I had the chance on Sept. 28 to chat with Amit Dhingra, assistant
professor of horticultural genomics and biotechnology at Washington
State University, Pullman.

1:03 p.m. Tom Karst: Thanks for taking time for a chat today. First of all, tell our readers a little about "what you do" with WSU and the tree fruit breeding program.
 ..
1:06 p.m. Amit Dhingra; I am part of the Breeding, Genetics and Genomics team at WSU where I in particular utilize genomics approaches to study plant processes underlying economically important traits, to discover crop specific genes, that can be rapidly employed for horticultural or physiological solutions or existing varietal improvement via directed sports (mutation) induction or used in breeding program for new variety development.

1:08 p.m. Tom:  I appreciated you showing me around the research farm in Wenatchee while I was reporting for stories for the Washington apple tab, and it was interesting to hear about the mapping of the apple genome. Why is that project significant and where does it stand right now, at least relating to practical implications for breeding?

1:09 p.m. Amit: My pleasure.

1:13 p.m. Each economically important trait is controlled by a gene or a set of genes working in an orchestrated way. Scientists have till now used indirect and rather long methods to pin point what region(s) of the genome is responsible for a given trait. This exercise does not always yield information on the actual gene. In fact, most of the time, scientists know the general area of the genome where the gene may be located. Therefore, having knowledge of the complete coordinates of apple genome is significant to be able to pin-point which gene(s) is responsible for making apple flavorful or cold tolerant. So far the apple genetics research has been like a city without a map. One knows the general region where the grocery store may be but doesn’t know where exactly it is.

1:14 p.m. Tom: Good analogy...

1:19 p.m. Amit: Right now the apple genome project in my program is funded by USDA, WSU and WTFRC and we have generated draft coverage of that. In addition, a group in Italy has also been sequencing the genome of the same apple and our combined data set provides an almost complete map of the apple genome. The research results should be published in a few months. Then, important genes or genetic regions related to commercial traits identified by several scientists all across the community can be placed back on the map, their coordinates can be identified and that knowledge can be utilized for breeding apples by design.

1:21 p.m. For example if we know from previous pathology studies that a gene named G provides resistance to powdery mildew. We can quickly search the genome sequence and find the chromosome where this gene is present and also what is its sequence. Then, the seedlings generated from a new cross between the parents can be screened using DNA technology for the presence or absence of the G gene. If it is present, then we keep the seedling. If not, we cull that seedling. This way we can increase the efficiency of the breeding process while generating powdery mildew resistant apple.

 Tom: I know this is a difficult question... but what types of advances do you see in tree fruit breeding in the next 10 to 15 years- whether in apples, pears or cherries. s you talk about powdery mildew and breeding, no doubt disease resistance will be valued by growers. Perhaps size, taste, and other characteristics as well...?

1:29 p.m. Amit: One certain aspect of using the DNA or genome-based knowledge would be to increase the efficiency of breeding. The way we read the genomes of any organism is going through an exponential upgrade every day. Today we can read the human genome (3.4 billion letters) in about a month. The cost is coming down considerably. In the future, we will read the genome of every seedling generated from a cross and be able to predict its profile using computers. It will of course require knowledge of what all (about 60,000 genes in apple) do or what their individual and collective function is. Then, we can breed apples by design for specific geographical areas, flavor, taste, size and different consumer preferences as well.

1:31 p.m. Tom: How many are working on tree fruit breeding, including the genomics program?

1:34 p.m. Amit: The major apple growing region is centered around Wenatchee. The apple breeder and physiologists are stationed at the WSU Tree Fruit Research and Education Center in Wenatchee. WSU Pullman is home to the biochemistry, genomics, genetics and bioinformatics programs that support the apple breeding program.

1:35 p.m. There are about 10 programs that are working on various aspects of apple improvement. USDA also has several scientists based in Wenatchee working as part of the larger team to address issues related to apple improvement. We like to call it apple improvement program.

1:38 p.m. Tom: I remember from our conversation that pear growers are also interested in what your program can offer. Do you also see room for improvement in pear varieties in the Northwest?

1:40 p.m. Amit: Yes. The methodology of genomics can be applied to any organism with DNA. The situation with pears is different as I have learned from the industry. There is always an interest regarding new varieties however, the existing varieties are very successful. My program is working with some growers on addressing some of the production and post-harvest issues with existing varieties.

1:42 p.m. Tom: Very good. Thanks for taking time today. One last question and I'll let you go. How did you first get involved with genomics and what motivated you to come to Washington state and be a part of the program there?

1:47 p.m. Amit: During my Ph.D in India I was involved in functional genomics of rice and our lab there eventually participated in sequencing the rice genome. So genomics is not anything new for me. I have worked in this area since 1995. While I was working as a post-doctoral scientist at University of Florida, the laboratory worked on strawberry genomics. I got an opportunity to get involved with strawberry research. As you know strawberry is a relative of apple, pear, cherry, peaches etc the position at WSU seemed both interesting and challenging. It has been a great place to learn from the industry and utilize my past experience to resolve important questions with this delicious yet enigmatic group of plants.

1:48 p.m. Tom: Good luck with your work and we'll be watching for new and improved tree fruit from WSU! Thanks again Amit