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.
My field day presentation at the Rhinelander Agricultural Research Station made the cover of the August 2016 issue of the Common’Tater.
In March 2016, the WPVGA SpudPro committee voted to name breeding line W5955-1 ‘Hodag’, after the mythical creature and local mascot of Rhinelander, Wisconsin. Here is one interpretation of the Hodag potato (note the sprouts), drawn by group member Cari Schmitz Carley, who grew up in Rhinelander:
The real Hodag potato is less frightening, as seen in the following photo, taken at the Hancock Field Day on July 28, 2016:
The Hodag variety has a number of favorable characteristics, including common scab resistance and long-term storage potential. Here is a photo of kettle-style chips from its first trial on a commercial processing line, after 8 months of storage at 48F.
Hodag should be managed for size carefully, as it produces large tubers and hollow heart has been observed in some environments. Here is a terrific factsheet by Felix Navarro with more information.
Maria Caraza has joined the lab as a PhD student in the Plant Breeding and Plant Genetics program. Maria has been involved with potato research for many years, including at the International Potato Center (CIP) in Lima, Peru, and for her MS degree at Dalhousie University in Halifax, Canada. Maria’s research focus will be on the genetics of skin set and color in red potatoes.
Last week was bittersweet, as we said goodbye to Lance (fourth from left) but also congratulated him on completing his MS in Plant Breeding and Plant Genetics. One focus of Lance’s research was to measure the genetic correlation between the Hancock Agricultural Research Station (where we conduct our preliminary and advanced yield trials) and two commercial farms, over a two year period. For every trait examined, including yield, shape, size distribution, and specific gravity, the research station seemed representative of the “population of environments” on the commercial farms. Lance used the uniplot visualization technique to reach these conclusions, as shown below for the % of marketable yield greater than 6 oz.
Each environment had a three digit code: the first letter indicating the location (H = Hancock, C = Coloma, N = Nekoosa) and the second two digits indicating the year. For environments that fall on the circle, the correlation equals the cosine of the angle defined by the points and center of the circle. This geometric interpretation becomes less exact as the points move toward the center of the circle (in which case the full correlation matrix should be consulted).
Lance is headed to Mount Vernon, Indiana, for a position in the Dow maize breeding program. He will be missed!
The Jansky and Endelman labs are collaborating on a project to use recombinant inbred lines for genetic mapping in potato. En route to that goal, we used the first F2 population to map 10 genes, including all 5 previously mapped genes for tuber pigmentation, the CHY2 locus for yellow flesh, the Ro locus for tuber shape, and new genes for eye tubers, jelly ends, and short anthers. Our publication also identified two misanchored super-scaffolds in version 4.03 of the potato reference genome.
Genome-wide association studies are widely used in diploid species to study complex traits in diversity panels and breeding populations, but GWAS software tailored to autopolyploids like potato has been missing…until now. Postdoc Umesh Rosyara is the first author on a publication illustrating the features of GWASpoly, an R package we developed for autopolyploids. You can also download the software.
Our paper on the first three years of the National Fry Processing Trial (NFPT) is now published in Crop Science.
Although I give presentations to potato growers and other scientists quite often, until two weeks ago I had never given a seminar to the general public about the potato breeding program. My seminar was part of the Northern Lights Tour for UW-Madison’s Wednesday Nite @ The Lab series and received some coverage on the nightly news in Rhinelander.