Mapping genes for color, eye tubers, jelly ends and more

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.

GWAS for autopolyploids

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.

Tissue culture

In an earlier post, I discussed our efforts to select new breeding lines with genetic resistance to potato virus Y.  This is just one part of a larger strategy for virus management in the breeding program.  Another key part that has been gaining momentum in recent weeks is our tissue culture collection.  Tissue culture allows us to maintain and propagate many plants in a small space, and to do so under aseptic conditions (i.e., without introducing disease).  Each plant grows in a test tube filled with semi-solid growth media, and many racks of tubes can fit inside an insulated growth chamber with controlled lighting and temperature:
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Once a new breeding line is deemed to have significant commercial potential, which typically occurs after 6 years of field testing, young sprouts from the tubers are introduced into tissue culture for the first time.  At this point the plants are most likely not disease-free because they have been propagated in the field for many years, so the plants are put through a virus eradication process that involves exposure to certain antiviral chemicals and environmental conditions.  Grace has just transferred our first batch of breeding lines onto the antiviral media, so we’ll provide more updates on their progress later this year.

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Marker-assisted selection for PVY

One of the key developments in plant breeding in the last 20 years has been the use of molecular markers to select for genetic traits in segregating populations.  Disease resistance is perhaps the prime example of a trait amenable to marker-assisted selection.  Thanks to the diligent work of Grace Christensen (research specialist for the breeding program), we are now able to use genetic markers to track two resistance genes for potato virus Y (PVY).  One gene, designated Ry(adg), was introduced to cultivated potato (S. tuberosum ssp. tuberosum) from S. tuberosum ssp. andigena, and the other gene, Ry(sto), was introduced from the wild species S. stoloniferum.  The presence of either gene confers extreme resistance to PVY, which is very desirable as PVY is the leading reason why seed potatoes fail certification in Wisconsin.

The markers for both genes can be assayed using PCR and gel electrophoresis.  The gel image below shows our result for the Ry(sto) marker known as YES3-3B.

STO analysis 2

The YES3-3B marker linked to Ry(sto) produces a 284 bp fragment, which is visible as a third band on the left side.  To ensure the assay was working, we included W8946-1rus as a positive control, which is known to have inherited Ry(sto) from the USDA-ARS breeding line PA98V1-2.  For a negative control we used the PVY-susceptible line W6234-1rus.  Of the four new breeding lines tested in this gel, only AW08417-6rus showed a banding pattern indicating the presence of Ry(sto).  The other three did not inherit the resistance gene.

End of the Season, End of an Era

On Monday we harvested our last field trial at the Hancock Research Station, marking the end of the 2014 field season for the breeding program.  One of the key changes we made this year was to group all Year 4+ breeding lines from the same market category into a single trial, rather than evaluating the Year 4 and Year 5 cohorts separately (and lumping all market types together).  The biggest trial was our chip trial at Hancock with 229 entries and 401 plots, followed by the fry processing trial containing 100 entries and 221 plots (also at Hancock). Our fresh market trials were subdivided into russet, yellow, and red categories, and portions of these trials were replicated on commercial farms in Wisconsin.

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One of the highlights from 2014 was the success of our crossing program. More than 500 cross-combinations were made, with a focus on elite x elite crosses to maximize the probability of finding progeny with commercial potential. We also enriched our breeding populations for PVY resistance by “backcrossing” PVY-resistant chip and russet breeding lines to elite types.

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On a bittersweet note, 2014 marks the end of Bryan Bowen’s career with the breeding program.  More than twenty years ago, Bryan moved to Rhinelander to manage the UW research station and has led the transformation of that facility into an indispensable resource for the breeding program.  I am very grateful for his mentoring during my first year on the job.

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Field Days 2014

On July 18 there was a field day at the Rhinelander Research Station to showcase the work of the potato breeding program and other research taking place there:

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A few days later we participated in the potato field day at the Hancock Research Station to tell growers about our new varieties:

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Crossing and “true” seed

Several weeks are spent each summer cross-pollinating our best breeding lines to generate tens of thousands of true seeds that are genetically distinct.  Here is a photo of Lance and Grace removing the anthers from collected flowers:

CollectingPollen

After drying overnight, the anthers are shaken and shed pollen that is collected in tubes.  The true seeds are inside the green fruit, or berries, that develop after pollination:

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true_seeds

 

These seeds are called “true” because they are seeds in the botanical sense, whereas the “seed” that is typically used for planting potatoes is actually a piece of tuber.