My published articles on daylily genetics.

Daylily Genetics 1: Understanding genotype and phenotype. The Daylily Journal. 2010; 65(1):12-14.
Daylily Genetics 2: Pathways to Color: From Phenotype to Genotype. The Daylily Journal. 2011; 66(1):42-50.
Daylily Genetics 3: Variegated or Broken Flower Colors: Jumping Genes? The Daylily Journal. 2011; 66(2):58-59.
Daylily Genetics 4: Pod or Pollen Parent: Do they Determine Different Seedling Characteristics? The Daylily Journal. 2011; 66(4):42-45.
Daylily Genetics 5: Foliage, Growth and Flowering. The Daylily Journal. 2012; 67(2):50-51.

They are crammed into too few pages and really would need hundreds of pages to do the topics justice so they are very "dense" going. They should all be available to A.H.S. members either through their printed journal or by downloading from the society web-site. One or two have been freely available from that same web-site in the past.

I am happy to discuss any questions related to these or similar topics - especially as that will be without page limits.

Chapter 2: Form and Species (just my take on it )

This chapter reviews the past use of F1/Mendellian hybridization models (sibling crosses to show simple white and purple pea flower color inheritance ratios) and then further explores McGarty’s F0/Gene-rations model (my word for his notation that shows how many generations a seedling is from its species and/or ancestors in order to track and show complex changes that the Mendellian model cannot). With the Mendellian model, plant breeders assumed a simple one-to-one mapping of colors to single genes, but this method quickly falls short of explaining the wide variation and gradations produced in daylily colors and patterns. So, to examine the more complex color expressions in hemerocallis, McGarty focuses our attention toward how color is produced first within the genetic/cell system itself, and then as part of an interconnected pattern of color production within petals and blooms.

Such a Range of Colors


The chapter opens by re-emphasizing the importance of using of our senses to observe, not just by looking, but by multiple senses, the unique characteristics and differences found in species plants. They are first and foremost the genetic pool of ancestors from which our modern-day cultivars have descended. Leaf and petal texture, various scents, the patterns in time for when they bloom, each characteristic is produced from genetic codes that get woven into subsequent generations. Physical systems form the outward details of what we all observe and highlights the importance of our own careful and detailed observation for understanding how daylily genes (the genotype) create the phenotype (external physical characteristics) of each plant.

One of the Foundational Species


Genotype refers to specific DNA and RNA that create protein codes resulting in the formation of genes in each cell that direct how physical attributes will appear and function. Because nucleic acids (the NA in DNA/RNA) can randomly re-combine, that creates a wide variety of how inherited characteristics may be expressed. For example, the F1 generation of offspring from McGarty’s own experimental breeding of fulva species with citrina species included offspring that had petal, stamen, and pistil lengths and widths that both undershot and overshot their species parents. This demonstrates that Mendellian-type associations of one-set-attribute-to-one-gene does not explain inheritance in daylilies, or only lengths and widths identical to either one of the parents would have been produced. Instead, the complex pattern of inheritance mixes, matches, and spreads attributes across a wider spectrum, while clustering most inherited attributes much like a bell curve around a general range of characteristics expressed by the parents.

Roots: Short and Bulbous, Mixed, and Long and Thin


He returns from his discussion on genes to focus once again on the importance of first looking at and then classifying the physical details of species plants. To start, he outlines the ways in which phenotype can be classified, and mentions that genotype classifications will be covered in a later chapter. The first of the phenotype classifications is: Form. Form refers to the physical nature of the different parts of the plant, and for purposes of his book, they are limited to roots, leaves, buds, flowers, and seed pods. Narrowing the focus like this should help us observe and remember differences as we learn how to identify our daylily species plants.

Leaves: Grass Thin, Full and Twisting, Classic Fan


The examination of roots will focus on the shape and size of the plant’s water absorbing system for nutrient storage and transport. Leaves with varying widths and lengths are the structures in which chlorophyll processes and creates energy for the plant. Buds of different shapes and sizes extend out from scapes of various thickness, height, and branching, depending on the cultivar. And species flowers, which now have descendants showing highly variable colors and physical characteristics, are formed with three inner petals, three outer sepals, six pollen stamens, and one female pistil that leads to an ovary. Pods are fertilized ovaries that produce and house seeds.

Buds: Balloon, String Bean, Whitish Color


I’ll stop here for now, as the remainder of the chapter is full of wonderful descriptions and pictures that explore differences in those five form characteristics found between the main species. I like to learn by recreating the process by which something is taught, and so I will see if I can assemble ATP database and other free-use photos to show what he describes of the identifying characteristics of the relatively few daylily ancestors behind today’s modern cultivars.

Petals and Sepals, Stamen and Pistil, Fertilized Seed Pod

chalyse, I can see you are putting a lot of time and work into this, I love the way you have gone about adding the ATP data base plant pictures as examples. This does emphasize the need to put pictures of all parts of the plant in the data base, not just blooms!

Thanks! ... in hoping people will become more interested in uploading photos of additional plant parts to the database! There are labels that apply to each part of these daylily plant forms:



Each segment of the daylily is important and can help to identify cultivars' physical characteristics. I know from experience that it can feel funny, for example, to photograph and upload roots (not a pretty sight next to all the lovely blooms!), but they are considered to be just as significant from a scientific viewpoint and their illustrations are historically important, invaluable and needed.

Hybridizers and home gardeners alike may also benefit from these kind of photos by perhaps learning such things as how to recognize root systems that will spread far and wide, longer or more bulbous roots that may weather drought well, or smaller, tidier root systems that may be easier to keep in pots. Each photograph of a different part of each cultivar gets a full acorn for uploading, so snapping pictures of the entire plant, foliage fans, its seed pods, the pollen anthers and pistil, and even the roots can be very "rewarding"!

this is terry mcgarty, i saw this discussion and thought it was worth commenting on

i do not know "maurice" so i cannot comment on his remarks but i saw what i believe are his comments a couple of years ago

flower color is an interesting area. i was stimulated to examine it a bit by reading alan turing last paper on tesselation, where he discusses colors in zebras and the like. however we have recently begun to understand patterns such as those on calico cats as being epigenetic in nature and not just genetic. yet even there we believe that a turing like tesselation may play a role.

i would be pleased to try and discuss, i avoid answer since many of these are works in progress, your questions. i prepared the document on the web site as a discussion piece and not as a definitive document. furthermore i got more heavily involved in the epigenetics issues and this had added significant complexity.

many of the constructs we have applied to various cancer pathways, since the coloring of cells is a pathway activation process just as the growth in cancer cells.

again if i can enter into a constructive dialog, get corrections on my draft, expand what has been done so far, i always enjoy collaborative discussions. i also as a common professional practice use my full name because that way you can also do your own due diligence.

again many thanks for your time spent slogging through the document, i also apologize for what is suspect are many typos, i have a bit of dyslexia and even with spell checking i often get the right spelling of the wrong words.

i look forward to your comments, feel free to contact me directly if you want. i am up in cambridge the rest of the week but am back on the week next.

regards

terry mcgarty
[email protected]

How wonderful to have you here Dr. McGarty ( @terry2 )! I had thought to email you to ask, invite, and thank you, but didn't want to impose, so you can imagine my delight at seeing your post. Thank you so much for joining in, and we in turn very much welcome any direction or re-direction, and hope very much for ATP members to enjoy the cordial discussion as we learn about the work you have so kindly shared.

I am very interested in the epigenetic (heritable changes not caused by DNA) loop of the genetic/environment feedback system you outlined in Chapter 2.1, and have returned to ponder it a number of times. I know that epigenetics seems to be the inescapable "extra ingredient" in so many health and life sciences, hiding in plain sight yet so complex and fluid that it has yet to be fully assimilated. Is it possible there would be way to (over) simplify the schematic in Figure 1 (Dynamic Gene Model) a bit further so that we can see an illustration or example system of it at work? I'm so visually oriented that I often cannot deeply grasp something until I see pictures.

And, I'll ask the first of many "dumb" questions (I adore doing that) ... can such an example be found, perhaps, in looking at both Turing's chemical substances in the genes of zebras that turn the black/white colors on and off, and the recent idea that stripes are found in patterns depending on the environment's volume of flies (which they may repel), and be something of what is meant by the genetic/epigenetic effects of flower pattern and colors? That an organisms coloring and patterns are a response to environmental requirements, as well as a product of the chemical nature within its physical life?

Your book is wonderfully accessible, and I'm so grateful for the chance to work through its very orderly and integrated progression of ideas. I only hope that I, and any others who'd like to do the same, will come closer to understanding by trying to summarize and discuss this new-to-us terminology. The theory, research, and access to ideas that you share illuminate a field that has been beyond reach before now, and will ultimately give us so much more understanding of our beloved daylilies. If we might learn more about the larger botanical world, our own physical systems, and even develop some first-step attempts at trying out some of these ideas with out own informal pollen dabbing, that would be superb.

Again, many thanks, and wishing you a pleasant rest of the week in MA, while looking forward to your return!

I would be more than happy to discuss various areas of your draft.

I do not use my full name on public insecure forums (such as this one). I used to, but I stopped doing that about six years ago when I found that the amount of detailed personal information freely accessible on the internet seemed dangerous. (The particular incident that made this obvious to me was that only knowing a person's maiden name from the 1970s I was able to find her current address, where she worked, where her mother lived, where her children went to school, a detailed floor plan of her house, etc.) This person had no web-site, belonged to know obvious internet groups, had no apparent public internet persona, etc.

You can 'identify' me in more detail by checking any of the articles in the Daylily Journal.

The discussion can be in this thread or offline - whichever you prefer. Lets start with the parentage of Hyperion, etc. (page 14, page 16, page 341 and following).

May I ask that your discussion of Hyperion's parentage move to email, tree-mail, or another thread @admmad? The hope for those of us who are interested is to read, discuss and learn here on the free ATP forum via this very accessible and helpful free e-book. The intent is to avoid pulling the ATP informal discussion into the realm of trying to settle which plants may be species or parents of particular lines - there seems to be ample evidence that there may be confusion and disagreement over any number and type of daylily records - and so it may be a larger kindness for you to engage in your inquiry separately.

I know that I, at least, would like the opportunity to finish learning from and discussing this book without the distraction of such long-running side-bars... ? I have already learned much from, and am very grateful for, the information as it stands; one scholarly author's writings, based on his work with MIT doctoral students. It has already shown its value to me in more general and practical topics to discuss.

Chapter 2: Form and Species - Conclusion (and, again, just my take on it)

Species Background

Originating in Russia, Japan, Korea and China, daylilies species are found in the wild on mountainous terrain. Breeding has taken the original yellow, orange, and brownish red colors forward into producing those that are purple, streaked pink and cream, near-blue, etc., and none of those colors are seen outwardly in the species. The simple shape and number of petals on daylily species have also come to include spiders, doubles, and many unusual forms.

The author points out that the focus of this book is not on definitive classification of species plants, but on employing what we know of some of the more detailed species to illustrate how we might recognize factors that differ even at the species level. For example, H. minor has grass-like leaves and its scape may be prone to bending toward the soil. Others, like H. middendorffii are very early bloomers. And, some species may even show slight variations between fans located in one environment versus another (perhaps something similar, though perhaps unrelated, to north-south differences we see today in how “toothed” flowers can look, or the performance of some of the patterned daylily cultivars?).

Roots

A couple of the daylily species plants, citrina and fulva, show the two extremes of root types found in daylilies.

H. citrina has dense roots that are long but not spreading (no rhizomes), cylindrical (no bulbs), and are covered with smaller hair-like roots. This is a photo of Crystal Blue Persuasion’s roots which seem to have similar characteristics:



H. fulva, on the other hand, has many bulbous roots that can store up nutrients deep under the soil and long runners that burrow out and away from the parent fan to create new shoots. I think there is a similar style in the roots of Paper Butterfly:



Scapes

The author includes definitions regarding scapes that I find very helpful. If I understand correctly, the scape starts at the bottom, without leaf. Then at some point upward it will have a bract (leaf-like growths) and that is where the stalk becomes what we would usually call a branch or branches (and/or where prolifs may appear) at or above those bracts. New branches also split out where bracts appear again higher up on that first main branch. I’d never actually noticed this, and it helps me to visualize the different parts of what before I’d only called "the scape." Here’s an ATP database photo that shows scapes with bracts, with a branch or branches above the bract (easier to see if you click the picture to enlarge it).



Branching

Daylily species have a variety of branching habits that help to identify them, from no branching to highly branched. For example:

No branching: dumortieri
Some branching: aurantiaca
Multiple branching: multiflora, fulva, hakunensis, coreana

Buds

Daylily flowers grow inside the buds, some of which may even appear just above a final set of bracts, without any stems. These buds that have no stems, connected directly above a set of final bracts, may be seen in the dumortieri and middendorfii species. In that case the junction between the bracts and the buds is not counted as further branching, and the buds are defined as “sessile” (attached directly to a base).



Species Flower Colors

Because there are so many differences in how species colors (and name spellings, etc.) are reported, I’m going to just show some of the ones represented in the ATP database. You may also want to peek at photos linked at http://www.hemerocallis-specie.... There may also be species and photos at AHS, but I am unable to find links to them.



Pods

Daylily pods may be used to identify various species plants, both from their range of size and by shape. Some are more oblong, others balloon out near the tip end, and some have coloring beyond the initial green on the outside of the pod.

Seeds

The size of seeds in daylily species plants may differ, from about 1/16 inch (H. minor) to about 1/3 inch (H. coreana) but are not considered good indicators, in and of themselves, to identify species (or modern cultivars, for that matter). In order roughly from smallest to largest, the author presents a photo with a number of species seeds: H. minor, H. thunbergii, H. hakuunensis, H. multiflora, H. citrina, and H. coreana.

Species Comparison

The chapter ends with various descriptive grids that have been developed or proposed for summarizing all of the species' differing characteristics by comparison and contrast. What follows directly after those grids, in an appendix to the chapter, will please anyone who is visually oriented:

An Awesome Pictorial Appendix in the Book Showing Twelve Daylily Species that are Behind Many Modern Cultivars
Page 84, and culminating in an integrated grid of pictures by page 102.
http://www.telmarcgardens.com/...

Here is where I would not even attempt to find photos to match those in the book; I have not found, through any other source I have been able to access, such a collection of photos that would even come close to matching it. Each of the twelve species in the book are showcased in simple, beautiful and very illustrative picture grids, sorted at first by photos of the main forms we've learned about (seeds, pods, flowers, buds, branching, leaves, and roots), and then presented en mass in a culmination of fully-gridded photo-rama pictures with all species forms side-by-side.

I wish I had read this far into the book two years ago when I first downloaded it. I will be printing out those identification tables and photos to use as a point of comparison and contrast as I look at their modern descendant daylilies growing in my own garden!

Tina et al

Just got back. You have a great list of issues. Just as a note I have used Podek's website as a great source.

Give me a day or two and I will write some thoughts on two topics:

1. What is a species? This one has been around for a long while. Mayr's answer was that they must be able to breed, but with hemerocallis they all seem to interbreed, thus the hybrids. Yet I have a half dozen different citrinas and the same for minors, not to mention others. Some bloom weeks before/after others. Are they the same of just variants?

2. Epigenetics. This has become my daily concern. There are many dimensions of epigenetics, such as the calico cat, which randomly silences one of the X chromosomes, but not really random. Otherwise there would be an even spread of hairs, not patches. Then the zebra, this is what got turing, there are patterns, and they may be quasi epigenetic. Then there are the patterning of daylilies, this follows Turing since they appear as "solutions" to certain flow equations. Thus they suggest perhaps some extracellular matrix control mechanism. There is still a lot of guess work here.

I also think in pictures, perhaps my dyslexia, great at math, bad speller!

Give me a day or two and I shall return

Regards to all

Terry

Would love to hear more, and gives me time to do some more chapter and background reading before getting in to the next book topic.

Thanks for the three lenses you provided around what epigenetics refers to - I'm sure I may not be the only one who is still working on wrapping my head around it, and any help in definition or examples is awesome. I'm thinking we are talking about structures or processes in daylilies (and possibly other color-patterned organisms) that have some natural control over how patterns and color changes appear? That some physical or chemical system is at work responding to signals and producing color changes in the petals? Is so, how do we get from the self species, to "dot" hybrids (early nomenclature for "eyes"), and edges, midribs, and so on? And, do we have some idea of how to mix and match pod and pollen parents so that we can try to get desired, or never before seen, results?

My eyes feel hungry for a visual progression through this color-changing process, and my head feels a bit a-spin with new hints about it - in the nicest of ways.

Just Thought it may be worth Sharing some recent ideas on Epigenetics, based on the Calico Cat!

OR; Alan Turing: Calico Cats, Zebras and Daylilies

Turing in 1954 wrote his paper on Tessellation, the patterns we often see on animals and plants. The question is; is Turing’s approach the right way to understand these patterns? Namely Turing proposed a hypothetical method whereby cells communicate with one another and that this communications is akin to flows of some, as of 1954, yet to be defined chemical substance or substances. Depending on the concentrations of these substances the cells then turned, for example, black or white, as in a zebra, and that this flow being coordinated in some manner yielded a pattern, not just a mass of black and white hairs.

Turing hypothesized, for example, that there may be two controlling molecules in varying densities and if one molecule was denser than the other it would turn on white and otherwise it would turn on black. But Turing said more, that the flow of the molecular density was not just random but that cells somehow participated in a distributed manner so that the densities flowed as waves, with peaks and valleys. Thus the Zebra stripes were a reflection of this flow. When the black molecule was at a high the hairs were black and when the white ones were high the hairs were white. The net result looked like waves of white and black.



Now a second model that has become of recent popularity is the explanation for the Calico Cat.



The explanation for this is dramatically different. Here Calico Cats are all female. The way it works is the epigenetic silencing of one of the X chromosomes. This allegedly is totally done at random. As seen above this of course is hardly the case. If every hair cell were random then we would expect to have a blend of two or more colors and not the patterns that we have above. This means that if this is epigenetic that spatially there is some mechanism that is not totally random. There is some form of cell to cell memory and cell to cell thresholding. Namely the hair stays black, brown or white for some spatial period and then switches to the other state. That is the Turing Tessellation effect. What then does that?

Now consider a third example; the daylily. We show a typical example below. Here we have an eyezone, the dark red around the milled and we even have red on the edges. This is again a tessellation type as described by Turing. There are areas where there is dark red and areas where there is light red or pink. Is this epigenetic, genetic, or a Turing tessellation.



In fact daylilies can show dramatic patterning as they get more sophisticated. The above is a simple form of patterning, a wave of dark and light red.

Thus what enables these patterns? In epigenetics of cats, it is the turning on and off of one X chromosome, but not really randomly, so there must be some mechanism that selects which one gets wrapped in an lncRNA and which does not. What is that activator? Not yet known.

In daylilies we know that color is driven by anthocyanin production. More of one and we get one color and more of the other another color. We also know that certain proteins, gene products, act as catalysts facilitating one anthocyanin path or another. Thus if one gene is producing then it may drive up pone anthocyanin or another. What turns these genes on and off? Perhaps epigenetic methylation as we see in many other examples. But that begs the question of what causes the methylation? It appears to be a pattern like that of the Calico Cat.

Thus the Turing Tessellation is a process that explains these patterns but the facilitator of that process, the extracellular or intercellular molecule is not known. Thus we have an interesting area of exploration. In addition we see similar effects in the field of metastatic cancers, where we get clusters of metastatic cells, and not just random aberrant one.

Terry

Some brief observations. Early species are coming out and as I have them recorded the following 3 may be of interest:

H minor

Notice the long bracts

H middendorfii

Simple sessile buds

H dumorterii

Note the reddish edge of the bud, the sepal back side will have that tint on it as well.

Love this info with the photos, makes me want to pay much closer attention to my plants. Can we get larger photos?

I have 4M photos but I do not know if they will be compressed. Let me know what you want. I will follow thru on an ongoing basis with the species as I understand them and their buds, flowers and seed pods.

Terry

Dave suggest 900 pixels wide as being about right for posting.

My brain hurts and my eyes are bleeding. Lol.

It's so much easier to see different characteristics in the garden now. What was just a fleeting glance at things that seemed unusual, before, is now a growing familiarity. Each cultivar shows off its own unique set of attributes, not just in blooms, and some seem like echoes from their species origins.

I hope its okay to mix in some of how this book is bringing a new approach to experiencing a daylily garden - I don't mean to confuse anyone to the point of tears, but I do want to share some of what I now can see, as all of this is shown to us. Some of these photos are not species, though some are (they'll be noted, and come from the ATP database). This new kind of focused observation really seems to bring things to light in new and helpful ways.

Here are some buds looking like they may be sessile (finally, learning some new gardening vocabulary :D ), though I don't know if all buds start out like this. They do seem a bit farther along than others that are already well separated by longer stems.


And, here are a couple that have some very long bracts. In a number of mine, the bracts are as long as the foliage! Maybe they are not so much "odd" as they are possibly an example of how extremes have been interbred through the ages?


Finally, a couple of fuzzy pics (the new camera and I are not getting along very well yet! :P ) showing a bud that is starting to pick up some color at the edge of each segment, soon to spread across the cells to cover the sepals. And, another fuzzy one showing buds closer to bloom that have some interesting pattern of color-rings on the sepals (darkest at tip, then a little lighter, then much lighter, until the shading stops with another ring of darker color).


One of the things I like most about this book (http://www.telmarcgardens.com/...) is the progression of how, and why, we can distinguish the species plants. First, they differ by blooming times, as this occurs in a natural rhythm to each daylily species ... those that bloom in earliest spring would not in nature be pollinated by those that bloom late in the season, so there is a really basic division between them there. And that is where this first set is grouped, earliest-blooming daylily species, as is so nicely shown in Chapter 2. I often need to review a chapter, sometimes reading it a few times, before all of the details start to sink in and the new terminology and ideas becomes more familiar.

So, it's making a lot of sense that we first start out by being shown that earliest-blooming group of: H minor, H middendorffi, and H dumorterii. Then we are shown what a deeper look reveals about how those three differ from each other.

This is likely H dumortieri, showing the buds and sepals with reddish-brownish coloring on the outside, but a clear yellow-gold on the inside sepal surface.


Then there is H minor. It is the lightest yellow of the three, with no dark color on the outside of the sepals. A nocturnal bloomer, it is also quite fragrant. Its very thin grass-like foliage can be seen against the backdrop of the wider leaves of its neighboring cultivars.


Species H middendorfii has flowers that open a bit wider than either of the other two, and it has a bit more of an orange-y tinge. Also shown is a photo of its sessile buds:

Great!

The problem I have is that the species do seem to vary a bit. I have a few students from China and as I collect some "originals" they do vary as well. I would be curious to see the genome differences. I am trying to persuade some colleagues with sequencing systems to give it a go on some spare time. Keep you all updated.

Things have started to grow now and the days star at 5 am!

Cheers

Terry

some more species pics

H minor (lemon yellow)



H minor branching (lots of branching)



H middendorfii (darker yellow)



note the color, branching, bracts