Frogsleap Farm

Frogsleap Farm

Friday, November 23, 2018

Introgression of traits from commercial tomato hybrids into heirloom types


Heirloom type tomatoes are the result of generations of selection for flavor.  However they typically lack other elements of fruit quality, such as tolerance to cracking/splitting and improved shelf life. Some heirlooms have low-level tolerance to some disease complexes, but lack the resistance to specific tomato pathogens that can greatly improve plant health and productivity.

On the other hand, many new commercial hybrids have multiple pest resistance to key disease and nematode pests, and improved tolerance to splitting, cracking and cat-facing.  Some commercial hybrids also demonstrate significant improvement in shelf life when compared to heirloom types.  However, strong selection pressure for fruit quality, fruit yield, plant health and traits that make the fruit “transportation friendly” has led to commercial hybrids that typically lack the excellent flavor of the best heirloom types.

The breeding challenge is to efficiently and effectively combine the great flavor of the best heirloom types with the improved plant health, fruit quality and productivity of newer commercial hybrids.  Harry Klee and colleagues at the University of Florida have attempted this by crossing a disease resistant commercial parent line to flavorful heirloom types to create novel hybrids (e.g. Garden Gem and Garden Treasure).   A step in the right direction perhaps, but it is a quick fix that likely falls short of what could be achieved in a breeding program designed to preserve or enhance flavor and stack dominant pest resistant genes on both sides of the hybrid pedigree. Introgression of traits associated with plant health (e.g . pest resistance) and fruit quality (e.g. tolerance to cracking) from newer commercial hybrids into selected heirloom types provides an opportunity to capture the “best of both worlds” in multiple parent lines that can be used to produce novel hybrids with a combination of high flavor, high yield, high fruit quality and multiple pest resistance/improved plant health – a trait combination that does not exist in the market today.

University tomato researchers have done an outstanding job of identifying sources of resistance to key tomato pests in tomato wild relatives, and then finding a molecular marker that co-segregates with the desired gene for resistance to the specific disease or nematode.  Selection for the associated genetic marker (i.e. marker assisted selection or “MAS”) allows tomato breeders to efficiently identify plants that carry the desired pest resistance gene (MAS reference).  Combining MAS with phenotypic selection in breeding populations derived from crosses between heirloom types and commercial hybrids allows the design of a breeding program that, over several generations of selection, stacks multiple pest resistance genes into stable inbred lines which have also been selected for high flavor and fruit quality.

2017 MAS nursery and trials

After 8 generations of MAS genotypic selection and two cycles of field phenotypic selection for flavor, fruit quality and fruit yield, we have created our first generation of multiple pest resistant experimental hybrids.  These were evaluated in open field and greenhouse trials in 2018.  We were able to document the multiple pest resistance (up to 10 pest resistance genes) of the hybrids and found individual test cross hybrids with heterosis for both fruit yield and fruit flavor.  

The best of these new hybrids tasted as good as or better than our best heirloom-derived lines, with generally improved fruit quality characteristics.  The first generation hybrids are cherry to saladette size – larger fruited types are a year or two behind.  The initial crosses were designed to generate breeding lines segregating for fruit color and stripes, so a diversity in fruit color, shape and size will be available in these new hybrid products.

In parallel we have been working on improving shelf life by selection per se, and by incorporating mutant alleles of RIN or NOR - key genes regulating fruit ripening in tomatoes.  Extended shelf life (XSL reference) will be a key feature of several of our new Cream of the Crop TomatoTM multiple pest resistant hybrids.  

Monday, January 1, 2018

New Year's News from Frogsleap Farm

We've each had 25+ year careers in plant breeding.  It’s been fun, but we are excited to be within 4 months of retirement. This will allow us to fully shift from working for someone else to working for ourselves, and from breeding agronomic crops to breeding fresh market tomatoes.  Tomato breeding started as a hobby about a decade ago and has grown into a passion.  We are extremely fortunate to have found an ideal partner that can handle the commercial side of our new business, and allow us to focus on breeding.  We will continue to post here and a few other places as Frogsleap Farm, but our products will be sold under the brand “Cream of the Crop Tomato” (link).   We hope to have our first products on the market next winter.


An earlier post on this site (link) was designed to provide a high level overview on the use of molecular markers in tomato breeding.  In 2015 we crossed our favorite FLF breeding lines to various commercial F1 hybrids carrying resistance to multiple tomato pathogens.  We used molecular markers associated with these disease resistance genes to identify segregating progeny that contained the desired combination of these new traits.  After 4-5 cycles (2-3 generations/yr) of Marker Assisted Selection (MAS) we now have mostly stable lines which are homozygous for some combination of the following resistance genes (and markers): tomato mosaic virus (Tm2a), tomato spotted wilt virus (Sw5), tomato yellow leaf curl virus (Ty1 and Ty3a), Verticillium wilt (Ve), Fusarium wilt (I1,I2 and I3), late blight (Ph2 and Ph3) and leaf mold (Cf9).  The project got legs this year with phenotypic evaluation of 1000+ genotyped plants in our Wisconsin breeding nursery, enabling us to combine selection for flavor and other fruit characteristics.  We are continuing to integrate multiple disease resistance into much of our heirloom-derived germplasm and will be making crosses this year to produce new F1 hybrids with resistance to most of these diseases. 


Jess taking leaf samples for marker analysis

2017 Wisconsin Molecular Marker Nursery

Septoria is a devil of a problem.  In our breeding nurseries in NC, PA and WI, Septoria is almost always the most damaging disease, Like clockwork it starts on the bottom leaves about early fruit set and then defoliates the plant from the ground up. There has been no good source of resistance in commercial germplasm (yes, this includes Iron Lady, the so-called tolerant/resistant hybrid from Cornell); but some lines are worse than others.  Over the years we thought we found sources of some tolerance – but it wasn’t repeatable the following year.  This year we found two lines with significantly less damage than the nearest neighbors, and for both this was the second such observation in consecutive years.  Both 2016 and 2017 were wet in the Midwest, we didn’t apply fungicides, and Septoria was rampant with extensive associated plant symptoms.  One of our new “tolerant” lines traces to a cross to a S. pimpinellifolium accession I got from Dar Jones, and tolerance looks excellent.  We will have these in broader testing next year. 

For several years we have been evaluating segregating progeny from heirloom beefsteak x cherry/saladette crosses.  In successive filial generations and cycles of selection (phenotypic recurrent selection) we have focused on large fruit size, excellent fruit quality and great flavor.  We are finally getting stable large fruited segregants in various colors – most with excellent flavor and great fruit quality.   This winter we will start making test crosses with these new breeding lines and begin the process of incorporating multiple disease resistance genes.

Three beefsteak segregates from cherry x beef crosses 
One of our most exciting projects is focused on Extended Shelf Life (ESL).  Various ESL strategies were also outlined in a previous post on this site (link), but since then we feel we have identified an excellent rin inbred that consistently contributes ESL traits combined with excellent flavor in F1 hybrids and we are jazzed about what may be a novel allele of “nor” (“non-ripening” gene) that appears to provide many of the core ESL attributes - but with normal carotenoid accumulation.  We have a new collaboration with a university plant biologist to explore mode of action of this trait, which appears to be novel in fresh market tomatoes.  The challenge with most delayed ripening strategies is getting the desired ESL phenotype without sacrificing fruit flavor and color.  We think this may be a breakthrough.

New ESL breeding line with delayed ripening and normal flesh pigmentation

This summer we had a very generous invitation to visit Japan and learn about their commercial tomato production system and current and future variety needs.   It is predominantly high input seasonal greenhouse production of cherry and grape types, the hybrids having a particular plant architecture and disease resistance profile.  It knocked our socks off.   We now have a segment of our breeding program targeting such products, starting with our crosses to commercial Japanese hybrids and progressing to MAS selected F2 progeny being planted this month in a greenhouse for the next cycle.

Learning the basics on their trellis system

A variety of farm produced juices from Japan

        Finally, to all our tomato friends – Happy New Year!