VitisGen2 Staff Spotlight – Cheng Zou

Cheng ZouCheng Zou joined the Cornell Biotech institute and began working as a postdoc in the VitisGen2 project in Jan 2018. She received her Ph.D in Plant Molecular Biology in Peking University in China, and then she did her first postdoc at Michigan State University with Prof. Shinhan Shiu, working on the evolution of gene regulation. She also completed a Masters’ Degree in Statistics at MSU during that time. After that, she went back to China to work at the Chinese Academy of Agricultural Science. With VitisGen2, Cheng is conducting bioinformatics analysis, such as designing rhAmpSeq primers and helping unlock genetics questions using bioinformatics analysis.

What got you interested in grape genomics?
I have studied many species in the Plant Kingdom, like Arabidopsis, rice, maize and wheat. Genomics studies of the Vitis genus is challenging due to its high diversity and heterozygosity. I like challenges in my research, and I also always like to solve problems that can help breeders to make better crops.

Hallway with computers lining the entire wall.

Genotyping data is stored in this room full of computers, on Cornell’s Ithaca campus.

What are some major challenges faced by plant breeders, and how will your work address them?
With its several thousand varieties, the Vitis genus is characterized by high levels of genetic diversity. These varieties are adapted to survive in a wide range of habitats and ecosystems. In order to make use of these abundant genetic resources we need markers to character them and trace them during the breeding. My work is to provide a tool that make the utilization of diverse Vitis species possible.

What is your role with the VitisGen2 project, and how does your research fit in with the overall goals of the project?
In my first year in the VitisGen2 project, my major project has been developing a marker system that works for the whole Vitis genus. With VitisGen1, the team has explored several platforms and found that the AmpSeq platform can eliminate issues found in traditional genotyping-by-sequencing. Preliminary efforts also indicated that using markers based on core-transcriptome worked more universally. Therefore, in VitisGen2, we combined the core genome marker development with an improved AmpSeq technology, called rhAmpSeq, to develop the markers that work for the whole Vitis genus. In total, we tested 2000 markers in four populations, and the transferability increased to 91.4%. This universal marker system is a potentially powerful tool for germplasm evaluation (including germplasm fingerprinting, genetic diversity analysis, and heterotic grouping), marker-assisted breeding, and primary quantitative trait loci (QTL) mapping.

What is the most exciting thing you’ve learned or done since starting work with VitisGen2?
When I first started, I was very nervous about the performance of these core-genome markers. But, after we genotyped four families that represent the wide diversity of the grape germplasm, we found that this set of markers outperform our previous platform in many ways. This might be due to two factors: the region we chose to genotype, and the rhAmpSeq platform. To explain further, there are two important questions when you design markers. One is which region you choose to genotype. There are millions of variations existing in the genome, and we first identified regions that are highly conserved in the ten genomes that we examined in the Vitis genus. Then we picked the region with moderate polymorphism (differences in the code between different individuals). The second question is how to perform the genotyping. Based on our previous research, we found that AmpSeq works for the Vitis genus.  In 2018, IDT started to test their new platform named rhAmpSeq, which has a new checkpoint for the primer binding to the target, which increases the accuracy and speed.   This strategy can be applied to any genus or clade that diverged about 20 million years ago. Many groups, such as the USDA Breeding Insight, CGIAR, and Bill and Melinda Gates Foundation are adopting rhAmpSeq as a primary genotyping technology. The CGIAR plans to use rhAmpSeq for all the grass species, and the USDA Breeding Insight plans to genotype the Vitis germplasm in the National Clonal Germplasm Repository (NCGR) using this platform.

What tip would you give someone just joining the project (or just beginning a career in genetics)?
I am really enjoy working on grapes. Many genetic tools were designed for humans or maize. We should be very cautious when we apply those tools to grape. The Vitis genus is highly diverse and heterozygous. Most grapevines are propagated by clonal or mass selection of plant material. All those factors will make it a very unique material to study.