Molecular characterization of a family of tandemly repeated DNA sequences, TR-1, in heterochromatic knobs of maize and its relatives

The non-Mendelian behavior of plant B chromosomes

B chromosomes, also known as supernumerary chromosomes, are dispensable elements in the genome of many plants, animals, and fungi. Many B chromosomes have evolved one or more drive mechanisms to transmit themselves at a higher frequency than predicted by Mendelian genetics, and these mechanisms counteract the tendency of non-essential genetic elements to be lost over time. The frequency of Bs in a population results from a balance between their effect on host fitness and their transmission rate. Here, we will summarize the findings of the drive process of plant B chromosomes, focusing on maize and rye.

Evolution of B Chromosomes: From Dispensable Parasitic Chromosomes to Essential Genomic Players

B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they mostly arise through rearrangements and duplications from standard chromosomes. They can occur in single or multiple copies in a cell and are usually present only in a subset of individuals in the population. Because B chromosomes frequently show unstable inheritance, their maintenance in a population is often associated with meiotic drive or other mechanisms that increase the probability of their transmission to the next generation. For all these reasons, B chromosomes have been commonly considered to be nonessential, selfish, parasitic elements. Although it was originally believed that B chromosomes had little or no effect on an organism's biology and fitness, a growing number of studies have shown that B chromosomes can play a significant role in processes such as sex determination, pathogenicity and resistance to pathogens. In some cases, B chromosomes became an essential part of the genome, turning into new sex chromosomes or germline-restricted chromosomes with important roles in the organism's fertility. Here, we review such cases of "cellular domestication" of B chromosomes and show that B chromosomes can be important genomic players with significant evolutionary impact.

The supernumerary B chromosome of maize: drive and genomic conflict

The supernumerary B chromosome of maize is dispensable, containing no vital genes, and thus is variable in number and presence in lines of maize. In order to be maintained in populations, it has a drive mechanism consisting of nondisjunction at the pollen mitosis that produces the two sperm cells, and then the sperm with the two B chromosomes has a preference for fertilizing the egg as opposed to the central cell in the process of double fertilization. The sequence of the B chromosome coupled with B chromosomal aberrations has localized features involved with nondisjunction and preferential fertilization, which are present at the centromeric region. The predicted genes from the sequence have paralogues dispersed across all A chromosomes and have widely different divergence times suggesting that they have transposed to the B chromosome over evolutionary time followed by degradation or have been co-opted for the selfish functions of the supernumerary chromosome.

A simple and efficient non-denaturing FISH method for maize chromosome differentiation using single-strand oligonucleotide probes

Single-strand oligonucleotides (SSONs hereafter) as probes are becoming a powerful method of chromosome painting in many species. In this study, nine SSONs ((ACT)₁₀, (ACT)₁₉, Knob-1, Knob-2, Knob-3, CentC69-1, MR68-3, K10-72-1, and TR1-357-2) were developed and used for chromosome identification in 16 maize (Zea mays L., 2n = 20) inbred lines and hybrids by non-denaturing fluorescence in situ hybridization (ND-FISH). Each SSON produced clear signals on 2-10 chromosomes of inbred lines B73 and Mo17. A multiplex probe set containing four SSONs ((ACT)₁₀, Knob-2, CentC69-1, and MR68-3) clearly characterized all maize chromosomes in the 16 lines by a single round of ND-FISH and revealed genetic variation at a chromosome level. For example, unique signals on chromosome 6 clearly distinguished all 16 genotypes. The SSONs and multiplex probe developed in this research will facilitate genotype identification and chromosome research in maize.

Fluorescence In Situ Hybridization Analysis Reveals Multiple Loci of Knob-associated DNA Elements in One-knob and Knobless Maize Lines

Fluorescence in situ hybridization analyses were conducted to examine the presence or absence of the 180- and 350-bp knob-associated tandem repeats in maize strains previously defined as “one-knob” or “knobless.” Multiple loci were found to hybridize to these two repeats in all maize lines analyzed. Our results show that the number of 180- and 350-bp repeat loci do not correlate with the number of knobs in maize and that these tandem repeats are not independently sufficient to confer knob heterochromatin, even when present at megabase sizes.

Intragenomic conflict between the two major knob repeats of maize

Examples of meiotic drive, the non-Mendelian segregation of a specific genomic region, have been identified in several eukaryotic species. Maize contains the abnormal chromosome 10 (Ab10) drive system that transforms typically inert heterochromatic knobs into centromere-like domains (neocentromeres) that move rapidly poleward along the spindle during meiosis. Knobs can be made of two different tandem repeat sequences (TR-1 and 180-bp repeat), and both repeats have become widespread in Zea species. Here we describe detailed studies of a large knob on chromosome 10 called K10L2. We show that the knob is composed entirely of the TR-1 repeat and is linked to a strong activator of TR-1 neocentromere activity. K10L2 shows weak meiotic drive when paired with N10 but significantly reduces the meiotic drive exhibited by Ab10 (types I or II) in Ab10/K10L2 heterozygotes. These and other data confirm that (1) there are two separate and independent neocentromere activities in maize, (2) that both the TR-1 and knob 180 repeats exhibit meiotic drive (in the presence of other drive genes), and (3) that the two repeats can operate in competition with each other. Our results support the general concept that tandem repeat arrays can engage in arms-race-like struggles and proliferate as an outcome.

Chromosomes with a life of their own

B chromosomes (Bs) can be described as 'passengers in the genome', a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. As with retrotransposons they can accumulate in number, but in this case by various processes of mitotic or meiotic drive, based on their own autonomous ways of using spindles, especially in the gametophyte phase of the life cycle of flowering plants. This selfish property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. Bs are inhabitants of the nucleus and they are subject to control by 'genes' in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a B chromosome, notwithstanding the fact that we are only now beginning to unravel the story in a few favoured species. In this review we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology.

Meiotic loss of the B chromosomes of maize is influenced by the B univalent co-orientation and the TR-1 knob constitution of the A chromosomes

The suppression of meiotic loss when the maize B chromosomes are unpaired is genetically determined. Two genotypes were selected in 1B x 0B crosses: the H line where the B transmission rate is Mendelian (50%) and the L line where the B is present in only about 40% of the progeny. Using the ZmBs probe located at the centromere and at the distal portion of the B chromosome in FISH, we found that the centromeric and telomeric ends of the B univalent co-orient at metaphase I. This feature seems to promote proper centromere orientation causing the lack of meiotic loss of the unpaired B. The co-orientation was observed in both lines, however in the L line the B univalents were not always properly oriented, showing amphitelic orientation in about 25% of the metaphase I cells. We also studied plants of the H and L lines with FISH to test the possible relation between the knob constitution and B loss. It has been found that the plants of both lines are similarly variable for the 180-bp knob repeat, but they differ in the TR-1 350-bp repeat, the L line having more TR-1 knobs. The use of a 45S rDNA probe which labels chromosome 6, allowed us to determine that this chromosome shows the main variability between the two lines: the L line has TR-1 in both arms, showing a large TR-1 knob on the long arm. The H line has only one, generally located on the short arm besides the NOR.

High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9

High-resolution cytogenetic maps provide important biological information on genome organization and function, as they correlate genetic distance with cytological structures, and are an invaluable complement to physical sequence data. The most direct way to generate a cytogenetic map is to localize genetically mapped genes onto chromosomes by fluorescence in situ hybridization (FISH). Detection of single-copy genes on plant chromosomes has been difficult. In this study, we developed a squash FISH procedure allowing successful detection of single-copy genes on maize (Zea mays) pachytene chromosomes. Using this method, the shortest probe that can be detected is 3.1 kb, and two sequences separated by approximately 100 kb can be resolved. To show the robust nature of this protocol, we localized nine genetically mapped single-copy genes on chromosome 9 in one FISH experiment. Integration of existing information from genetic maps and the BAC contig-based physical map with the cytological structure of chromosome 9 provides a comprehensive cross-referenced cytogenetic map and shows the dramatic reduction of recombination in the pericentromeric heterochromatic region. To establish a feasible mapping system for maize, we also developed a probe cocktail for unambiguous identification of the 10 maize pachytene chromosomes. These results provide a starting point toward constructing a high-resolution integrated cytogenetic map of maize.

High frequency of centromere inactivation resulting in stable dicentric chromosomes of maize

Somatic chromosome spreads from maize (Zea mays L.) plants containing B-A translocation chromosomes undergoing the chromosome type breakage-fusion-bridge cycle were examined by FISH. The size and type of extra chromosomes varied among cells of the same individual. A collection of minichromosomes derived from the chromosome type breakage-fusion-bridge cycle was examined for the presence of stable dicentric chromosomes. Six of 23 chromosomes in the collection contained two regions with DNA sequences typical of centromeres. Functional analysis and immunolabeling of CENH3, the centromere-specific histone H3 variant, revealed only one functional centromere per chromosome, despite the duplicate centromere sequences. One plant was found with an inactive B centromere that had been translocated to the short arm of chromosome 9. The translocated centromere region appeared identical to that of a normal B chromosome. The inactivation of the centromeres was stable for at least four generations. By using dicentrics from dispensable chromosomes, centromere inactivation was found to be quite common under these circumstances.

Cytogenetic mapping in maize

Cytogenetic maps depict the location and order of markers along chromosomes. Cytogenetic maps are important in genome research as they relate the genetic data and molecular sequences to the morphological features of chromosomes. In this paper, we discuss various methods used in cytogenetic mapping in maize, with special reference to fluorescence in situ hybridization (FISH) of single-copy sequences on meiotic pachytene chromosomes.

Genome conflict in the gramineae

The genomes of grasses and cereals include a diverse and large collection of selfish genetic elements, many of which are fossil relics of ancient origin. Some of these elements are active and, because of their selfish nature and the way in which they exist to perpetuate themselves, they cause a conflict for genomes both within and between species in hybrids and allopolyploids. The conflict arises from how the various elements may undergo 'drive', through transposition, centromere and neocentromere drive, and in mitotic and meiotic drive processes in supernumerary B chromosomes. Experimental and newly formed hybrids and polyploids, where new combinations of genomes are brought together for the first time, find themselves sharing a common nuclear and cytoplasmic environment, and they can respond with varying degrees of instability to adjust to their new partnerships. B chromosomes are harmful to fertility and to the physiology of the cells and plants that carry them. In this review we take a broad view of genome conflict, drawing together aspects arising from a range of genetic elements that have not hitherto been considered in their entirety, and we find some common themes linking these various elements in their activities.

Sequences associated with A chromosome centromeres are present throughout the maize B chromosome

Maize chromosome spreads containing the supernumerary B chromosome were hybridized with probes from various repetitive elements including CentC, CRM, and CentA, which have been localized to centromeric regions on the A chromosomes. Repetitive elements that are enriched or found exclusively near the centromeres of A chromosomes hybridized to many sites distinct from the centromere on the B chromosome. To examine whether these elements recruit kinetochore proteins at locations other than the canonical B centromere, cells were labeled with antibodies against CENH3, a key kinetochore protein. No labeling was detected outside the normal centromere and no evidence of B chromosome holocentromeric activity was observed. This finding suggests that, as in other higher eukaryotes, DNA sequence alone is insufficient to dictate kinetochore location in plants. Additionally, examination of the B centromere region in pachytene chromosomes revealed that the B-specific element ZmBs hybridizes to a much larger region than the site of hybridization of CentC, CRM, and CentA and the labeling by anti-CENH3 antibodies.

Molecular Organization of Large Fragments in the Maize B Chromosome: Indication of a Novel Repeat

The supernumerary B chromosome has no apparent effects on plant growth, and its molecular makeup is difficult to unravel, due to its high homology to the normal complement, which prevents conventional cloning. This difficulty was overcome previously by microdissecting the B chromosome under the microscope to result in 19 B clones, one of which is B specific and highly repetitive, dispersing over one-third of the B long arm and most regions of the centromeric knob. To gain insights into the molecular structure of the B chromosome, this sequence was used to screen a genomic library constructed from W22 carrying 16 B’s. Five clones (>10 kb each) were isolated, and all were repetitive, showing homology with A chromosomes in Southern and FISH analyses. Two of them were further characterized and sequenced. Each is composed of several restriction fragments with variable degrees of repetitiveness. Some of these are B specific and others have variable degrees of homology with the A chromosomes. The order of each characteristic group is not contiguous; they intersperse within those of other groups. Sequence analysis reveals that their sequences (∼26 kb) have no homology with any published gene other than sequences of transposable elements (retrotransposons and MITEs) and the B as well as the A centromeres. We uncovered a 1.6-kb CL-repeat sequence, seven units of which were present in the two clones in defective forms. Those repeats mostly arrange in tandem array in the B chromosome. Moreover, we detected transposition of a retrotransposon and a MITE element involved in the genesis of these two sequences.