Dr. Cari Schmitz Carley

Congratulations to lab member Cari Schmitz Carley on her successful PhD thesis defense! Cari made several contributions to advance genomics-assisted breeding for potato, including developing software to determine allele dosage in autotetraploids, selecting parents based on genomic-estimated breeding values, and determining the genetic correlation between locations in the National Chip Processing Trial. We wish Cari the best in her new position with the potato genetics and breeding program at the University of Minnesota.

Genomic selection in potato is here

For the past five years, the Endelman lab has been working toward the goal of implementing genomic selection for potato breeding, and it is finally ready to use! Details can be found in our new publication in Genetics, but the main practical message is we were able to predict yield, specific gravity, and fry color with accuracies of 0.4–0.5 based on a training population of 400 chip processing clones. Breeding value predictions were used to select parents after 3 years of field testing in early 2018, rather than waiting 4 or 5 years like before. We are now extending this research to other market types and traits.

Field Day 2017

The focus of the SpudPro field day this summer was W8890-1R, which is in its first field year of foundation seed production. This clone has excellent color, good skin set, and high yield potential with a smaller size profile at full maturity. Here is a photo of W8890-1R compared to other red clones at the Hancock Research Station, harvested by hand on July 20:

From Hancock we traveled a few miles to the south to see a one-acre trial of W8890-1R at Coloma Farms:

Maria wins grad student competition at PAA!

Congratulations to lab member student Maria Caraza (second from right) on winning first place in the graduate student oral competition at the 2017 Annual Meeting of the Potato Association of America, in Fargo, ND.

Maria’s presentation was titled “Using Image Analysis to Quantify Skin Set and Color in Red Potatoes.” Her research has given us a more precise understanding of the differences in skin color and skin set for red clones in the breeding program. Both traits are important for developing varieties with good appearance, and proper skin set also protects the tuber from disease during storage.

SpudPro homepage

The WPVGA SpudPro committee facilitates production of the initial foundation seed for new varieties from the UW-Madison breeding program. Meetings of the committee provide an opportunity to share information about new varieties with stakeholders. These presentations are now being archived on the SpudPro homepage.

Personnel updates

A few weeks ago, the lab group (and significant others) got together for a summer cook-out and to say farewell to postdoc Laura Shannon, who is starting her own potato breeding and genetics research program as an Assistant Professor at the University of Minnesota!

We also recently welcomed two new people to the lab. Postdoc Sushan Ru (far right, second row) completed her PhD at Washington State University and will be investigating the use of genotyping-by-sequencing in potato. The other new group member is Filipe Matias (far right, first row), a visiting PhD student from the University of São Paolo ESALQ who is studying genomic selection in the autotetraploid (like potato) forage grass Brachiaria.

New publications

Two new publications from the group appeared online at the start of the new year! The first paper concerns ClusterCall, a new R package for making tetraploid genotype calls from the potato SNP array. Because commercial potato germplasm is autotetraploid, there are three possible heterozygous genotypes for bi-allelic SNPs, which complicates conversion of the raw signal intensity into reliable marker data. ClusterCall automates this process and provides a concordance metric that can be used to filter out unreliable markers. The R package and a tutorial can be downloaded from the software section of the website.

The second paper describes how data from the potato SNP array was used to curate pedigree records for more than 700 elite varieties and breeding lines. Pedigree errors can arise in several ways, and correcting them is important for legal, cultural, and technical reasons. Our research is notable because not only did we identify numerous genotypes with mistaken parentage, in many cases the true parents were discovered unambiguously. For example, Hodag is a new chip processing variety released in 2015, with recorded parentage Pike x C31-5-120 (a genetic stock from UW). From the marker data we discovered that C31-5-120 is not the male parent; the true father is Dakota Pearl.

SpudPro Field Day 2016

The SpudPro committee of the Wisconsin Potato and Vegetable Growers Association (WPVGA) meets 2-3 times per year to discuss new varieties coming out of the breeding program. This summer we met in a Plover-area hotel for the business meeting and then headed to Plover River Farms, where Mike Copas (Senior Agronomist, RPE) discussed some preliminary results from a trial comparing our advanced breeding line W9133-1rus against the leading fresh market russet varieties, Goldrush and Russet Norkotah.

Three other advanced lines, W8893-1R, W9433-1rus, and W9576-11Y, are being tested on a larger scale (0.5 to 1 acre) by commercial growers this year. We look forward to learning more from the growers about the performance of the breeding lines at the fall SpudPro meeting.