Diploid x Higherploid or Higherploid x Diploid

Rose Genetics Ploidy Level
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21

My main gripe is with the notion that anything that seems complicated, highly technical and scientific-y must be believed, however thin the evidence and poorly reasoned the arguments. If we ignore enough of the data – genetic or morphological – it is easy enough to claim that species A and species B are nearest cousins.

In the back of my mind there are some of these DNA papers that I read years ago, written by people known to me. Checking the details, I learned that the program used by the author(s) calculated 4000 equal probability phylogenetic trees, then printed a few representative examples. What’s the point?

Imagine taking a test and answering that you have determined 4000 equally probable answers, and cannot vouch for accuracy of the one or two representative examples you chose to write down.

Some of these papers seem to be based on the assumption that every species evolves in isolation. And if two species are different enough to be distinguished, then differences must also be revealed in all the genetic and morphological details. Random gene mutations, of course, should not be limited to the obvious distinctions.

I think it would be useful to test the methods and assumptions of these researchers with some plants of known origin. I have previously mentioned some 2nd generation seedling of hybrids of Mimulus cardinalis and M. Lewisii that were transplanted to a wild area where neither parent species could be found. After a few years, the hybrid swarm had become resolved by bumblebees and hummingbirds into the original species … as far as anyone could tell. Would the DNA evidence show that the two species evolved recently from a common ancestor?

Years ago I read ‘Introgressive Hybridization’ by Edgar Anderson. It has stuck with me. Species can mate, then regain themselves in slightly altered forms. This is not a rare event. But the formation of “hybrid swarms” may be less common, and of shorter duration, than we might have assumed.

Another gripe is the notion that all measurements should be of value. This is not true. Some measurements are merely confusing, even when one tries to compare equivalent parts. Why should we consider the length of a sepal to be a significant measurement when flowers vary so much in size? Raw numbers may suggest overlap, whereas ratios may reveal clear differences. Anderson showed how this works in the superficially similar Iris virginica and I. versicolor, and some other species.
http://bulbnrose.x10.mx/Heredity/Anderson/AndersonIris1928_2/AndersonIris1928_2.html

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Species can mate, then regain themselves in slightly altered forms. This is not a rare event.

True enough, and this is really just the special case, involving pure species, of the general back-cross method we used to call ‘fixing’ a trait.

Imagine taking a test and answering that you have determined 4000 equally probable answers

Not every answer is equally probable, at least in the Basyean methodologies. It’s very similar to modeling hurricane tracks where you get a spread but when you run the algorithm enough times they converge on a most likely path.

The genetic matching algorithms used by the genealogy companies also generate false positives. They use marker sets having around 600K SNP’s. I don’t know what the comparable size would be for the rose genome. I haven’t fully read the TAMU paper posted last week in another thread but I think I saw where they mentioned the size of their marker set. I think they were mapping diploids, as well, and polyploids would presumably require exponentially more markers.

23

Just before the rose paper came out, I was working on a different subject, the saltcedar. Using genotyping by sequencing the authors of that study created a lot of SNPs. They cut a 3000Mbp genome with a restriction enzyme that gives pieces on average length of 4000 Bp. That means they had 750,000 pieces (3 billion divided by 4000). If they successfully sequence 64 bases at each end of each piece they could have 1.5 million SNPs. Many of these would be worthless duplicates in repetitive regions, or wouldn’t get enough sequence reads to be reliable. So they kept just the ones that had a least 7 matching reads. They threw out others for various reasons like not having a difference between the two (presumably homozygous) species that were being compared as parents of hybrids.

The 3 billion is a moderately small genome for something with n=12, diploid =24. But the number of interesting “genes” is going to be comparable to that of roses with n=7, diploid = 14. What you end up with is a whole lot of SNPs per chromosome but of course not equally spaced. The average length of the restriction fragments is 4000, but many many are much longer or shorter than that. So some regions will be nicely covered and others will be sparse.

this strategy has worked reasonably well for agriculture crops such as sorghum, maize, rice (for which the whole genome is sequenced), soybeans.

24

In the saltcedar case, the two species being crossed (spontaneously ,naturally) breed freely wherever they come into contact. So although the parent species can be distinguished from one another, many of the fragments that could be SNPs turn out to be identical between species. In the end only a few thousand were useful when looked at across populations. Those were ones that differed between parent species, and that could be separated in different progeny. Same appears true in the rose paper where there is a whole lot more mapping information to start with, based on the strawberry genome. If we can make crosses, by definition there is a lot of similarity between species at the chromosome level, so lots of potential SNPs aren’t actually polymorphic between species or populations within our complicated hybrid families that we call tea roses or gallicas or floribunda or whatever…

The rose folks ended up with a few thousand SNPs reasonably well distributed along all the chromosomes. But even with that many, most actual genes are very small compared to the distances between SNPs. Sequencing the entire genome is the next essential step. There is a sequencing factory that is working its way through plant genomes and trying to keep busy. So their turn will come.

25

Somewhere in here we get into the problem of defining species. Among the DNA crowd there are some who would like to ignore the messy biological aspects of habitat, mating preferences, climate and geological history. To them, evolution is all chemistry. Differences in genotype define species, not the phenotype.

Back when I worked at a biotech company (I was in IT), I attended the seminars to keep up with the latest. I encountered a few people who must have known far more about the chemistry than I did (do), but who were dreadfully ignorant of biology. I asked one guy how temperature might affect a particular process. He replied that plants have a way of maintaining a stable temperature, which was news to me. And another guy clung to the archaic notion that reproductive isolation was an inevitable consequence of divergence. He seemed a bit startled when I told him that Rosa species from around the world are cross-compatible even after being isolated for (apparently) millions of years. And he was even more disturbed when I mentioned hybrids of roses and apples.

DNA evidence is very valuable when combined with other evidence. It should not be used instead of the rest. For example:
Noguchi, J., and H. De-Yuan. 2004. Multiple origins of the Japanese nocturnal Hemerocallis citrina var. vespertina (Asparagales: Hemerocallidaceae): Evidence from noncoding chloroplast DNA sequences and morphology. Int. J. Plant Sci. 165(1):219–230.

The authors found that what was thought to be a single species involved three different lineages that converged on a similar, general phenotype without cross-breeding.

A similar example is found in the Andean genus Rhodophiala. Again, DNA evidence points to at least three separate lineages, this time involving different genera. In one lineage, the chromosome number changed. The species of Rhodophiala are cross compatible, even though they have not (to my knowledge) been backcrossed to species of their presumed ancestral genera.

One more thing. Back in the day, I discussed SNPs with a co-worker. I understood the concept, and was intrigued by the possible uses. However, around that time the subject of RNA interference was developing. Abruptly, single nucleotide differences took on new aspects … and a lot of the “junk” DNA was being found to be not so junky after all.

And this leads to some other questions. I look for papers on RNA, but so many seem to be involved with using siRNA and miRNA as tools for this or treatments for that. What interests me (at the moment) is whether a given RNA snippet might be acting on two more RNA transcripts. For example, two genes might be co-promoted and work together in one environment. In a different context, one might be blocked by RNAi. Would a single nucleotide change be enough to isolate the two genes?

In a broader scenario, all the genes are being “performed” (up- and down-regulated) by RNAi. Do the necessary changes occur primarily in the RNA snippets, in the gene transcripts, or some of both?

By the way: I looked into some of the more recent RNAi research and quickly learned that the field has grown A LOT in recent years. The little I thought I understood has been replaced with different concepts and models.

26

The RNA as control molecule is very muddling. This afternoon I was at a poster session talking to an undergrad about his lab’s work on micro-RNA and how it is controlled by RNAi. Sometimes it is direct interaction of one RNA with another. Sometimes it is done by intervening proteins so that one RNA molecule can control several different genes, or maybe even several different micro-RNAs which each control several genes. There are complex regulatory networks within cells, and organisms.

Hybrid vigor, discussed in another thread, depends on interaction of the networks of two different lines genetic lines such as in the classic case of hybrid maize. Up and down-regulation of different genes in different pathways leads to something we like and call hybrid vigor, or perhaps it is broad adaptation, or more particularly adaptation to human manipulated environments. In many environments bigger is not better, for instance when some one nutrient is limiting growth. In another environment it might be a different nutrient. Each environment selects lines to grow best under the limitation of its location. But suppose that in a human manipulated environment, neither nutrient is limiting. Then a crossing mix of the two lines, which “ignores” the adaptation to nutrient limits will have hybrid vigor. It grabs he best of both worlds.

You can ring a thousand changes on this theme, which I totally made up just now speaking of nutrients, but which also applies to light, heat, water, daylength, temperature swings, wind, competitors, predators, diseases. How the RNA controls on networks, and on other epi-genetic changes such as DNA methylation is still wide open for exploration.

27

Larry,
I hadn’t thought about that. I know that bigger is not always better, the the connection to nutrients is worth pondering.

I read a fascinating article about fertility and micronutrients, but lost it. More than one, actually.

The tropical hibiscuses are lumped together as Hibiscus rosa-sinensis, but this is a complex of species complexes. The various localized forms are scattered among islands that differ in their chemistry. A coral atoll has different nutrients than a collapsing volcano, which is different from a break-away sliver of a continental land mass.

The various species rely on different micronutrients for something (I forget what) affecting fertility. All is well until gardeners started crossing a species from this island with a one from that island. The F1 hybrids were fine, but the F2 and later generations gave a perplexing segregation for sterility and fertility. Now one can find micronutrient supplements to restore fertility, but beginners may still be caught off guard when they begin crossing.

The other article dealt with animals I vaguely recall a mention of silkworm moths, and a mammalian hybrid or two where the males suffered a micronutrient deficiency that contributed to their sterility.
Karl
ps.
Now I have to start another bibliography.
Trace Elements in Plants p. 77 (2012)
By M.Ya. Shkolnik
Shcherbenev (1973) successfully hybridized quinces with apples by supplying boron and gibberellic acid.

28

hybrids of roses and apples.

I waited to see if anyone else would take this bait but I guess it’s up to me - wot?

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The Catholic Digest 2(12): 20-23 (1938)
The Rose Wizard
Frederick M. Lynk, S.V.D.
I was very anxious to see a sample of his rose apple, or edible rose. Twenty of these had been stolen, too, but he found one of a smaller size, opened the fruit with my pocket knife and showed me how closely the structure resembles that of an apple, outside and inside, core and all. “The natives of Burma subsist on it,” he said, when I asked him whether one could really eat them; “but,” he continued, “the rosa pomifera does not taste like an apple, but like a rose.” Rose and apple, as he pointed out, evidently are of the same broad botanic family. By hybridizing rosa pomifera with a Spitzenberg apple, he obtained a better-sized fruit than that of rosa pomifera. It had a decided apple character and delicious flavor. It took years of cross-fertilization to produce a plant, which not only blooms like a beautiful rose, but when the petals are gone develops into an edible fruit.
http://bulbnrose.x10.mx/Roses/breeding/Schoener/SchoenerCD1938.html

henry_kuska
The following is from an article that appeared in the 1960 Canadian Rose Annual pages 69-70. Of interest are the several crosses of roses with other members of the Rosaceae family. Although the crosses at that time were sterile, it is possible that with modern techniques such as chromosone doubling fertile plants could be made.
http://bulbnrose.x10.mx/Roses/breeding/ShepherdHybrids1960.html
Title: Hybridizing Limitations
by Roy E. Shepherd, Medina, Ohio
“The writer has succeeded in budding a rose on to an apple branch and in crossing a rose with a member of the blackberry family, but the bud remained dormant and the seeds did not germinate. Dr. J. H. Nicolas, formerly Research Director for Jackson and Perkins, was more successful as he raised three seedlings of a cross between an apple and a rose. They were similar to the latter in general appearance but showed evidence of apple influence in the bark, foliage, and in the peculiarly colored double apple-like blossoms. The latter, incidentally, were somewhat similar to those produced by Bechtels Crab but not as well formed or as large. The plants were barely remontant and after blooming they were inactive until fall when a second spurt took place. Further experience with Rose x Apple and Rose x Hawthorn crosses gave similar results and all proved to be sterile. They were therefore valueless for use as parents in further breeding along this line.”

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Yeah, wow. I wonder which direction of cross would be more likely to succeed with apple x rose.

31

Larry,
I remember back in high school biology class, that RNA was regarded as a necessary but unlovely sister of the more glamorous DNA. My how times have changed. And when I was at Appliedbiosystems, someone had a bumper sticker: DNA is Life, all the rest is interpretation. Now we see that DNA is merely a bit of hardware in the RNA-Protein machine that can be changed as required.
Karl

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When were you at Appliedbio?

33

The immediate problem I see is the assumption that all chromosomes are created equal. As I have been trying to show by various examples, the sets of traits that can distinguish species may function a units in breeding even though they involve multiple genes affecting different parts of the plant. One chromosome may not carry all the relevant genes, but apparently it can carry a regulatory control that governs the co-expression of those genes. That’s why a Canina x Rugosa hybrid that was missing one chromosome showed no obvious Rugosa influence. A sister seedling with all its chromosomes did show the paternal influence.

Furthermore, these regulatory units (I don’t know what else to call them) differ in their relative dominance. This relative dominance may be altered by environmental conditions. Hurst (1925) described this situation:

Naturally with four double septets working equally and independently in an octoploid species, only about one-fourth of the characters of each septet can be represented at one time. An analysis shows that in a plant of > R. acicularis > Lindl. carrying four years’ growth of surculi, stems, branches and branchlets, about one-half of the characters of each of the four septets B, C, D and E were represented (fig. 174 e and f).

http://bulbnrose.x10.mx/Roses/Hurst/HURST2.HTM
I didn’t copy the figure, sorry to say.

It seems that two diploid species may share a great many genes, even whole chromosomes, while still remaining distinct because of a single chromosome that runs the show.

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Karl, I did get pdfs of those papers from back in the good old days about diploid vs higherploidy. Send me a message and I will send them as an attachment that you can post up. My address is a simple ldavis (From back around 1988) and as everyone knows including web crawlers if they have some AI behind them, I work at an edu cational institution commonly called ksu around here. I’ll let you assemble the pieces.

35

Larry,
I got them both OCRed. The first covers the diploid hybrids, the second has diploids with polyploids (regular and irregular).
http://bulbnrose.x10.mx/Roses/breeding/RatsekDiploids1939.html
http://bulbnrose.x10.mx/Roses/breeding/RatsekDipPoly1940.html

The authors give Hurst’s letter code for each, but miss the point of his work entirely.

Hurst OBSERVED that five sets of fifty characters hang together in Rosa species from around the world. Botanists in general seem to be incapable of considering more than a handful of traits at one time. In 1925, when Hurst began discussing his research, it seemed to him that the only way so many traits could be maintained together was for whole septets of chromosomes to be inherited together. This does happen in Oenothera spp., but that mode of inheritance is not observed in roses.

Hurst wrote that this was only a “working hypothesis”, but other researchers set to work disproving hi “theory”.

Then history happened, as it often does. Hurst inherited a thriving nursery, but devoted his time, money and efforts to genetic research. The stock market crash of 1929 hurt him. And when WWII came along, Major Hurst had military duties to occupy most of his time. He died in 1947.

C. D. Darlington had no love for Hurst. He even called Hurst a charlatan, but only after Hurst was dead. But coincidentally (?), 1949 Darlington published a paper, “On An Integrated Species Difference”. He reported two cases in Rubus that made a compelling argument that the traits distinguishing raspberries from blackberries must be linked together on a single chromosome. Of course, he never acknowledged that the same mechanism might account for Hurst’s observations in the closely allied genus Rosa.
http://bulbnrose.x10.mx/Roses/Hurst/DarlingtonVersatility1949.html