistachios despite their economic importance, great nutritional value and sustainable crop qualities. A team of UC Davis researchers has now generated the most comprehensive genome sequence of the pistachio, alongside an in-depth account of pistachio nut development.
This research study involved the collaboration of two labs focused on the Kerman cultivar of the pistachio nut. The new genome sequencing of the pistachio was accomplished by Grey Monroe’s team, while Bárbara Blanco-Ulate’s team focused on characterizing four distinct development stages of the pistachio.
Monroe, an assistant professor in the department of plant sciences at UC Davis and head of the Monroe Lab, said that this new type of in-depth sequencing was made possible by new advancements within DNA sequencing.
“In the realm of genetics, we are in a time of a lot of technological advances; one of those advances is around new technologies in DNA sequencing,” Monroe said. “The sequencing method we used is called circular consensus sequencing, which is available through the company Pacific BioSciences. They have something they call HiFi sequencing, which is what we used.”
As described in the team’s published study in the New Phytologist Foundation, young leaf tissue samples from Kerman trees were collected and flash-frozen in nitrogen for HiFi sequencing. HiFi sequencing employs fluorescent light signals to identify DNA bases and modified bases.
Once this initial sequencing is accomplished, Monroe’s team begins analyzing the data collected through extensive coding and writing computer software; this process is called bioinformatics. The team can then generate a data file with the genome sequence enclosed.
This data is then applied to the work being done within Blanco-Ulate’s lab to achieve a detailed analysis of the pistachio development processes. Blanco-Ulate’s team specifically focuses on characterizing four stages of development in the Kerman cultivar.
Jaclyn Adaskaveg, a postdoctoral research contributor and member of Blanco-Ulate’s lab, described the methods used.
“We were able to characterize the development every week as we collected samples across a 24-week period and did different phenotyping on each sample,” Adaskaveg said. “We looked at the different coloring on the pistachio, what the kernels looked like and other characteristics. We also gathered information on how its size is increasing and the hardness and texture of the shell itself.”
After examining many of the physiological aspects of development, Blanco-Ulate’s team complemented the data collected with a transcriptomic study, which is an account of gene expression at different periods. This allowed them to characterize individual stages of development in a way that had not previously been defined in depth.
“The transcriptomic study was across mainly the kernel development, which is about 12 weeks, during which we were able to integrate these two data sets and identify genes that were involved in key aspects of pistachio development,” Adaskaveg said. “We could see what genes were present, when protein was developing or what genes were driving [fat accumulation].”
This new information about each stage of development can serve as great insight for a variety of groups while also offering a new understanding of crop development and harvesting strategies.
“Pretty much anybody who works in pistachios can now use this tool,” Monroe said. “For example, here at UC Davis, we have plant breeders who are now going to use this as a tool for their plant breeding program.”
Real-world application of this research has already been displayed and as time continues on, the hope is that this new tool continues to prove beneficial. With this research, the future developments regarding pistachios remain boundless.
“We’ve now been able to give the pistachio world a lot more resources to work with,” Adaskaveg said. “There wasn’t really as high of a definition of a genome prior and we weren’t able to apply that to the development yet, so this will hopefully have really good applications for farmers and growers.”
Written by: Madeline Hass— science@theaggie.org
