Review of Plant Cytogenetics

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1 Review of Plant Cytogenetics Updated 2/13/06 Reading: Richards, A.J. and R.K. Dawe Plant centromeres: structure and control. Current Op. Plant Biol. 1: R.K. Dawe Centromere renewal and replacement in the plant kingdom. PNAS 102: Optional (but really interesting): Lee, H.-R. et al Chromtain immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. PNAS 102: Nasuda, S. et al Stable barley chromosomes without centromeric repeats. PNAS 102: I. Basic terminology Chromosome: A molecule of DNA, and associated proteins bound together. Each chromosome contains: Centromere: specialized region that is the last part of a replicated chromosome to disjoin at meiosis or mitosis Kinetochore: protein structure surrounding centromere that coordinates spindle attachment and chromosome movement Telomere: specialized regions at both ends of the chromosome Euchromatin: stains normally, gene rich region Heterochromatin: stains darkly, gene poor region What composes telomeres and centromeres at the molecular level? Telomeres are composed of short tandem repeats of DNA that are added to chromosome ends by the enzyme telomerase. These repeat sequences are fairly well conserved across all eukaryotes, and the repeat sequence TTTAGGG is conserved in most plant species (Gill and Friebe, 1998). Centromeres also contain blocks of repeated DNA sequences, but these sequences seem much less conserved across species. Centromere regions range from about 1 Mbp (Arabidopsis) to more than 100 Mbp (wheat) in size (Bennetzen 1998). Richards and Dawe (1998) suggested that centromere DNA sequences are not always sufficient, nor are they always necessary for specification of centromere activity. The observation that there is little sequence conservation among the known centromere repeats is consistent with the idea that primary DNA sequence may provide only part of the information necessary to specify centromere function. The remaining information is thought to be 1

2 epigenetic, superimposed on the primary nucleotide information, in the form of stable, self-propagating chromatin states. This suggests that DNA sequence analysis alone will not tell us too much about what a centromere is! The centromere seems to be the result of an interaction between various DNA sequences and the chromosome-associated proteins. Interestingly, although centromeric DNA sequences seem to be highly variable, one of the key proteins they interact with to produce kinetochores is a highly conserved protein called CenH3, which is a variant histone protein. This protein is found in yeast, insects, vertebrates, and plants. There may be other centromeric proteins that are rapidly evolving, however, to maintain the interaction between the conserved CenH3 and the rapidly changing centromeric DNA sequences. The most detailed analyses of plant centromere DNA sequences have been in rice. Cultivated rice (Oryza sativa) centromeres contain two domains: a 155 bp sequence called CentO that is tandemly repeated many times (and called satellite DNA because most such repeats have different bulk density than the rest of the genome and can be separated on density gradients), and a set of retrotransposon-derived sequences, called CRR, that are dispersed among these repeats and also found in the centromeres of other grass species. Lee et al. (2005) analyzed the sequences of centromeres from 17 different species in the Oryza genus and found that they did not all share a common centromere repeat sequence. Some of the wild species have quite different centromeric repeats, indicating the rapid evolution of the sequences that can occur. Even more surprising is the result from Nasuda et al. (2005) that artificially broken barley chromosomes that completely lack the centromeric associated repeats can still function by organizing kinetochore formation. How are centromeres defined genetically? See final section of this lecture (will be covered only if we have time). Chromatid: One molecule of the double helix of DNA in a replicated chromosome. Following DNA replication and before meiosis or mitosis, each chromosome has two chromatids joined at the centromere. Homologous chromosomes: Chromosomes that carry the same genes in the same order and that pair at meiosis. May have different alleles at common genes. Homoeologous (homeologous) chromosomes: Chromosomes that carry some, but not all, of the same genes (or related genes). They do not pair at meiosis, or pair with low frequency. 2

3 Genome: All the genetic information (DNA, chromosomes) in a cell of an organism. Often the nuclear genome is implied, but don t forget about the mitochondrial and chloroplast genomes! Locus: Allele: A particular location on a chromosome. It may refer to a gene that codes for a protein (e.g., the waxy gene in corn). Or it may refer to a region of the chromosome that does not code for a protein (e.g., UMC187, a corn RFLP locus identified by a genomic clone). So, all genes are loci, but not all loci are genes! Alternate form a locus. Designated by A, a implying dominance of the A allele over the a allele. Or by A 1, A 2,, A n to account for multiple alleles without implying dominance relationships. Breeding works by selecting for different alleles, not different genes! Nomenclature of chromosome numbers and DNA content. n = gametophytic chromosome complement 2n = sporophytic chromosome complement x = number of chromosomes in one complete homoeologous set of chromosomes. 2x = number of chromosomes in a diploid sporophyte 4x = number of chromosomes in a tetraploid sporophyte. etc. Examples Diploid Maize 2n = 2x = 20 Triploid Banana 2n = 3x = 33 Tetraploid Alfalfa 2n = 4x = 32 Hexaploid Wheat 2n = 6x = 42 Octoploid Sugarcane 2n = 8x = 80 So, most cells in a maize plant have 2n = 2x = 20 chromosomes, but maize pollen cells each have n = x = 10 chromosomes. Compare: Relative amount of DNA in a cell C = constant the relative amount of DNA in a gametophytic cell 2C = relative amount of DNA in a sporophytic cell before DNA replication 4C = relative amount of DNA in a sporophytic cell after DNA replication and before mitosis/cell division. 3

4 Euploidy Absolute amount of DNA in a cell C-value Given in picograms (10-12 g) 1 pg = x nucleotides (base pairs) See Arumunagathan and Earle (1991) for C-values for many plant species. Haploid: A sporophytic plant having the gametophytic chromosome number (n), and derived directly from a gametophyte (without fertilization). If the species is diploid (2n = 2x), a haploid of that species has a single set of the chromosome (n = x). If the species is polyploid (2n > 2x), a haploid of that species has more than a single set of the chromosomes (n > x), but is still called a haploid. For example, a haploid derived from tetraploid alfalfa (2n = 4x = 32) has two copies of the basic chromosome set (n = 2x = 16) Doubled Haploid: Haploidy can be induced in some species (e.g., in barley, tobacco with some regularity; in maize, alfalfa, wheat, oat, potato it is done with greater difficulty). This can be accomplished by anther/pollen culture, interspecific crosses, or with some reproductive mutants. Doubling is achieved with colchicine or by tissue culture techniques. Why make doubled haploids? Since haploids have only one allele per locus (if from a diploid species), doubled haploids are immediately completely homozygous at every locus. This may be useful for breeding purposes (homozygosity in one generation vs. selfing for many generations) and for genetics applications (linkage mapping is simplified). Polyploid: A species having more than two basic sets of chromosomes per sporophytic cell. Many species are polyploids (70% of grasses, 23% of legumes, for example). Types of polyploids (Stebbins): Nomenclature: A represents the set of chromosomes in the A genome. B represents the set of chromosomes in the B genome, etc. Autopolyploids: many sets of a single genome: AA 6 AAAA Allopolyploids: two or more distinct genomes: AA + BB 6 AABB or AB 6 AABB. (Note that A and B can be homoeologous sets of chromosomes; i.e., they are similar sets of chromosomes, but A chromosomes do not pair with B chromosomes at meiosis.) Segmental allopolyploids: genomes are somewhat differentiated, but pairing of chromosomes from different genomes is still possible: A 1 A 1 + A 2 A 2 = A 1 A 1 A 2 A 2. Autoallopolyploids: a mixture of common and distinct genomes. 4

5 Pairing of chromosomes at meiosis: Bivalents (II) two chromosomes pair at meiosis I Trivalents (III) three chromosomes pair at meiosis I Quadrivalents (IV) four chromosomes pair at meiosis I Allopolyploids do not have pairing higher than bivalents. Autopolyploids may have pairing higher than bivalents. In some cases, autopolyploids have only bivalents, but the crucial distinction is that any of the more than two homologous chromosomes can pair, there is no restriction of which two homologs pair. Because the terms auto- and alloploidy imply an evolutionary history that is often not really known, the terms disomic and polysomic polyploids are preferred. These terms are based solely on the pairing relationships among the chromosomes, and do not imply the evolutionary origin of the polyploidy species. Disomic polyploid: only bivalents occur at meiosis, and each chromosome can pair with only one other chromosome in the genome. Polysomic polyploid: each chromosome can pair with more than one other chromosome in the genome; groups of more than two chromosomes may pair at meiosis. Amphiploid: a man-made polyploid synthesized by doubling the chromosomes of an interspecific hybrid. Some examples include Triticale (wheat x rye) and Raphanobrassica (radish x cabbage). Some examples to clarify: Maize: 2n = 2x = 20. The basic chromosome set has 10 distinct chromosomes. Each sporophytic cell has 2 copies of each chromosome. Wheat: 2n = 6x = 42. The basic chromosome set of wheat has 7 distinct chromosomes. Bread wheat has three related genomes, A, B, and D. Chromosome 1 of genome A is structurally similar to chromosome 1 of genome B and chromosome 1 of genome D, chromosome 1 of genome A only pairs with chromosome 1 of genome A! Alfalfa: 2n = 4x = 32. The basic chromosome set of alfalfa has 8 chromosomes. Cultivates alfalfa cells each have four copies of each of the 8 chromosomes. Any one of these four copies of a common homolog can pair with any of the other three at meiosis, even though quadrivalents rarely form. 5

6 Now that you grasp the basic rules, it is time to learn that in reality, the distinction between diploidy and polyploidy can be fuzzy. Many diploid species are in fact paleopolyploids meaning that they have many duplicated genes, implying a polyploid ancestor in their evolutionary history, but through evolution, the species developed regular disomic inheritance. Paleopolyploidy was discovered originally with molecular linkage maps (in corn and soybean). A single RFLP probe often identifies more than one locus in these species, and conserved linkage arrangements among some of the duplicated loci ( large-scale duplications ) were observed. Whereas a single duplicated locus is not evidence for ancient polyploidy, larger stretches of multiple duplicated linkage arrangements are! More recently, DNA sequencing has provided additional evidence that paleopolyploidy is common. The complete DNA sequence of Arabidopsis, which has one of the simplest regular diploid genomes among plants, reveals large scale duplication events within the genome, suggesting ancient polyploidy. The result of this large-scale duplication is that genetic redundancy is common in plants: More than one gene may code for similar functions. Knocking out even a simple phenotype may be difficult if more than one locus affects the phenotype. Duplicate epistasis may be common in plants. But, if the duplications are sufficiently ancient, the duplicated genes may evolve new functions or function under different conditions or developmental stages. II. Meiosis Compare diploid, allotetraploid, autotetraploid for one set of homologous or homoeologous chromosomes III. Polyploid segregation ratios. What are the expected segregation ratios of a single locus in a tetrasomic polyploid? They depend on the recombination frequency between the locus and the centromere. As an example, we demonstrate segregation ratios at three hypothetical loci on, A, B, and C, that differ in their recombination frequencies from the centromere. The A locus is tightly linked to the centromere, so that no recombination occurs between the locus and the centromere. The A locus segregates exactly like the centromeres themselves. At meiosis I, two homologous centromeres move to one pole, and the other two centromeres move to the other pole. So, if the plant is tetra-allelic, A 1 A 2 A 3 A 4, then at meiosis I (following DNA replication and chromosome doubling), the following segregations are possible (and equally likely): 6

7 MI A 1 A 1 /A 2 A 2 + A 3 A 3 /A 4 A 4 A 1 A 1 /A 3 A 3 + A 2 A 2 /A 4 A 4 A 1 A 1 /A 4 A 4 + A 2 A 2 /A 3 A 3 At meiosis II, one copy of each centromere and one allele of each locus in parent cell move into each daughter cell: MI MII A 1 A 1 /A 2 A 2 + A 3 A 3 /A 4 A 4 A 1 A 2 / A 1 A 2 / A 3 A 4 / A 3 A 4 A 1 A 1 /A 3 A 3 + A 2 A 2 /A 4 A 4 A 1 A 3 / A 1 A 3 / A 2 A 4 / A 2 A 4 A 1 A 1 /A 4 A 4 + A 2 A 2 /A 3 A 3 A 1 A 4 / A 1 A 4 / A 2 A 3 / A 2 A 3 This results in the equal probability of the following gametic types: A 1 A 2, A 1 A 3, A 1 A 4, A 2 A 3, A 2 A 4, A 3 A 4 (1/6 frequency each). This mode of inheritance is called random chromosome segregation. The C locus is far from the centromere, so that the C locus and the centromere are genetically unlinked. In this case, sufficient crossing-over occurs between the centromere and the C locus that any one allele at the C locus can be grouped with any set of three other alleles after the first meiotic separation if the chromosomes form quadrivalents. If the C locus has a recombination frequency of 50% with the centromere, the gamete frequencies from genotype C 1 C 2 C 3 C 4 are: (1/28) C 1 C 1 (4/28) C 1 C 2 (4/28) C 1 C 3 (4/28) C 1 C 4 (1/28) C 2 C 2 (4/28) C 2 C 3 (4/28) C 2 C 4 (1/28) C 3 C 3 (4/28) C 3 C 4 (1/28) C 4 C 4 To figure out these gamete frequencies, realize that there is only one possible way to get a C 1 C 1 gamete, but there are four ways to get a C 1 C 2 gamete: the first C 1 chromatid segment can be paired with either the first or the second C 2 chromatid segment, and the second C 1 chromatid segment can be paired with either the first or the second C 2 chromatid segment. This reasoning applies to all of the other heterozygous gametic combinations. When the locus exhibits these segregation ratios, it is called random chromatid segregation. Notice that an outcome of this type of segregation is that alleles on sister chromatids may end up in the same gamete; this result is called double reduction. The frequency of double reduction is measured as the frequency of gametes containing sister 7

8 chromatid alleles and is denoted as α. So, under random chromatid assortment, the frequency of double reduction = α = sum of frequencies of C 1 C 1, C 2 C 2, C 3 C 3, C 4 C 4 = 1/7. What happens if C has 50% recombination frequency with the centromere, but quadrivalents do not form? Consider the gamete frequencies of a C 1 C 2 C 3 C 4 plant with only bivalent pairing. First consider the possible pairing arrangements: MI (1/3) C 1 C 1 /C 2 C 2 + C 3 C 3 /C 4 C 4 (1/3) C 1 C 1 /C 3 C 3 + C 2 C 2 /C 4 C 4 (1/3) C 1 C 1 /C 4 C 4 + C 2 C 2 /C 3 C 3 Now, allow for recombination between centromeres and chromosomes during MI: MI metaphase (1/12) C 1 C 1 /C 2 C 2 + C 3 C 3 /C 4 C 4 (1/12) C 1 C 2 /C 1 C 2 + C 3 C 3 /C 4 C 4 (1/12) C 1 C 1 /C 2 C 2 + C 3 C 4 /C 3 C 4 (1/12) C 1 C 2 /C 1 C 2 + C 3 C 4 /C 3 C 4 (1/12) C 1 C 1 /C 3 C 3 + C 2 C 2 /C 4 C 4 (1/12) C 1 C 3 /C 1 C 3 + C 2 C 2 /C 4 C 4 (1/12) C 1 C 1 /C 3 C 3 + C 2 C 4 /C 2 C 4 (1/12) C 1 C 3 /C 1 C 3 + C 2 C 4 /C 2 C 4 (1/12) C 1 C 1 /C 4 C 4 + C 2 C 2 /C 3 C 3 (1/12) C 1 C 4 /C 1 C 4 + C 2 C 2 /C 3 C 3 (1/12) C 1 C 1 /C 4 C 4 + C 2 C 3 /C 2 C 3 (1/12) C 1 C 4 /C 1 C 4 + C 2 C 3 /C 2 C 3 8

9 MI metaphase MI anaphase (1/12) C 1 C 1 /C 2 C 2 + C 3 C 3 /C 4 C 4 C 1 C 1 / C 3 C 3 // C 2 C 2 / C 4 C 4 or C 1 C 1 / C 4 C 4 // C 2 C 2 / C 3 C 3 (1/12) C 1 C 2 /C 1 C 2 + C 3 C 3 /C 4 C 4 C 1 C 2 / C 3 C 3 // C 1 C 2 / C 4 C 4 (1/12) C 1 C 1 /C 2 C 2 + C 3 C 4 /C 3 C 4 C 1 C 1 / C 3 C 4 // C 2 C 2 / C 3 C 4 (1/12) C 1 C 2 /C 1 C 2 + C 3 C 4 /C 3 C 4 C 1 C 2 / C 3 C 4 // C 1 C 2 / C 3 C 4 (1/12) C 1 C 1 /C 3 C 3 + C 2 C 2 /C 4 C 4 C 1 C 1 / C 2 C 2 // C 3 C 3 / C 4 C 4 or C 1 C 1 / C 4 C 4 // C 2 C 2 / C 3 C 3 (1/12) C 1 C 3 /C 1 C 3 + C 2 C 2 /C 4 C 4 C 1 C 3 / C 2 C 2 // C 1 C 3 / C 4 C 4 (1/12) C 1 C 1 /C 3 C 3 + C 2 C 4 /C 2 C 4 C 1 C 1 / C 2 C 4 // C 3 C 3 / C 2 C 4 (1/12) C 1 C 3 /C 1 C 3 + C 2 C 4 /C 2 C 4 C 1 C 3 / C 2 C 4 // C 1 C 3 / C 2 C 4 (1/12) C 1 C 1 /C 4 C 4 + C 2 C 2 /C 3 C 3 C 1 C 1 / C 2 C 2 // C 3 C 3 / C 4 C 4 or C 1 C 1 / C 3 C 3 // C 2 C 2 / C 4 C 4 (1/12) C 1 C 4 /C 1 C 4 + C 2 C 2 /C 3 C 3 C 1 C 4 / C 2 C 2 // C 1 C 4 / C 3 C 3 (1/12) C 1 C 1 /C 4 C 4 + C 2 C 3 /C 2 C 3 C 1 C 1 / C 2 C 3 // C 2 C 3 / C 4 C 4 (1/12) C 1 C 4 /C 1 C 4 + C 2 C 3 /C 2 C 3 C 1 C 4 / C 2 C 3 // C 1 C 4 / C 2 C 3 At meiosis II, one copy of each centromere and one allele of each locus in parent cell move into each daughter cell. This results in the following gametic types: MI anaphase MII C 1 C 1 / C 3 C 3 // C 2 C 2 / C 4 C 4 or C 1 C 1 / C 4 C 4 // C 2 C 2 / C 3 C 3 C 1 C 3 / C 1 C 3 / C 2 C 4 / C 2 C 4 or C 1 C 4 / C 2 C 3 / C 1 C 4 / C 2 C 3 C 1 C 2 / C 3 C 3 // C 1 C 2 / C 4 C 4 C 1 C 3 / C 2 C 3 / C 1 C 4 / C 2 C 4 C 1 C 1 / C 3 C 4 // C 2 C 2 / C 3 C 4 C 1 C 3 / C 1 C 4 / C 2 C 3 / C 2 C 4 C 1 C 2 / C 3 C 4 // C 1 C 2 / C 3 C 4 C 1 C 3 / C 1 C 4 / C 2 C 3 / C 2 C 4 C 1 C 1 / C 2 C 2 // C 3 C 3 / C 4 C 4 or C 1 C 1 / C 4 C 4 // C 2 C 2 / C 3 C 3 C 1 C 2 / C 1 C 2 / C 3 C 4 / C 3 C 4 or C 1 C 4 / C 2 C 3 / C 1 C 4 / C 2 C 3 C 1 C 3 / C 2 C 2 // C 1 C 3 / C 4 C 4 C 1 C 2 / C 2 C 3 / C 1 C 4 / C 3 C 4 C 1 C 1 / C 2 C 4 // C 3 C 3 / C 2 C 4 C 1 C 2 / C 1 C 4 / C 2 C 3 / C 3 C 4 C 1 C 3 / C 2 C 4 // C 1 C 3 / C 2 C 4 C 1 C 2 / C 3 C 4 / C 1 C 4 / C 2 C 3 9

10 C 1 C 1 / C 2 C 2 // C 3 C 3 / C 4 C 4 or C 1 C 1 / C 3 C 3 // C 2 C 2 / C 4 C 4 C 1 C 2 / C 1 C 2 / C 3 C 4 / C 3 C 4 or C 1 C 3 / C 1 C 3 / C 2 C 4 / C 2 C 4 C 1 C 4 / C 2 C 2 // C 1 C 4 / C 3 C 3 C 1 C 2 / C 2 C 4 / C 1 C 3 / C 3 C 4 C 1 C 1 / C 2 C 3 // C 2 C 3 / C 4 C 4 C 1 C 2 / C 1 C 3 / C 2 C 4 / C 3 C 4 C 1 C 4 / C 2 C 3 // C 1 C 4 / C 2 C 3 C 1 C 2 / C 3 C 4 / C 1 C 3 / C 2 C 4 Summing over all the possibilities, the gametic frequencies are: (1/6) C 1 C 2 (1/6) C 1 C 3 (1/6) C 1 C 4 (1/6) C 2 C 3 (1/6) C 2 C 4 (1/6) C 3 C 4 This is identical to random chromosome segregation! So, if the chromosomes do not form quadrivalents, then loci segregate following random chromosome segregation, no matter what their position is relative to the centromere. To summarize: If the locus is very near the centromere, random chromosome segregation occurs. If the locus has 50% recombination from the centromere, and quadrivalents form, random chromatid segregation occurs. If the locus has 50% recombination from the centromere, and quadrivalents do not form, random chromosome segregation occurs. Finally, consider a locus, B, that is not completely linked nor completely unlinked from the centromere. The frequency of double reduction at this locus will likely be somewhere between 0 and (1/7), and this will depend on the formation of quadrivalents and the probability of recombination between the centromere and locus B. We can write general formulas for gamete frequencies of an autotetraploid as a function of α, the probability of double reduction. Note that: α = 0 for loci undergoing random chromosome segregation, α = 0 if quadrivalents do not form (as in alfalfa), α = 1/7 for loci undergoing random chromatid segregation, 10

11 0 < α < 1/7 for loci that are only partially linked to the centromere. Bingham et al. (1968) estimated the frequency of double reduction in autoteraploid maize and reported that: α = 2.2% for wx α = 18% for Sh They suggested that the estimate of α = 18% for Sh exceeded the theoretical maximum (14%) because of sampling error. In general, though, the estimates follow roughly what is expected based on the position of these loci with respect to the centromere: on chromosome 9, wx is 5 cm from the centromere, and Sh is about 30 cm from the centromere. In a quadrallelic genotype, B 1 B 2 B 3 B 4, each double reduction gamete occurs with frequency α/4. (Note that this gives 1/28 when α = 1/7 in random chromatid segregation). The other types of gametes occur at a frequency of (1 α)/6: Gametes from double reduction Gametes not from double reduction Gamete Frequency Gamete Frequency B 1 B 1 α/4 B 1 B 2 (1 α)/6 B 2 B 2 α/4 B 1 B 3 (1 α)/6 B 3 B 3 α/4 B 1 B 4 (1 α)/6 B 4 B 4 α/4 B 2 B 3 (1 α)/6 B 2 B 4 (1 α)/6 B 3 B 4 (1 α)/6 Sum α Sum 1 α Genotype frequencies can then be easily derived from a Punnet square of the appropriate gamete frequencies. Special cases: Diallelic genotypes (with two alleles per locus, B and b): Genotype of Parent Plant BBBb BBbb Bbbb Gamete Frequency BB (2 + α)/4 (1 + 2α)/6 α/4 Bb (2 2α)/4 (4 4α)/6 (2 2α)/4 bb α/4 (1 + 2α)/6 (2 + α)/4 What are the genotype frequencies resulting from self-pollination of each of these three types of diallelic parents? 11

12 Offspring Genotype of Parent Plant BBBb BBbb Bbbb Genotype Offspring genotype frequencies BBBB [(2 + α)/4] 2 [(1 + 2α)/6] 2 α 2 /16 BBBb (2 + α)(2 2α)/8 (1 + 2α)(4 4α)/36 (2 2α)α/8 BBbb (2+α)α/8+[(2 2α)/4] 2 [(1+2α)/6] 2 +[(4 4α)/6] 2 (2+α)α/8 +[(2 2α)/4] 2 Bbbb (2 2α)α/8 (1 + 2α)(4 4α)/36 (2 + α)(2 2α)/8 bbbb α 2 /16 [(1 + 2α)/6] 2 [(2 + α)/4] 2 Notice that if α = 0, then neither a bbbb nor a Bbbb genotype can arise from selfpollination of a BBBb genotype. Also, in this case, the genotype frequencies that arise from the self-pollination of a Bbbb plant are (1/4) BBbb, (1/2) Bbbb, (1/4) bbbb. From these results, it should be clear that homozygous genotypes are rarer in polysomic polyploids than in diploids. Segregation ratios in allopolyploids Let A represent a locus on one chromosome of a disomic tetraploid, and let B represent a locus on its homoeologous chromosome. If a plant with genotype A 1 A 2 B 1 B 2 is selfed, the following gamete ratios result (verify this by considering the behavior of the homoeologous chromosomes at meiosis): Gamete Frequency A 1 B 1 1/4 A 1 B 2 1/4 A 2 B 1 1/4 A 2 B 2 1/4 The following genotype frequencies occur in its selfed progeny: Genotype Frequency A 1 A 1 B 1 B 1 1/16 A 1 A 1 B 1 B 2 1/8 A 1 A 1 B 2 B 2 1/16 A 1 A 2 B 1 B 1 1/8 A 1 A 2 B 1 B 2 1/4 A 1 A 2 B 2 B 2 1/8 A 2 A 2 B 1 B 1 1/16 A 2 A 2 B 1 B 2 1/8 A 2 A 2 B 2 B 2 1/16 12

13 You will notice that this is simply a diploid segregation ratio with two unlinked genes. In fact, breeders treat disomic polyploids as diploids for the purposes of genetics, with the realization that many genes are likely duplicated on homoeologous chromosomes. What do the different inheritance patterns of polysomic and disomic polyploids suggest about their breeding behavior? Mac Key (1970) observed that virtually all polysomic polyploids are primarily outcrosses, whereas virtually all disomic polyploids are primarily self-fertilizing species. He proposed that the reason for this lay in their different inheritance patterns. It seems that in most diploids and in polysomic polyploids, heterozygosity is related to vigor (this does not necessarily imply overdominant gene action, it is likely primarily due to deleterious recessive alleles at different loci in repulsion phase linkage). Therefore, polysomic polyploids tend to be outcrossers in order to maximize heterozygosity. In contrast, disomic polyploids can fix heterozygosity in the homozygous state because alleles at duplicated loci on homoeologous chromosomes can interact like different alleles at the same locus in a diploid or polysomic polyploid. Thus, using our previous example, if the A1B2 allelic interaction were favorable, it can be fixed in the A 1 A 1 B 2 B 2 homozygote. Thus, for disomic polyploids, self-fertilization can serve to prevent the disruption of favorable allelic interactions. Note that this implies that dominance intra-locus interactions of diploid genomes are converted to epistatic inter-locus interactions in disomic polyploids. IV. Defining centromeres genetically Centromeres were defined genetically with a special mutant stock in Arabidopsis called quartet. Plants homozygous for the quartet mutation do not produce normal pollen grains, instead they produce pollen as groups of four microgametophytes that represent one microgametic tetrad. That is, one cluster of four microgametophytes represent the four products of a single meiosis. Each tetrad of pollen can be separated and used to pollinate an emasculated tester plant, producing four seeds. These four seeds then can be analyzed using tetrad analysis procedures originally developed for fungi. By considering pairs of loci, one can classify each tetrad as parental ditype (PD), nonparental ditype (NPD), and tetratype (TT), see figure from Copenhaver et al. (1998): 13

14 Copenhaver et al. (1998) screened 57 tetrads with 52 DNA markers, and later, Copenhaver et al. (1999) screened more than 1000 tetrads with DNA markers, including the centromere-associated 180 bp repeat. By identifying marker pairs on different chromsomes that showed few or no tetratype tetrads, they were able to genetically define the centromeres on the linkage maps defined by the genetic markers (see Figure 4, Copenhaver et al. (1998)). To clarify their method, consider four loci on linkage group 1, two of which (A and B) are very near the centromere, such that crossovers between them and the centromere are rare, and the two of which (D and E) are far enough from the centromere that crossovers regularly occur between it and the centromere. Then consider a second linkage group with loci F (near its centromere) and G (far from its centromere). Two parental lines with genotypes A 1 A 1 B 1 B 1 D 1 D 1 E 1 E 1 F 1 F 1 G 1 G 1 and A 2 A 2 B 2 B 2 D 2 D 2 E 2 E 2 F 2 F 2 G 2 G 2 are crossed to form the heterozygous genotype A 1 A 2 B 1 B 2 D 1 D 2 E 1 E 2 F 1 F 2 G 1 G 2, which also has the quartet mutation, so it forms pollen tetrads. This heterozygote is used to pollinate a tester genotype A 3 A 3 B 3 B 3 D 3 D 3 E 3 E 3 F 3 F 3 G 3 G 3. The 14

15 four testcross progeny corresponding to a pollen tetrad can be identified, permitting unordered tetrad analysis. Assume that loci A and B flank the centromere so closely that crossovers very rarely or never occur between them and the centromere. Then consider the effect of a single crossover that occurs between loci B and D on linkage group 1 (C represents the centromere): Chromatids at Meiosis I Chromatids in resulting gametes A 1 -C-B D 1 -E 1 A 1 -C-B D 1 -E 1 A 1 -C-B D 1 -E 1 A 1 -C-B D 2 -E 2 A 2 -C-B D 2 -E 2 A 2 -C-B D 1 -E 1 A 2 -C-B D 2 -E 2 A 2 -C-B D 2 -E 2 After this pollen tetrad is used to fertilize the tester stock, four progeny result. Ignoring the tester alleles, and considering the A and B loci, the progeny represent a Parental Ditype tetrad: A 1 B 1 A 1 B 1 A 2 B 2 A 2 B 2 Ignoring the tester alleles, and considering the A and D loci, the result is a Tetratype: A 1 D 1 A 1 D 2 A 2 D 1 A 2 D 2 The latter result also applies to the A and E pair, the B and D pair, and the B and E pair: A 1 E 1 B 1 D 1 B 1 E 1 A 1 E 2 B 1 D 2 B 1 E 2 A 2 E 1 B 2 D 1 B 2 E 1 A 2 E 2 B 2 D 2 B 2 E 2 (all are tetratypes) Now consider the D and E loci; the result is a Parental Ditype: D 1 E 1 D 2 E 2 D 1 E 1 D 2 E 2 Remember that these tetrads are unordered, so the ditype shown above cannot be distinguished from the following order: 15

16 D 1 E 1 D 1 E 1 D 2 E 2 D 2 E 2 What happens if there are two crossovers between loci B and D? Non-parental ditypes for loci B and D can occur from a 4-strand double crossover that occurs between loci B and D, but this result could have also been due to a crossover that occurred between the centromere and locus A. A 2-strand double crossovers in the B-D interval will result in parental ditypes for B and D (indistinguishable from a zero-crossover meiosis), and 3- strand double crossovers will results in tetratypes for B and D. Considering these results, you can see that by comparing pairs of loci on the same chromosome, you cannot distinguish between a low frequency of tetratypes that occurs because the two loci are both near the centromere or because the two loci are simply tightly linked and not near the centromere. But, what happens if you consider pairs of loci that are on different chromosomes? Since the markers were already used to create a complete linkage map, you can know if the marker loci are on the same chromosome or not. Consider the case where there is a crossover between B and D on chromosome 1 and between F and G on chromosome 2. The following tetrads could result: B 1 F 1 B 1 F 2 B 1 F 1 B 1 F 2 B 2 F 2 B 2 F 1 B 2 F 2 B 2 F 1 (no tetratypes possible) PD NPD D 1 F 1 D 1 F 2 D 1 F 1 D 1 F 1 D 1 F 2 D 1 F 2 D 2 F 2 D 2 F 1 D 2 F 1 D 2 F 2 D 2 F 1 D 2 F 2 PD NPD TT B 1 G 1 B 1 G 2 B 1 G 1 B 1 G 1 B 1 G 2 B 1 G 2 B 2 G 2 B 2 G 1 B 2 G 1 B 2 G 2 B 2 G 1 B 2 G 2 PD NPD TT D 1 G 1 D 1 G 2 D 1 G 1 D 1 G 1 D 1 G 2 D 1 G 2 D 2 G 2 D 2 G 1 D 2 G 1 D 2 G 2 D 2 G 1 D 2 G 2 16

17 PD NPD TT So, when you look at two loci on different chromosomes and find no tetratypes, you know that they are both tightly linked to their cetromeres, because the two loci themselves are not linked to each other. Thus, Figure 4 of Copenhaver et al. (1998) illustrates the frequency of tetratypes between loci near the centromere on chromosomes I through IV on the one hand and all of the loci on chromosome V. The four lines correspond to the four centromere-associated loci on the other chromosomes, and they all indicate that their proportion of tetrads in pairs with chromosome V are minimum around position 74 cm, indicating that is the position of the centromere on chromosome V: This technique also allowed them to study crossover interference, which we will discuss in a later section. References 17

18 Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: Bingham ET, Burnham CR, Gates CE (1968) Double and single backcross linkage estimates in autotetraploid maize. Genetics 59: Mac Key J (1970) Significance of mating systems for chromosomes and gametes in polyploids. Hereditas 66:

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