Fruit Genetics Friday #8: Picking a Scab Resistance Gene

I know the title is a pretty bad pun, and not even that accurate. Sorry. Anyway, here's the bit about scab resistance I hacked out of the draft on the WineCrisp apple:

The Vf gene comes out of a selection Malus floribunda. The original introgression of the Vf gene (or genes, but more on that later) was done by Purdue back in the 1940's, and has been used heavily in breeding, including as a fairly early target of marker assisted selection (a detailed history of scab resistance breeding is available from Purdue. I'll hit the highlights here.)

There are at least seven distinct loci governing resistance to apple scab, each named according to the original source (the "V" is for Venturia inaequalis, the name of the pathogen):

Vf - Malus floribunda
Vm - Malus micromalus
Va - 'Antonovka'
Vb - Malus baccata Hansen's #2
Vbj - Malus baccata ssp. jackii
Vr - Malus pumila R12740-7A
Vr2 - Malus pumila GMAL 2743

There are distinct races of the scab pathogen, though, and they react differently to the different resistances. Race 5 overcomes Vm, for example, while Race 2 overcomes the resistance in some M. baccata. In 40 years of breeding, no resistance breaking isolate of Vf was identified, but towards the end of the twentieth century reports began to surface in Europe of strains which could overcome Vf.

As I hinted before, it's probably more appropriate to refer to the Vf locus, rather than the Vf gene, because the Mendelian Vf gene is in reality a collection of genes. (Although I use it as much as anyone else (probably more), the word "gene" is actually kind of a problematic one anyway--it's really better to use "locus", to refer to a specific point in the genome, or "allele" to refer to a specific sequence at that locus.) Sequencing showed the so-called Vf gene to be a cluster of four genes, Vfa1, Vfa2, Vfa3, and Vfa4. Clusters of resistance genes aren't uncommon and have been shown in lots of species--it may be the extra copies strengthen the resistance by increasing expression, or allow a broader resistance by having multiple versions. It's also possible that resistance alleles are more likely to evolve from duplicated genes, because the plant can better survive mutations in a gene it already has backup copies of. In this case, Vfa3 has sustain some pretty serious mutation, and no longer produces a full length transcript. Although the similarity among the remaining four led researchers to suggest that all activate the same defensive systems, Vfa1 and Vfa2 (along with the partial transcript of Vfa3) are primarily expressed in immature leaves, while Vfa4 is expressed in mature leaves. Of these, Transgenic apples transformed with each of these apples showed that susceptible varieties expressing Vfa1 and Vfa2 became resistant, suggesting these two genes are capable of conveying resistance.

The Vf locus was really one of the first fruit genes to really be thoroughly investigated and described, from its introgression from a wild species, description as a Mendelian trait, and detailed dissection on the molecular level. Although other source of scab resistance are gaining in importance, and molecular tools such as linked markers developed to improve their usefulness to breeding programs, the Vf locus remains possibly the most studied disease resistance locus in any fruit crop. (I'm just speaking off the top of my head...Anybody think of any other contenders?)

Fruit Genetics Friday #7: Plant Sex Chromosomes Part II: Strawberries

A couple weeks back, in the very infrequent Fruit Genetics Friday series, I discussed sex chromosomes in fruit, specifically papaya. At the time, the only two fruit crops I knew of with sex chromosomes were papaya and kiwi. Monday I opened my e-mail to a paper, forwarded to me by a friend who is also one of the authors, describing a very interesting development in this area:

Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome (Heredity)

(Unfortunately, for non-subscribers, this will just be an abstract, but I'll try to hit the good stuff).

People were excited about the discovery of sex chromosomes in papaya, because it represented one of the most primitive sex chromosomes yet found in plants. Well, it turns out that F. virginiana, one of the ancestors of our cultivated strawberry, has sex chromosomes too (counter to what I said in that earlier post, incidentally), and these are even younger in their development! They're also really unusual in how they operate. In papaya and kiwi, as well as most other plants and lots of animals, the homogametic sex is the female (as in 'XX') and the heterogametic sex is male ('XY'). This seems to be the more typical arrangement, but strawberries, oddly enough, have the opposite arrangement.

So if you recall the arrangement in papaya, you had two critical loci. One, which we'll call "F" is a suppressor of femaleness, and the other is a promoter of maleness, which we'll call "M". So the two "wild type" chromosomes (which I'll call X and Y, since it puts it in terms people are familiar with and is essentially correct, even though the terminology isn't really used consistently in plants) consist of:

f---m (X chromosome)

F---M (Y chromosome)


So a female would be XX, or (fm)/(fm), so no maleness promoted and no femaleness suppressed. And male would be XY, with the femaleness suppressed, and maleness promoted. Hermaphrodites are generally a mutation of the Y chromosome (which we'll call the Y⁺ chromosome), so that the suppression of female development ceases to function, but male development still takes place:

(f)---M (Y⁺ chromosome)

So the sexes are basically female (XX), male (XY), and hermaphrodite (XY⁺). (because the YY isn't viable, you can't get a homozygous, true-breeding hermaphrodite).

Well, turns out strawberry has a different arrangement. The roles of the genes are kind of reversed. You have a dominant promoter of femaleness (which we'll call 'G' (for "gyn-", as used in the paper)), and a dominant gene for male sterility (which the paper calls 'A', as in "andro-"). And in this case we'll use Z and W (the system from birds) rather than the XY system.

So the arrangement is:

g---a (Z chromosome)

G---A (W chromosome)

So the sexes are female (ZW) and male (ZZ). This actually fits with some old research dating as far back as the 1920's suggesting that the female is the heterogametic sex. This was backed up by Ahmadi and Bringhurst, who suggested a single locus with three alleles, F, H, and M (in decreasing order of dominance). I kind of suspect many of these single locus, three allele systems, which have been proposed in other species as well, turn out to be variations on the two locus system, like in strawberry or papaya.

Here's a cool bit: The strawberry sex chromosome is pretty primitive, and so recombination in between these loci isn't fully suppressed, and you actually get crossover between them 5.7% of the time. As a result, you can get variations, namely hermaphrodites (resulting from a G/a recombinant) or a neuter (the result of a g/A recombinant). That suggests something which is only barely functioning as a sex chromosome.

Because the sex chromosome seems to have evolved very recently, what I'm curious about is how widespread in related species it is. I think it quite likely that the other major octoploid species, Fragaria chiloensis, and its offspring with F. virginiana, the cultivated F. x ananassa, share this scheme. But do the lower ploidy strawberries?

If diploid strawberries possessed sex chromosomes previous to the evolution of octoploids, then the octoploids should have eight sex chromosomes. Having this many would probably result in a mess (although it seems to work out alright for the short-beaked echidna), and the fact that sex inheritance seems to be pretty simple suggest that if the octoploid had eight sex chromosomes, then six of them have probably ceased to function as such.

Though there may be some exceptions (there are a bunch of east Asian diploid species I'm not really familiar with) the diploids I'm aware of, F. vesca, F. viridis, and F. nubicola seem to be almost (but not quite) uniformly hermaphrodite. Yet a number of higher ploidy species in addition to the octoploids, including the hexaploid F. moschata and the tetraploid F. orientalis are at least partially dioecious. It may be that polyploidy, by creating "backup" copies of the chromosomes possessing the sex controlling loci, allows divergence of one pair into more specialized sex chromosomes.

I'd be curious to know if closely-related genera such as Rubus and Potentilla share this system. Research suggests that in both of these species, the females are the heterogametic sex. If they possessed similar sex chromosomes, that would suggest that the strawberry's sex chromosomes have remained in their primitive state for a long time, or that something about the common ancestor was prone to the development of such an arrangement.

The other, perhaps less novel, but no less cool, aspect of the paper is that it introduces the first SSR-based map of the octoploid strawberry. Including two markers linked to the sex loci!

Anyway, all told, pretty cool, huh?

Fruit Genetics Friday #6: Sex and the Single Papaya

I came across this article while Googling for information on date palm sex inheritance the other night:

A primitive Y chromosome in papaya marks incipient sex chromosome evolution (Nature)

Unless you're a Nature subscriber, however, you can only read the abstract there, so try this for a more complete overview:

Scientists discover that papayas have sex chromosomes (University of Georgia)

It's an older article, but not one I'd seen. However it was not on date palm, so it was not immediately and directly relevant and I thought I'd wait until Friday to make it the launching point for another installment in this series.

The inheritance of sex in humans is probably one of the very first traits students learn the genetics behind (along with a vastly over-simplified and essentially incorrect description of the inheritance of eye color). It's a simple system, with a pretty distinct, binary (for the most part) phenotype, and it's something everyone cares about. Of course, sex isn't unique to humans. Plants and animals have distinct sexes as well--though sometimes they aren't quite so distinct. In fact, a majority of plants (and most fruit crops) are hermaphrodites (ie, they are simultaneously male and female), and there is evidence that suggests this is the ancestral state of plants as a whole--sex is a later invention.

Inheritance of sex in plants varies from species to species, and in fact may have evolved independently over a hundred times. It turns out, however, that an amazing lot of species have developed a similar system to people: females are homozygous (XX), and males are heterozygous (XY). Just like in humans, this will generally work out to a 1:1 ratio of male:female in the offspring. However, since sex is a little more flexible in many plants, some male plants will set the occasional fruit (interestingly, it virtually never happens the other way around, with male flowers on females). These self-pollinations show a 3:1 of males to females (or, occasionally 2:1, if the YY plants aren't viable). So we know that male is the heterozygous sex. Because of this, a locus denoted Su^F, for supressor of femaleness, was theorized. However, as the trait was further studied, it became clear, in part through cytological studies of chromosome deletion, that there were multiple loci involved, at least one or two more, involved in anther development. Hermaphrodites can result from mutation in one or the other of these genes.

In virtually all species, these genes are closely linked together. This makes sense, when you think about it: having "maleness" conditioned by multiple genes only works if you don't occasionally lose them to recombination. If a species is going to evolve separate sexes, and maintain them, these genes need to consistently work together to produce functional males. In some species these genes are an autosome (one of the standard, non-sex chromosomes) just like any other gene. However, despite the tight linkage, autosomes undergo crossing-over and recombination, so there will always been some risk of the linkage being broken up.

Enter the sex chromosome. Not all species that have sexes have sex chromosomes, getting by just fine keeping the required genes on an autosome. However, a sex chromosome has a major advantage, and that is to prevent recombination in the critical bit of genome. The human X and Y chromosomes may pair cytologically, but they're not two slightly different copies of the same thing the way the maternal and paternal copies of most chromosomes would be--there's vast differences in the content of the two (there would have to be given the size difference). I presume that's why the trait is denoted XX/XY not Xx/xx or Su^F/Su^f in people--we're really talking whole chromosomes assorting here, not just a trait.

(Note that although the XX/XY scheme is pretty common, it's by no means the only one out there. Birds have a ZW/ZZ scheme (just the same, but females are the heterozygous sex), and in some species there is no Y...just one or two copies of the X. The monotremes (such as the playtpus or the echidna) have one of the most bizarre schemes of all with multiple versions of both X and Y--for example in the short-beaked echidna it's XYXYXYXYX for males and XXXXXXXXXX (yes, there is one unpaired X in the male). I'm going to deal with XX/XY scheme exclusively for now, for fear of making things even less intelligible than they are now.)

Having two distinct sex chromosomes is useful in that by having two very different chromosomes, you suppress recombination, thus keeping things together appropriately. However, the trick is to have two different chromosomes that nonetheless pair up during meiosis, so that you always get one of each in each gamete. This can be accomplished because a portion of each sex chromosome remains similar (and thus capable of recombination). In people, a small area at one end of the X and Y chromosomes is identical and functions essentially as an autosome. Because this area does have a mate to seek out at meiosis, it pulls the non-pairing, non-recombinant bits along with it.

So how is recombination suppressed in the rest of it? The specifics aren't entirely clear, but basically the end result is that the Y chromosome ends up highly degenerate, accumulating deletions and mutations until, in some cases like humans, only a tiny handful of functional genes remain on it. That's probably why in many cases YY individuals aren't viable at all--they're missing functional copies of critical genes.

Plant Y chromosomes, it turns out, are on the whole not nearly as far gone as their mammalian counterparts. That's part of why people got excited about the papaya sex chromosomes. In papaya, normal recombination still occurs over 90% of the chromosome (compare that to less than 10% in humans), with only a small portion, which contains the male-determining genes, with evidence of heavy mutations and translocations. Because of this, it appears to be a sex chromosome in a very early stage of development, and provides a clear piece of evidence for the idea that sex chromosomes developed from autosomes. Recent work by geneticists shows that the non-recombinant region of the Y chromosome has a comparative lack of functional genes, and they estimate that the sex chromosomes evolved 1.3 to 2.8 million years ago, a mere twinkling of an eye in evolutionary terms.

Sex chromosomes appear to be more the exception than the rule in cultivated plants, however. One very good reason for this is probably the fact that most crop plants are hermaphrodites, and thus unlikely to be species with highly developed sex determination mechanisms. Some species (such as grapes) exist as males and females in the wild, but largely only as hermaphrodites in cultivated plants (the grape sex locus appears to be on an autosome). As far as I know, there are only two fruit crops that possess sex chromosomes: papaya (Carica papaya) and kiwi (Actinidia species). However, given how much more subtle the difference in previously described plant sex chromosomes are, there might well be some we have not yet discovered in fruits.

Papaya throws another wrinkle into the story by having hermaphrodites as well as male and female plants. Papaya cultivars, which are seed propagated, fall into two categories: those whose seeds give rise to male and female plants, and those that give rise to female and hermaphrodite plants (a majority of commercial cultivars are of that type, which makes sense, because who would want the non-fruitful male plants around). It appears that there may be two "flavors" of Y chromosome, one with a functional Su^F-type gene, and one without (but still possessing the necessary genes for anther development). This is supported perhaps by the fact it does not seem possible to generate a true breeding hermaphrodite papaya, perhaps because YY plants are not viable. In other words:

X_fX_f = female
X_fY_M = male
X_fY_H = hermaphrodite
Y_MY_M = not viable
Y_MY_H = not viable
Y_HY_H = not viable

Now that I've prattled on for a zillion words or so, I'd like to end on a brief note of caution...I'm not a papaya geneticist, so I may have gone horribly wrong in some of this, but this is the situation as I understand it.

The same goes for my understanding of kiwi, but I think it's interesting to note that although many kiwi species are polyploid, sex determination remains determined by a single gene pair, despite the sex chromosomes being duplicated (contrary to some early papers which suggested they were not, so that 2n=58=2x+XY but 2n=170=6x+XY...turns out that it's just really hard to count that many chromosomes...the hexaploids really had 174). So it looks as though there's a single pair of sex chromosomes that retains the ability to determine sex. (This also appears to be the case in octoploid strawberry, although the sex genes are on an autosome(s)).

Anyway, there it is. Probably the least exciting discussion of sex you've come across. (This will have to do for the time being instead of the persimmon sex post I mentioned in the comments a few days ago...I'm not sure of what became of it...I wrote it in Word because I was offline and on a plane at the time, and now I'm not sure where it is. Might be on the work laptop...(Sorry, Brandon.))

Fruit Genetics Friday #5: The Jostaberry

Most of my "Fruit Genetics Friday" posts have really been basically genetics posts with a little gloss of fruit thrown in to tie them into the prevailing theme. So I thought for a change I'd do something very specifically fruit-focused, a little more of a story of breeding than a genetics lesson.

Currants and gooseberries are both members of the genus Ribes, a group of fruit much appreciated in Europe but unfortunately often forgotten on this side of the Atlantic. I've heard a number of reasons suggested as to why Ribes fruit haven't really become big players in the New World, despite successfully adopting nearly every other major European fruit, and having a selection of wild Ribes of our own. I could (and, quite possible, might still) write a whole post on these, but I don't want to dwell on that in what is supposed to be a genetics post. Suffice it to say that if you're American and haven't had any of the fruits mentioned in this post, you're not alone. (But you are missing out).

Given their obvious morphological similarities, the idea of crossing currants and gooseberries probably occurred almost as soon as people began developing intentional hybrid fruit. No doubt more than a few attempts were fueled by the gooseberry breeding craze which swept England in 1800's (a worthy subject for a later post).Perhaps the first was the product of a Mr. W. Culverwell, an Englishman who in 1880 produced what was called Ribes culverwelli by crossing a black currant with a gooseberry. Producing hybrid seedlings turned out not to be too terribly hard, so long as the black currant was used as the female parent.

Such crosses yielded a range of diploid progeny, with a wide range of characteristics, some resembling their currant parent, some gooseberries, many somewhere in between. Unfortunately, they all had one thing in common: they were virtually sterile. Those that did set fruit did so parthenocarpically (ie, without fertilization) and so were dead ends when it came to breeding.

The Germans made some of the most concerted efforts, and in 1926 Paul Lorenz began making crosses at Berlin's Kaiser Wilhelm Institute. By World War II he had over 1,000 F₁ seedlings growing, but unfortunately in the chaos and destruction of the war, only eight plants remained. In 1946, these survivors were incorporated into a program at the newly founded Erwin Baur Institute.

It was there that Rudolf Bauer finally struck upon a method of generating fertile hybrids between black currants and gooseberries. By treating the sterile hybrids with a solution of colchicine, he was able to restore fertility.

Here I'll slip into a little more science: Colchicine is an alkaloid derived from autumn crocus (Colchium autumnale) that has been put to a variety of uses over the years. Medically, it is used to treat both cancer and gout, although it's worth noting that it's teratogenic and widly toxic, two major downsides to any medicine (though manageable with adequate care). It's value in breeding was discovered in 1937 by Albert Blakeslee, who found that plants soaked in solutions of colchicine had multiple sets of chromosomes in their cells. Turns out, colchicine inhibits spindle formation during mitosis. So basically, the chromosomes double, but the cell fails to divide, resulting in a cell with double the normal complement of chromosomes.

This is pretty useful in and of itself: polyploid plants tend to be bigger, and that often includes fruit. Lots of crop plants are polyploid (the first Fruit Genetics Friday, #1b, featured polyploidy, so I won't dwell on its many virtues here). However, from a plant breeding point of view it's greatest virtue is perhaps the ability to restore fertility in "mule" hybrids. It does this by providing chromosomes with a mate to pair with in meiosis.

For example: Imagine that a normal black currant or gooseberry has three pairs of chromosomes (they don't, they have eight, but let's keep this simple), for a total of six chromosomes. Each gamete (pollen cell or ovule) will have three, one from each pair, and these will combine to form a plant with the normal three pairs. However, the gooseberry and black currant have diverged enough evolutionarily that the chromosomes no longer recognize each other. Because of this, they don't pair normally during meiosis and can't form viable gametes. The result is a sterile plant.

So imagine the chromosomes as shown below ('c'-black currant, 'g'-gooseberry, '='-successful pairing):


Black Currant:
1_c=1_c
2_c=2_c
3_c=3_c

Gooseberry:
1_g=1_g
2_g=2_g
3_g=3_g

Diploid F₁ Hyrbid:
1_c 1_g
2_c 2_g
3_c 3_g


The chromosomes in the hybrid don't match up, so they don't pair. Colchicine gets around this by providing each chromosome with a mate, its exact duplicate:


Tetraploid F₁ Hyrbid:
1_c=1_c
1_g=1_g
2_c=2_c
2_g=2_g
3_c=3_c
3_g=3_g


Using this strategy, Bauer was able to improve the fertility of those eight survivors, and use them as the basis for further breeding. Although the collection was once again cut back severely when the institute moved to Cologne, he eventually generated 15,000 fertile tetraploid hybrid seedlings. From these he selected three hybrids, which he dubbed 'Jostaberry' as a group ("Josta" comes from the beginnings of the common names of both species in German, Johannisbeere and stachelbeere). However, there has been some confusion since then, and Jostaberry has been distributed as single clone, despite the fact that it was originally three distinct genotypes (two of which were siblings). It is not clear which of the existing clones are the original three (assuming all three survive). In addition to the original 'Jostaberry' introduction to the U.S., the Corvallis repository has two other clones, and a Swiss nursery has named two others of uncertain origin, 'Jostina' and 'Jogranda', so it's possible the originals are still out there.

The Jostaberry has much to recommend it (although it requires lots of pruning and does still suffer some residual problems with fruit set), especially in its resistance to white pine blister rust and its lack of thorns, and there has been a little subsequent interest in improving it. George Waldo, working with USDA in Oregon, did some further breeding, but there has been little activity since then, hampered by low yields and a limited market. In addition to the varieties mentioned above, the only other slections circulating are perhaps a dozen ORUS selections from the USDA, some of which are still available in nursery catalogs. Although a minor fruit today, it remains an example of what can be accomplished with a clever breeding strategy.

Fruit Genetics Friday #4: Transposable Elements and Fruit Color

After I wrote that big long 'Micah Rood' post, I felt a powerful hankering to spend a little time getting back to some down-and-dirty molecular stuff. This is surprising because when I finished my Ph.D. I thought I'd never, ever feel the urge to even look at molecular genetics again. (I actually do occasionally venture over to the molecular side of things in the course of my job, but it's really mostly some one else's job, which is exactly how I like molecular biology to work). But I figure that it's been a long, long time since I wrote a big dense genetics post here (heck, it's been a long, long time since I wrote much of anything here), and if I'm going to even pretend to have this "Fruit Genetics Friday" thing I'm going to have to have something to post some Friday, so I might as well give it a shot. For those of my readers who are intensely non-science and are here merely out of simple love of eating and/or growing fruit, my apologies. Though really, at this stage, you ought to just be pleased to see me posting at all.

Anyway, if you recall (if you don't, feel free to look at it now), back in the discussion of the 'Micah Rood' apple, I mentioned transposable elements as a possible cause of a sudden shift in coloration. Whole books and whole careers have been spent on transposable elements, and I'm hardly an expert, so I'm not going to attempt to burden you with an in-depth discussion of the many types and the different mechanisms involved. The short version is this: Transposable elements are basically freeloaders, little chunks of DNA with the power to move themselves around the genome. Exactly when and why they do this is not always very well understood. Usually they can do this relatively harmlessly--a lot of most higher organisms' genomes are comprised of "junk" DNA (though not of much of it seems to be junk as we once thought). As long as they land somewhere unimportant in the genome, they're pretty harmless. If they land in the middle of a gene, though, they will often disable the gene. If the gene was something important, one may see a pretty stunning change. If the transposable element later "jumps" out of the gene, it may or may not return to normal--frequently the gene won't get repaired correctly, leaving a small "scar" in the sequence at the point from which the transposable element departed. Most genomes are chock-full of transposable elements (by some estimates half of human DNA), but relatively few of them are active, because as they accumulate mutations themselves, the lose the ability to jump. Because particular sequences seem to be especially attractive targets for specific transposons, some species have specific traits that seem particularly prone mutation due to transposon insertion.

Fruit color changes in grape are relatively common (in the sense that lots are known, not that you would likely ever encounter one in your lifetime). Probably the best known are 'Pinot gris' and 'Pinot blanc', both mutations of the venerable 'Pinot noir' variety. (The difference between the two is that 'Pinot gris' is a chimera (like 'Pinot Meunier'), carrying the mutant color gene only in one cell layer, while 'Pinot blanc' has it in all layers). 'Frontenac gris' is a white mutant of 'Frontenac', a relatively recent wine grape release from the University of Minnesota. Both of these cases involve black fruited varieties producing white fruit, but the process can go the other way as well. 'Verdelho roxo', 'Ruby Okuyama' and 'Flame Muscat', are red mutants of the white grapes 'Verdelho', 'Italia' and 'Muscat of Alexandria', respectively. Occasionally the mutant forms of these will revert back to the original color.

The causes of many of these mutations are unknown, but it seems that most white fruited grapes result of a transposable element called Gret1 (Grape retroelement 1). This transposable element is of a type called a retroelement (because it copies itself through an RNA intermediary phase, much like retroviruses, to which they are likely related). Gret1 has a tendency to land next to a gene called VvMybA1. While the gene's function isn't entirely clear, it's part of a class of genes called transcription factors, which regulate the expression of other genes. While Gret1 doesn't actually disrupt the gene itself, it does land in the promoter region and thus may affect the expression of the gene.

It turns out that in nearly all white grapes, both copies of VvMybA1 (one each from the male and female parents) have a copy of Gret1 in their promoters, while black fruited varieties have one or more copy without this insert. Recent red fruited mutants of white varieties appear to have lost one copy of Gret1, apparently leaving an additional bit of genetic detritus behind, partially disrupting the promoter. It's theorized that the white fruit characteristic developed in Vitis vinifera, the European grapevine, only once.

Interestingly (to me anyway), while white-fruited selections of other grape species lack the Gret1-VvMybA1, it does appear that at least a couple may have developed white fruit as the result of Gret1 insertions elsewhere. Both 'Pixiola' (a white fruited selection of V. aestivalis) and 'Bougher' (a white V. riparia) feature Gret1 insertions in the gene F3H. F3H is involved in anthocyanin production, and coincidentally, F3H appears to also be the source of the yellow fruit mutation in the diploid strawberry, Fragaria vesca.

(For you really hardcore genetics types, you can see the relevant papers here, here, and here. (And a bonus strawberry paper here.))

Fruit Genetics Friday #3: Self-Incompatibility

When shopping for fruit and nut trees (or just flipping idly through nursery catalogs), one common issue is that many species require another of their species to provide pollen in order to set fruit. Most fruit crops produce flowers which are both male and female, and produce plenty of pollen. In some cases odd ploidy can result in plants incapable of producing viable pollen at all (or very small amounts, anyway), and a few species are dioecious (having male and female flowers on separate plants). But in many cases, the plants in question produce perfectly good pollen. Nursery catalogs are full of little pollination tables and warnings of "requires a pollinator" or, strangely enough, something along the lines of "[Cultivar X] will not pollinate [Cultivar Y]".

The reason for this is a phenomenon called self-incompatibility (SI). As inconvenient as it is for those of us who would like to just plant our favorite cultivar and nothing else, self-incompatibility serves a useful purpose evolutionarily. The whole point of sexual reproduction is to encourage assortment and exchange of genes, and yet by generally self-fertilizing (which they do by having male and female reproductive organs mature simultaneously and adjacent to each other), many species have sacrificed this evolutionary opportunity in exchange for a better chance of producing offspring, with the downside that those offspring will be merely reassortments of the parent's genes, not new mixtures of two individuals. Self-incompatibility evolved to prevent self-pollination in such cases, helping to avoid inbreeding depression.

There are two major SI systems in fruit crops, and both are really quite simple, though the implications are not necessarily so. Both involve interactions involve alleles of a single gene, called the "S" locus, which is why the basic genetics of it were worked out nearly a hundred years ago.

Gametophytic self-incompatibility, the most common form, is most commonly seen in sweet cherry (Prunus avium, which, coincidentally, I'm eating a giant bag of right now), though it's also found in a number of other fruit and nut species including almond, Japanese apricot, roses, arctic bramble and assorted diploid blackberries and raspberries. Under this scheme, the haploid genotype of the pollen is the factor determining whether pollination can occur. Each pollen grain receives one of the two S-alleles of the parent, and that pollen is unable to germinate on flowers of individuals which possess the same S-allele. So, for example:

If you have a cherry tree with the S-genotype of S1S2, the pollen grains produced will be either S1 or S2. Neither can fertilize the tree's own flowers, since both S1 and S2 are present in the female. But say a neighoring tree is S1S3. It can produce S1 and S3 pollen. The S1 grains won't be able to germinate on either tree's flowers, but the S2 grains of the first tree can fertilize the second, and the second's S3 grains can fertilize the first. If we propose third tree, S4S8, appears on the scene, then both the other plants, having neither S4 or S8, will be able to fertilize it, as well as the reverse. There are quite a few different S-alleles in cherry, so the odds of getting two cultivars with the exact same complement is pretty small, but it can happen (for example, 'Bing' and 'Emperor Francis' are both S3S4). A nice diagram of gametophytic SI is available here.

The other system is called sporophytic incompatibility. This one's a bit less common, particularly in fruit. The example that springs to mind is hazelnut (Corylus species). The situation is similar to the gametophytic system, in that it depends on a pair of S-alleles. But there is one critical difference: in gametophytic SI, the compatibility phenotype of the pollen grain depends on the genotype of that grain, while under sporophytic it is the genotype of the parent that matters. So while a S1S2 GSI plant produces pollen grains with S1 or S2 genotypes, and corresponding S1 or S2 compatibility phenotypes. However, under SSI, while pollen grains are still genotypically S1 or S2, they all will share the dominant S-alleles phenotype (in this case S1). So a S1S2 SSI plant would produce pollen grains carrying the S2 allele, but effectively S1 for pollination purposes, so it could pollinate a S2S3 plant. An interesting twist is that while GSI plants are always heterozygous (with one minor exception which I will get to), SSI plants can carry two identical S-alleles, because it the actual genotype of the pollen is not related to the phenotype. It also adds the extra complication of the needing to know the dominance hierarchy of the S-alleles (which, inconveniently, is not simply numerical order. It's actually something like: (3, 8), (6), (1, 5, 7, 10, 12, 14, 15, 16, 17, 18, 20, 21, 24), (2, 25), (19), (9, 11, 22, 26), (23), (4), with dominance running from dominant on the left to recessive on the right (alleles in the same set of parentheses are roughly equivalent in dominance).

Researchers have, however, managed to come up with a convenient end-run around GSI in cherry. Scientists pollinated 'Emperor Francis' (S3S4) with irradiated pollen from 'Napoleon' (also S3S4). Normally, with both parents having the same S-alleles, no cross could occur. But a few seeds did set, because the radiation had damaged the chromosomes in some of the pollen grains, and, completely randomly, had damaged the S4 allele carried in one of them. The resulting seedling was JI 2420, which broke the rule I just mentioned above by being S4S4. However, one of those S4's was non-functional, and could pollinate any sweet cherry, including itself. The value of this was obvious, and JI 2420's amazing allele was immediately incorporated into a new cultivar, called 'Stella'. Nearly all self-compatible sweet cherries carry S4', the modified S4 from 'Stella'. While the trait is undeniably useful, the dependence on a single source is worrisome from a genetic diversity standpoint, and Amy Iezzoni, cherry breeder from Michigan State, has suggested that there may be some undesireable linkages associated with Stella's S4' gene. (Another self-compatible selection, JI 2434, came from the same experiment as JI 2420 and has been found to carry a second self-compatibility gene, this one a modification of the S3 allele (cleverly indicated S3'). So there's at least another option out there. Similar self-compatibility alleles exist in almond, Japanese apricot, and probably Rubus, having occurred naturally and been selected.

So next time you see those compatibility tables in the nursery catalog, see if you can puzzle out the S-allele genotypes based on the information given. And don't forget to buy a pollenizer!

Fruit Genetics Friday #2: Polyploid Inheritance

Last time on Fruit Genetics Friday, I discussed the basics of polyploidy. Polyploidy has lots of implications for fruit breeding, and some of the most profound are in terms of inheritance.

Inheritance in polyploids is different than in diploids, though the fundamental pricinpals remain the same. I'm going to assume once again that you've all got the dominant vs. recessive bit pretty much down. I'll use thornlessness in tetraploid blackberries as an example, since I've worked with it a bit. There are a couple of types of thornlessness in blackberries, but the most common is a recessive gene derived from Rubus ulmifolius var. inermis and passed on via 'Merton Thornless', s. In a diploid, you might have SS (thorny), Ss, and ss (thornless). In the tetraploid you get a few more genotypes:

SSSS (Thorny)
SSSs (Thorny)
SSss (Thorny)
Ssss (Thorny)
ssss (Thornless)

One thing you may notice is that it's a lot harder to see the recessive trait expressed. This can be a problem if you're breeding for a trait which is recessively inherited. The more slots to be filled, the more likely one of them is going to come up with the dominant and mask your desired trait.

Just how these four get passed on depends on what type of polyploid you're dealing with. If our tetraploid is an autoploid, we basically wind up doing the scaled version of the old familiar diploid inheritance. Instead of choosing 1 of 2 alleles from each parent, we just choose 2 of 4 instead. So if we are selfing a cultivar which is SSss, we get:

Gametes produced (frequency):
SS (1/6)
Ss (4/6)
ss (1/6)


To the following offspring (frequency):

SSSS = SS & SS (1/6 x 1/6 = 1/36) (Thorny)

SSSs = SS & Ss or Ss & SS (1/6 x 4/6 + 4/6 x 1/6 = 8/36) (Thorny)

SSss = SS & ss or ss & SS or Ss & Ss
(1/6 x 1/6 + 1/6 x 1/6 + 4/6 x 4/6 = 18/36) (Thorny)

Ssss = SS & Ss or Ss & SS (1/6 x 4/6 + 4/6 x 1/6 = 8/36) (Thorny)

ssss = ss & ss (1/6 x 1/6 = 1/36) (Thornless)

So, as I noted before, even if your parents have half their alleles the recessive, only 1 in 36 of the offspring will show the trait (compare this to 1 in 4 for a comparable situation in a diploid). These ratios also assume random chromosome assortment. Random chromosome assortment is considered a given in diploids, and more or less most of the time it is in autoploids, as well, but one consequence of having multiple possible partners for each chromosome is that sometimes the fact that they can form configurations other than simple pairs leads to complications, particularly something called random chromatid assortment. I won't go into the details here because it's a mess, but suffice it to say, weird things happen, including getting progeny with genotypes impossible under normal assumptions (such as SSSs x SSSs yielding some offspring with ssss, for example).

The situation is different with an alloploid. If you recall, alloploids have distinct sets of chromosomes from differing origins (in this case we'll call them A and B). These sets are going to pair with each other, so you get regular pairing like in a diploid, effectively giving you the equivalent of two genes with two copies each, rather than four copies of a single gene. In some ways this simplifies things, but it also adds a few twists. For example, not all SSss individuals will pass on the trait the same way, because it matters which genomes the alleles are in. If both genomes have one copy of either allele (we'll express it [Ss][Ss], with the first pair of brackets the A genome, the second the B), then we see something like this:

Gametes produced (frequency):
SS [S][S] (1/4)
Ss [S][s] (1/4)
sS [s][S] (1/4)
ss [s][s] (1/4)

You might have noticed that it'd be much easier to find a ssss seedling in this case, 1 in 16. However, another SSss individual may have its genes configured differently. If both copies of the recessive are in one genome and both copies of the dominant in the other ([SS][ss], we see something more like this:

Gametes produced (frequency):
Ss [S][s] (all)

See what's happening? The A genome is [SS], so it can only contribute an S to a gamete. The B genome is [ss], so it can only contribute an s. Thus all gametes will be the same, and in fact, all selfings will result in the same genotype, in this case SSss ([SS][ss]), the same as the parent. So it would be impossible to find any thornless plants at all, no matter how many seedlings you grew out from the selfing.

To add yet another wrinkle to this, in higher order polyploids, you can have segmental alloploids, where portions of the genome behave like autoploids within an alloploid. So one could have a hexaploid [SSss][Ss], for example, in which the A genome exhibits inheritance like an autotetraploid, and the B genome behaves like a diploid. Crazy stuff.

The big lesson here is, of course, polyploids are darn complex (which is why the inheritance of many important traits, even in well-studied polyploid species, is still unknown except in vague terms). In fact, they are complex enough that I'm thinking this probably wasn't a wise topic to tackle, particularly early in this series, but I promised it, so there it is. Enterntained me to write it, anyway. Feel free to ask questions, and I'll do what I can to explain.

"Next Week" on Fruit Genetics Friday: Self-Incompatibility. Why do some fruit crops require a second variety to pollinate, and why do some pollen source work better than others?

I'm willing to entertain requests, too, by the way...I don't have any kind of master plan for this series, besides a vague hope to make it quasi-regular in its timing, and I've always gotten great article suggestions from my readers in the past (some of which I've followed through on, and some of which have fallen through the cracks.)

Fruit Genetics Friday #1b: Polyploidy(And yeah, I know it's Saturday...)

Well, here I am at 1:34am in the lab, waiting an hour so I can dump a little media onto a couple of plates and go home, so I thought maybe to pass the time I'd give you folks a real post for a change.

This is Fruit Genetics Friday #1b, because there's another #1 that covers the real basic stuff that isn't finished, and might never be. Frankly, basic genetics, while certainly cool, gets a little old to write a ton about, and I'm guessing my average reader remembers the really basic stuff. If you don't, feel free to ask questions. I won't think any less of you for it.

So on to the fruit genetics and one of my favorite topics, polyploidy:

One of the first major wrinkles one runs into when trying to understand the genetics of many fruit crops is polyploidy. Remember how people (and most animals and many plants) have two of each gene, one copy from each parent? That makes them diploid. That's sort of the basic model, and in the animal world it's the most common one. But in plants (and a few insects, reptiles, and amphibians), it's not uncommon to have more than the basic two sets of chromosomes, a condition called polyploidy ("di" meaning two, vs. "poly" meaning many, see?). Estimates are all over the place, but somewhere in the vicinity of 70% of plant species (angiosperms, anyway) are or have been polyploid at some point in their evolutionary past. An awful lot of crop species are polyploid, partly because one of the traits of polyploids is that they tend to be bigger than the their diploid counterparts, and in general bigger has been considered better when it comes to crop development.

For example, I started my career working with a diploid species, grapes, did my M.S. working with tetraploid blackberries (four sets of chromosomes), and now work with strawberries, which are octoploid (eight sets of chromosomes.) The cultivated strawberry is among the crops with the highest ploidy level, although there are blackberry species with as high as twelve sets of chromosomes (dodecaploid maybe? I get mixed up past ten. By the way, standard shorthand for these things is to use "x" to represent the basic chromosome set for a species, so a diploid is denoted as 2x, and tetraploid, 4x, etc.)

Just like diploids, when polyploids reproduce, they form eggs and pollen cells containing half the normal complement of chromosomes. This generally works pretty well if you've got an even number of sets of chromosomes, but it becomes a problem in odd-ploid plants. If you've got three copies of a particular chromosome, and the cells splits to form two pollen grain, what happens to the extra? The answer varies...sometimes one cell gets it and the other doesn't, sometimes it's just lost. The result, anyway, is reproductive cells that are complete mess a lot of the time. This results in sterile plants. A good example of this is the cultivated banana, which is triploid. Wild, diploid bananas are full of seeds, but because cultivated types can't produce viable sex cells, no fertilization takes place, and we get our nice soft, seedless bananas (although some one once told me that about one in every five or ten thousand bananas will contain a viable seed, the result of the off chance that a particular combination of chromosomes works out).

There are two types of polyploids, which are formed in two different ways. The simplest kind of polyploid is called an autoploid. In an autoploid, all the chromosome sets come from the same species. This can come from a spontaneous doubling in a vegetatively propagated plant (this happens when a cell basically makes a mistake mid-division and fails to divide after duplicating it's chromosomes). This has, for example, resulted in a handful of grape cultivars, such as 'Pierce', which was identified as a large-fruited shoot on an 'Isabella' vine. The other possible cause is the tendency of plants to occasionally produce sex cells with double the normal genetic complement, which are called "unreduced gametes". These unreduced gametes can also join to produce autoploids.

The other kind is called an alloploid. Alloploids have two or more different types of chromosomes, generally from ancestors of two or more different species. In octoploid strawberry we use the notation AAA'A'BBB'B' to indicate that the eight sets of chromosomes come in four different types, from four different ancestral species. Most crosses between species fail, resulting in sterile progeny (because unlike sets of chromosomes will not pair, it is next to impossible to form viable gametes, just like in an odd-ploid plant). However, if at some point the resulting plant doubles its genetic contents, the problem is solved. A new hybrid with genomes AB can't reproduce, because A chromosomes won't pair with B chromosomes. However, if AB becomes AABB, then the A chromosomes will pair with the other A chromosomes, and the B with the B, and fertility is restored, though frequently at less than perfect levels.

These potential problems with fertility are part of why artificial polyploids have been successful in only a relatively few cases. Even if a plant has big fruit, if it has sterility problems and has trouble actually producing that fruit, it's not going to be a hit. There are other problems, too, though they vary somewhat from species to species. In addition to fertility issues, polyploids tend to be less tolerant of cold, have less rugged shoots, and sometimes have disease issues as well.

Well, my labwork is calling. Next installment I'll look at inheritance in polyploids, and why it's so darn kooky. (I'm hoping to post a list of polyploid fruits here for you, but it's 2:30am, I've got lab work to do and a baby squawking, and I can't get the table HTML right, so it's got to wait.) I realize this may be a tad technical for some folks...like I said, let me know if there's something you're curious about and I didn't do a good job explaining it.

Anyway, good night, folks.

Update: Here's the little table I promised you folks. I really need to get me some fancy program to do my HTML...it's too tiring to do a big table, so this is hardly an exhaustive list, just some examples

Update 2: The table is screwing things up, and my imperfect knowledge of HTML leaves me helpless when it comes to fixing it. So no more table. Sorry. I'd try to sort it out, but I'm way, way, too tired. So anyway, polyploids include blackberries, strawberries, sour cherries, European plums, bananas, blueberries, persimmons, some apples and mandarins, etc.