Download Control of Chromosome Pairing and Genome Evolution in Disomic

Control of Chromosome Pairing and Genome Evolution in Disomic Polyploids
Updated: 2/17/06
Readings:
Naranjo,T. and E. Corredor. 2005. Clustering of centromeres precedes bivalent
chromosome pairing of polyploid wheats. Trends in Plant Sci. 9:214-217
Feldman, M. and A.A. Levy. 2005. Allopolyploidy - a shaping force in the evolution of
wheat genomes. Cytogenet. Genome Res. 109:250-258.
I. Chromosome pairing in disomic polyploids
Why do homologous, but not homoeologous, chromosomes pair at meiosis in disomic
polyploids? If homoeologous chromosomes have similar structures and gene order, what
is to prevent them from pairing at meiosis?
The best studied example of genetically-controlled control of chromosome pairing in a
disomic polyploidy is the Ph1 gene in wheat. It helps to know the outline of evolution of
the bread wheat genome. Wheat has three genomes, A, B, and D, and different diploid
relatives of bread wheat contain one or the other of those genomes:
T. urartu
(2n = 2x = 14)
genome AA
Ae. speltoides
(2n = 2x = 14)
genome SS ~ BB
T. turgidum
(2n = 4x = 28)
genome AABB
T. aestivum
(2n = 6x = 42)
genome AABBDD
Ae. tauschii
(2n = 2x = 14)
genome DD
How does an AABB progeny result naturally from a cross of AA x BB? The most likely
route to allopolyploidization is the formation of an AB F1 hybrid with limited fertility,
which then produces 2n (AB) eggs and 2n (AB) pollen, which unite to form a fertile
AABB tetraplo id.
Once the allopolyploid is established, intergenomic pairing (pairing of homoeologues)
must be restricted, or meiotic irregularities may result, reducing fertility.
Sears and Okamoto at Univ. of Missouri and Riley and Chapman in the UK in 1958
independently demonstrated that the absence of chromosome 5B of bread wheat caused
an increase in pairing among the remaining homoeologous chromosomes and a decrease
in pairing between homologues. The locus controlling the control of pairing was named
Ph1 (Pairing homoeologous 1) and was mapped with deletion stocks to a region on the
long arm of 5B (5BL).
What is the mechanism of action of Ph1? How does it restrict pairing to homologues?
There are (at least) two major competing theories:
1. Ph1 promotes premeiotic association of homologous chromosomes:
The idea is that Ph1 regulates the position of chromosomes in the nucleus – both in
mitosis and meiosis – so that homologues are more closely aligned even before meiotic
prophase begins, and this results in homologues being more likely to pair at meiosis.
This idea is reviewed by Feldman (1993).
Evidence for premeiotic association: Martinez-Perez et al. (2001) demonstrated that in
the absence of Ph1, homoeologous chromosomes associate in some somatic cells (root
xylem cells), but in the presence of Ph1, only homologues were associated in these
somatic cells. As far as I know, this is the first report of somatic chromosome pairing in
plants, which is important in itself, but it suggests that if Ph1 regulates pairing in somatic
cells, then it certainly can be operating premeiotically. Martinez-Perez et al. (2004) also
demonstrated premeiotic association of homologous centromeres in polyploidy wheat in
the presence of the Ph1 gene, whereas this association does not occur in the absence of
Ph1 or in diploid wheats (Naranjo and Corredor, 2004).
2. Ph1 regulates synapsis and crossing-over at meiotic prophase:
The idea is that chromosomes can search each other out more or less at random during
prophase, and that Ph1 controls how specifically the chromosomes will pair. In the
absence of Ph1, if two homoeologues come together at prophase, they can synapse and
recombine, whereas in the presence of Ph1, homoeologues may associate briefly, but
they will not pair, so that the chromosomes remain unpaired and continue to “search”
until they find their homolog.
Evidence for this is the Luo et al. (1996) experiment:
Chromosome 1Am of Triticum monococcum can be substituted for one copy of the
normal chromosome 1A of bread wheat. Chromosomes 1Am and 1A are “closely
homoeologous” and pair at meiosis and recombine genetically as if they were
homologous in the absence of Ph1. However in the presence of Ph1, they recombine
little, if at all. This provided a system with which they could test the role of homologous
vs. homoeologous centromeres and telomeres on recombination between chromosomes in
the presence of Ph1.
Because chromosomes 1Am and 1A recombine in the absence of Ph1, it is possible to
recover genetically recombined chromosomes that carry some genes from 1Am and some
1A. Luo et al. used two different recombinant 1Am – 1A chromosomes to study the
importance of homology in different regions of the chromosome:
To understand this material, we need to review some ane uploid terms:
Euploid has normal 2n sporophytic chromosome complement or an exact multiple of that
number (thus, euploids include haploids, diploids, tetraploids, etc…)
Aneuploid has one or a few chromosomes extra or fewer than the normal 2n number
Monosomic has 2n – 1 chromosomes: it is missing one of a homologous pair
Double monosomic has 2n – 1 – 1 chromosomes: it is missing one each of two
homologous pairs
Nullisomic (not used in this experiment) has 2n – 2 chromosomes, it is missing both
chromosomes of a homologous pair.
Monotelosomic has 2n - 1 chromosomes, and that chromosome that is lacking its
homolog is missing one of its arms. In this experiment they used monotelosomic 1AL,
which has all normal chromosomes except that it no normal chromosome 1A, but one
telosomic 1AL which has the long arm, but not the short arm of chromosome 1A.
Ditelosomic has 2n chromosomes, but one homologous pair is represented by telosomics.
This means the genome is deficient for one chromosome arm.
Double ditelosomic (DDt) has 2n + 2 chromosomes, but one homologous pair is
represented by two pairs of telosomics, one pair for each chromosome arm. In this
experiment they used DDt1A, which has 20 normal pairs plus two 1AL telosomic
chromosomes and two 1AS telosomic chromosome s.
Recombinant Substitution Line (RSL) is a line that has all the same chromosomes (and
alleles) of a standard stock but one chromosome is different (in this case it is a
recombined chromosome relative to the standard chromosome 1A).
Mapping populations used in Luo et al. (1996): RSL1Arec x Chinese Spring (CS) ph1:
1Arec
CS 1A
CS mt1AL
X
(transmits ½
nullisomic gametes)
RSL1Arec x CS ph1 F1
Some progeny are monosomic –
monotelosomic, identify by
karyoptype and discard.
Other progenies are monosomic for (a
possibly recombined) chromosome 1, keep
these and analyze with chromosome 1
markers to determine allelic composition
of chromosome 1
Only monosomic progenies are desired, because each such progeny represents a single
recombinant chromosome from the F1, and this recombinant chromosome can be
maintained intact (with no further recombination) over selfing generations, so it is a
“permanent” recombinant progeny. 96 monosomic progenies were recovered from this
cross and the genetic map of this population serves as a control because recombination is
essentially normal in the absence of Ph1.
Another control population is made from the cross of DSCnn1A to Chinese Spring (CS).
DSCnn1A is identical to Chinese Spring except its chromosome 1A pair is from the
cultivar Cheyenne. This allows measurement of recombination between homologous
chromosomes 1A in the presence of Ph1.
To study the effect of homologous centromeres with other homoeologous portions in the
same chromosome on recombination, two different recombinant chromosome
substitution lines were crossed to CS in the presence of Ph1. If Ph1 acts only on
centromeres to cause chromosomes with homologous centromeres to pair and recombine,
then recombination between these recombinant chromosomes and CS 1A should be
normal even in the presence of Ph1.
RSL 82 has a CS centromere and long arm, but most of its short arm (including one
telomere) are derived from 1Am. RSL104 has a CS centromere and both telomeres are
from CS, but has two interstitial segments derive from 1Am. See Figure 1 from Luo et al.
(1996). Each of these lines was crossed to CS with Ph1 to form a mapping population (in
which case only recombination within the homoeologous segment can be studied,
because the other regions are from CS, so are not polymorphic with CS), and also to
DSCnn1A with Ph1 to form a mapping population in which recombination can be
measured along the length of the chromosome.
Results are shown in Figures 2 and 3 of Luo et al. (1996). When Ph1 is present,
recombination is normal in homologous chromosome segments, but entirely excluded
from homoeologous segments. This is true whether both telomeres are homologous or
not. The conclusion is that even after chromosomes pair, Ph1 acts to discriminate
homologous from homoeologous chromosome segments within paired chromosomes, and
prevents complete synapsis in homoeologous segments.
Luo et al. (1996) concluded from this that Ph1 does not control pre- meiotic association of
homologous centromeres, instead it controls synapsis and recombination at meiosis. My
own conclusion is that Luo et al. (1996) did not disprove that Ph1 controls pre- meiotic
association based on centromere homology; to test that hypothesis, they could have
studied recombination between chromosomes homologous except for having
homoeologous centromeres. It seems that this result can be reconciled with Feldman’s
hypothesis that Ph1 controls centromeric associations between homologues even before
meiosis by hypothesizing that Ph1 controls both premeiotic association and synapsis and
recombination during prophase.
Genome evolution in allopolyploids
What happens when two quite similar genomes that evolved to operate “independently”
come together in an allopolyploid? Recent studies have suggested that allopolyploidy in
itself is a major force for genome evolution.
Case study 1: allopolyploid Brassica (Song et al., 1995)
The species in the genus Brassica include three diploid species and three allopolyploid
species derived from pairwise combinations of the diploid genomes:
B. nigra
(black mustard)
(2n = 16, B genome)
B. carinata
(2n = 34, BBCC)
B. juncea
(2n = 36, AABB)
B. campestris = B.
rapa (turnip)
(2n = 20, A genome)
B. oleracea
(broccoli, cauliflower)
(2n = 18, C genome)
B. napus (canola)
(2n = 38, AACC)
Song et al. (1995) created new allopolyploids from hybrids of B. rapa and B. oleracea
(corresponding to B. napus allopolyploids) and from hybrids of B. rapa and B. nigra
(corresponding to B. juncea allopolyploids). The AB and AC F1s were treated with
colchicines to double their chromosomes and form the allotetraploids AABB and AACC.
In addition, reciprocal crosses were made for each allotetraploid. The F1s were selfed to
form F2s, and a single F2 from each F1 was selfed to the F5 generation, and nine F5
plants from each synthetic allotetraploid were genotyped with 70 RFLP probes.
An example of their results are shown in Fig. 1…why do the F2s sometimes differ from
the parents? Why do the F5s sometimes differ from the F2s?
All of their data are summarized in Table 1.
They suggested the following mechanisms for the observed results:
They suggested the following mechanisms for the observed results:
“The changes we observed could have resulted from several different processes, such as
chromosome rearrangement, point mutation, gene conversion, DNA methylation, and
others yet to be described.” Loss of chromosomes was not a factor, because all plants
had the expected chromosome number.
Chromosome rearrangement: “we observed a high frequency of aberrant meioses with
chromosome bridges, chromosomes lagging, and multivalents. These aberrant meioses
probably indicate intergenomic chromosome associations and could have resulted in loss
of RFLP fragments through subsequent segregation of recombined or broken
chromosomes. A small frequency of these events could result in gain of novel fragments
due to recombination events within the probed regions.
Gene conversion: “Intergenomic associations also could provide the opportunity for gene
conversion- like eve nts, and as evidence for this, we observed simultaneous loss/gain of
parental restriction fragments for some of the probes.” They refer to gene conversion
resulting from non-homologous recombination in yeast as an example of such events.
Changes in DNA methylation: likely, but not of major importance, because digestion
with isoschizomer enzymes Hpa II (cuts CCGG but not CpCpGG, CpCGG, or CCpGG)
and Msp I (cuts CCGG or CCpGG but not CpCpGG or CpCGG) revealed no differences
in 7 of 9 probes.
Directional genome change:
In the AB polyploid, mostly B fragments were lost, whereas in the BA polyploid, about
equal numbers of A and B-derived fragments were altered. They suggested that this was
due to an incompatibility reaction between the A cytoplasm and the B nuclear genomes.
In the AC and CA polyploids, no directional change was observed. They suggested that
the difference between the AB/BA and AC/CA polyploids was due to the fact that the A
and C genomes are more closely related than are the A and B genomes.
Implications of results:
Suggests that rapid genome changes can occur in the early generations following
interspecific hybridization and allopolyploid formation. This variation may enhance the
rate of evolution of allopolyploids. The question remains, does such rapid change occur
in other new allopolyploids?
Case study 2: allopolyploid wheat (Ozkhan et al. 2001)
Ozkhan et al. (2001) specifically studied 8 DNA sequences that exist in all diploid wheat
species, but are missing from all but one genome in allohexaploid wheat. Thus, these
represent sequences that were eliminated from the allohexaploid genome at some point
during evolution. The question addressed in this study was: are these sequences
eliminated in the first few generations of the allohexaploid? i.e., are these sequences
eliminated rapidly or only over long evolutionary periods?
They made F1 hybrids between various, diploid, tetraploid, and hexaploid species, and
created allohexaploids from these hybrids with colchicines treatment (or in a few cases,
these occurred spontaneously). The allohexaploids represented some genomic
combinations that exist naturally (such as AASS, which are similar to AABB genomes,
or AABBDD, like bread wheat), and others that do not exist in nature (Table 1). They
studied the F1 generation (e.g., AB), and selfed generations derived from 22 different
allopolyploids created from the F1s (e.g., AABB).
Results:
They found that in natural allopolyploids, 75 – 100% of the sequences were eliminated
by the S2 generation. In non- natural allopolyploids, 50 – 58% of the sequences were
eliminated by the S2 generation. Only one case of a “gain” of a novel band not present in
the parents was reported, and it disappeared in a later generation.
They suggested that the faster elimination of duplicated sequences in natural polyploids is
a reason that such allopolyploids were successful in being established as species.
They found that, in every case, the genome from which sequences were eliminated in the
synthesized allopolyploids matched those in the natural polyploids.
Because the patterns of loss were repeatable across different allopolyploid combinations,
and because the patterns of loss matched that in natural allopolyploids, they concluded
that the observed sequence elimination was “rapid, nonrandom, and directional.”
In contrast to Song et al. (1995):
They suggested that intergenomic recombination was NOT responsible for sequence loss.
What was their evidence for this?
They suggested that cytoplasm of the allopolyploids was NOT responsible for which
sequences were lost, because combinations with the same nuclear combinations but
different cytoplasms did not differ for their pattern of sequence loss.
Implications: “Our results imply that rapid and nonrandom sequence eleimination is an
essential aadjustement required for the harmonious coexistence of the two or more
different genomes in the nucleus of wheat allopolyploids... Such nonrandom elimination
of DNA sequences augments the divergence of homoeologous chromosomes, that is, it
accelerates the evolution of genomic alloplyploids from segmental allopolyploids; thus it
can provide the physical basis for the diploid-like meiotic behaviour (i.e., the exclusive
pairing of homologous chromosomes) of the newly formed allopolyploids.”
Perhaps rapid genome change is the first step in diploidizing the allopolyploid, and the
action of Ph1 is another step that reinforces genomic changes.
BUT:
Note that not all studies of newly formed allopolyploids have found rapid genomic
changes like those reported by Song et al and Ozkhan et al. First, Axelsson et al. (2000)
reported essentially no genomic changed in newly a synthesized Brassica AABB
allopolyploid, in contrast to the Song et al (1995) study. Also, Liu et al. (2001) reported
that newly synthesized cotton (Gossypium) allopolyploids showed no changes among
some 22,000 loci!
Recent studies have focused on the role of epigenetic changes that occur in newly formed
polyploidy species, in addition to the genetic changes discus sed in this lecture. Gene
expression in general seems to be affected by changes in ploidy. Epigenetic changes that
have been observed in new polyploids include the silencing of one set of progenitor genes
through DNA methylation changes (without involving the actual loss of such genes).
Osborn et al (2003) reviewed the genetic and epigenetic changes in newly formed
polyploidy species and discussed ways in which these changes could promote the natural
fitness of new polyploids, helping to establish them as species.
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