Molecular karyotyping and aneuploidy detection in Arabidopsis thaliana using quantitative fluorescent polymerase chain reaction

Certain cellular processes are sensitive to changes in gene dosage. Aneuploidy is deleterious because of an imbalance of gene dosage on a chromosomal scale. Identification, classification and characterization of aneuploidy are therefore important for molecular, population and medical genetics and for a deeper understanding of the mechanisms underlying dosage sensitivity. Notwithstanding recent progress in genomic technologies, limited means are available for detecting and classifying changes in chromosome dose. The development of an inexpensive and scalable karyotyping method would allow rapid detection and characterization of both simple and complex aneuploid types. In addition to the problem of karyotyping, genomic and molecular genetic studies of aneuploids and polyploids are complicated by multiple heterozygous combinations possible at loci present in more than two copies. Quantitative scoring of allele genotypes would enable large-scale population genetic experiments in polyploids, and permit genetic analyses on bulked populations in diploid species. Here, we demonstrate that quantitative fluorescent-polymerase chain reaction (QF-PCR) can be used to simultaneously genotype and karyotype aneuploid and polyploid Arabidopsis thaliana. Comparison of QF-PCR with flow cytometric determination of nuclear DNA content indicated near perfect agreement between the methods, but complete karyotype resolution was only possible using QF-PCR. A complex karyotype, determined by QF-PCR, was validated by comparative genomic hybridization to microarrays. Finally, we screened the progeny of tetraploid individuals and found that more than 25% were aneuploid and that our artificially induced tetraploid strain produced fewer aneuploid individuals than a tetraploid strain isolated from nature.

Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response

Polyploidy, the inheritance of more than two genome copies per cell, has played a major role in the evolution of higher plants. Little is known about the transition from diploidy to polyploidy but in some species, triploids are thought to function as intermediates in this transition. In contrast, in other species triploidy is viewed as a block. We investigated the responses of Arabidopsis thaliana to triploidy. The role of genetic variability was tested by comparing triploids generated from crosses between Col-0, a diploid, and either a natural autotetraploid (Wa-1) or an induced tetraploid of Col-0. In this study, we demonstrate that triploids of A. thaliana are fertile, producing a swarm of different aneuploids. Propagation of the progeny of a triploid for a few generations resulted in diploid and tetraploid cohorts. This demonstrated that, in A. thaliana, triploids can readily form tetraploids and function as bridges between euploid types. Genetic analysis of recombinant inbred lines produced from a triploid identified a locus on chromosome I exhibiting allelic bias in the tetraploid lines but not in the diploid lines. Thus, genetic variation was subject to selection contingent on the final ploidy and possibly acting during the protracted aneuploid phase.

Reduced metaphase I associations between the short arms of homologous chromosomes in a Hordeum vulgare L. x H. bulbosum L. diploid hybrid influences the frequency of recombinant progeny

Hordeum vulgare (cultivated barley) x H. bulbosum (bulbous barley grass) hybrids have been used to obtain disease-resistant recombinant lines (RLs). The RLs contain chromatin transferred from the wild species mostly onto the long arms of recipient barley chromosomes. To determine whether differences in meiotic metaphase I (MI) associations between the long and short arms of homologous chromosomes can account for the preponderance of introgressions on the long arms, we carried out fluorescent in situ hybridisation on MI chromosome preparations obtained from pollen mother cells of a diploid interspecific hybrid. By using various probes, we established that MI associations between the long arms occurred more frequently than between the short arms for the five chromosomes tested.

Nuclear instability and its manipulation in plant breeding

Nuclear instability occurs spontaneously in a typically very small proportion of cells of every individual, even in crop varieties. Of greatest interest to the cereal breeder are instabilities in the germ line, which produce off-types among progeny, or in the endosperm, which reduce grain quality. Nuclear instabilities in crop plants merit cytological investigation for several reasons: first, to ensure that biologically possible standards of genetical purity are set for varieties in agriculture; secondly, because once understood, nuclear instability may be usefully applied in plant breeding; thirdly, because nuclear instability is thought to have played a major role in crop plant evolution - understanding the past may help in predicting which new genome combinations will be successful crop species; fourthly, because failure to achieve adequate nuclear stability has played a major role in preventing so many potentially useful plants from becoming crops. These points are illustrated mainly by reference to three different nuclear instabilities, namely: (1) haploid barley production by genome elimination in some Hordeum vulgare x H. bulbosum crosses; (2) the action of the tri gene in barley to produce about 50% diploid embryo sacs; (3) aberrant endosperm development in hexaploid triticale. Improved seed type in triticale has been achieved by a controlled reduction in rye telomeric heterochromatin. This approach may open the way for a new type of plant breeding, selecting for nucleotypic variation in the amount of non-coding DNA sequences. Understanding the cellular mechanisms responsible for nuclear stability (or instability) is essential if controlled plant modification based on precise nuclear engineering is to become possible. This understanding can come only from sustained fundamental research.

Cytogenetics of ditelotetrasomics for short arms of four chromosomes of barley (Hordeum vulgare L.)

Plants with a pair of extra homologous telocentric chromosomes in addition to the normal chromosome complement are called ditelotetrasomics. Six types of ditelotetrasomics of barley have been obtained. Four types obtained in the selfed progenies of telotrisomics (Triplo 2S, Triplo 5S, Triplo 6S, and Triplo 7S) are reported in this paper. The ditelotetra 2S showed a stronger expression of the diagnostic characteristics of Triplo 2S. It was weak and small, with narrow, short, dark-green leaves, and was almost completely pollen and seed sterile. However, three other ditelotetrasomics (ditelotetra 5S, 6S, and 7S) did not show specific diagnostic characteristics and were similar to normal diploid plants, with the exception of ditelotetrasomic 5S, which showed some effects. At meiotic diakinesis and metaphase I, these ditelotetrasomic plants showed chromosome configurations of 6II+1IV, 7II+1 teloII, 6II+1III+1teloI, or 7II+2 teloI. Most of the sporocytes at anaphase and telophase in the first and second meiotic divisions showed almost normal chromosome behavior. Quartets were mostly normal with no micronuclei. Approximately 30% of the selfed progenies of these three ditelotetrasomics were ditelotetrasomics and almost 50% were telotrisomics, indicating a high percentage of male and female transmission of the extra telocentric chromosomes.

Cytogenetics of four telotrisomics in barley (Hordeum vulgare L.)

Four barley telotrisomics (Triplo 3S, 5S, 6S, and 7S) were studied. No major qualitative differences in morphology between the telotrisomics and their diploid sibs were found. The pollen and seed fertility of these telotrisomics was comparable to their diploid sibs. The meiotic study showed that the average frequency of 6II + 1III at diakinesis and metaphase I was 84.2% and 71.7%, respectively. The normal chromosome separation ranged from 77.2% to 89.4% at anaphase I through telophase II. The transmission rate of the extra telocentric chromosomes averaged 28.4% upon selfing and 28.7% through the female. All four telotrisomics showed various degrees of pollen transmission, the average being 3.6%. Ditelotetrasomic plants (2n = 14 + 2 homologous telocentrics) were obtained in the progenies of selfed monotelotrisomic plants of all four types. These ditelotetrasomic plants were viable and showed various degrees of seed fertility.

Chromosomal location of resistance to barley yellow mosaic virus in German winter-barley identified by trisomic analysis

In order to localize a gene for resistance to Barley Yellow Mosaic Virus (BaYMV) of German resistant varieties, cvs. 'Ogra' and 'Sonate' were crossed to a complete trisomic (2n=2x+1=15) set of 'Shin Ebisu 16'. Tests for resistance in F2 strongly support the conclusion that the German gene for resistance to BaYMV is located on barley chromosome 3.

The cytogenetics of a triploid Hordeum bulbosum and of some of its hybrid and trisomic derivatives

The progeny from a cross between diploid H. vulgare and triploid H. bulbosum were mostly triploid (VBB) hybrids, the other progeny were haploid (V) barley (H. vulgare). From a cross between diploid and triploid H. bulbosum, four of the seven possible trisomic lines were isolated. The Giemsa banded karyotype of H. bulbosum was produced, and two of the lines were identified as trisomic for chromosomes 6 and 7. The cytology and transmission rates of the trisomics were examined.

Acrotrisomic analysis in linkage mapping in barley (Hordeum vulgare L.)

Three acrotrisomic lines, Triplo IL(1S), 3L(3S), and 4L(4S), each carrying an extra acrocentric chromosome, were used for cytogenetic linkage mapping of barley chromosomes. The cytological structures of the acrocentric chromosome of the three acrotrisomic lines were studied with an improved Giemsa N-banding technique. The long (1L) and short arm (1S) of chromosome 1 had deficiencies of approximately 38% and 65%, respectively. The percentages of deficiencies were 0 and 77.8% for 3L and 3S, and 31.7 and 59.3% for 4L and 4S, respectively. All three genes tested (br, f c , gs3) in 1S and all three genes tested, f8, n and 1k2 in 1L showed a disomic ratio indicating that they are located in the deficient segments. Two genes (a c , yst2) located in the middle segment of 3S in linkage map showed a trisomic ratio, and two others a n , x s showed a disomic ratio. The only gene(f9) tested in 4L showed a trisomic ratio. Two genes (1g4, g1) located in the proximal segment of 4S in the linkage map showed a trisomic ratio, whereas two genes (br2, g13) located distally in 4S showed a disomic ratio, indicating that the breakage occurred between g1 and br2. This experiment demonstrates a new method for physical localization of genes on chromosome segments in material such as barley in which pachytene analysis can not be effectively used for accurate determination of break points in structural changes. Problems associated with this new technique are discussed.

The karyotype of tuleen 346 barley

Tuleen 346 barley is a triple homozygote for 3 unequal interchanges, T1-5v, T2-6y and T3-7d, which were induced independently in the variety, 'Bonus'. It has great potential value in studying differences in behaviour and position among chromosomes within the same cell in barley and its hybrids since at least 5 and usually all 7 chromosome types can be identified in Feulgen preparations, compared with only 3 types in normal barley. Measurement of chromosome arm and satellite lengths in 10 haploid root-tip metaphases showed that in all comparisons except of the longest with the next longest, the 7 chromosome types were distinct in total length (P<0.001-0.05) and in 8 of the 10 cells, the longest chromosome had a smaller arm ratio than the next longest. In these preparations, each of the 5 shortest chromosomes was easily identifiable by size and morphology. The longest chromosome was about 2.2 times as long as the shortest. C-banding showed that each of the 7 chromosome types had a clearly unique band pattern. The C-band patterns of interchange chromosomes confirmed and increased the precision of previously published breakpoint locations, viz. the short arms of chromosomes 1, 2, 3 and 7 and the long arms of chromosomes 5 and 6.

Trisomics of ryegrass and their transmission

Primary trisomics of perennial ryegrass, Lolium perenne L., were studied for meiotic behaviour, fertility, morphology and trisome transmission. Trisomics differed from each other in mean meiotic association, pollen fertility, seed set and morphology. The combined cytomorphological data suggested that the investigated trisomic plants included trisomes 2 to 7. No pollen transmission of trisomes was detected. Female transmission of trisomes ranged from 12% for tri 3 to 37% for tri 4 with a mean of 24% for the six trisomes. Trisome transmission was not related to either chromosome size or trivalent/univalent frequency, although the larger trisomes formed trivalents more frequently than the smaller trisomes.

Trisomics from triploid-diploid crosses in self-incompatible Lycopersicum peruvianum : II. Transmission of trisomics

The transmission rate of trisomy was determined for two primary trisomic types, triplo-1 and triplo-3, of the self-incompatible species Lycopersicum peruvianum. Chromosome counts in somatic metaphases of root-tip squashes from 112 progeny plants showed that 8 individuals (7.2 %) were trisomic and 104 (92.8%) were diploid. The average frequency of transmission approximated 2.6% in triplo-1 and 8.6% in triplo-3. Data are presented on the karyotype and the morphological features of the 8 trisomics detected in the progenies of triplo-1 and triplo-3 and the various factors affecting the transmission rate of trisomy are discussed.The transmission rate of trisomy was also determined for the trisomic plant 269 which displayed a complete deletion of the satellited part of chromosome 2 and was characterized by ovate fruits. Out of 18 progeny plants analysed, 8 (44.4%) were trisomic and 10 (55.6%) were diploid. Cytological and morphological analyses of the 8 trisomic individuals revealed that only two of them (11.1 %) resembled the parental trisomic. A number of diploid and trisomic progenies exhibited a partial or a complete deletion of the satellited segment of chromosome 2.

CYTOGENETICS OF WIEBE'S 16 CHROMOSOME BARLEY

A cytogenetic study was made on Wiebe's stock of barley (H. vulgare L.) with 16 chromosomes in which the extra chromosome was derived from a shortened section of a T5-7a translocation. Predominantly 8 chromosome pairs (8″) were observed at MI. Transmission of the extra chromosome through both egg and pollen was regular. The absence of pairing between the extra and homologous segments of normal chromosomes was attributed to the presumed absence of terminal sections of the extra chromosomes. A low frequency of a quadrivalent involving normal chromosomes indicated the presence of a translocation.

CYTOGENETICS OF SOME MONOTELOTRISOMICS IN BARLEY

Linkage markers and translocation stocks were used to identify four monotelotrisomics in barley as 14 + 1S, 14 + 2L, 14 + 4L, and 14 + 5S. In morphology they displayed the same deviations from disomic plants as the corresponding primary trisomics but to a lesser extent, ranging from an approach to the disomic for 14 + 1S to close resemblance to the trisomic for 14 + 2L. At meiotic metaphase, an average of 61.1% of the cells contained heteromorphic trivalents, with tandem-chain and ring-rod configurations predominating. The extra telocentrics were transmitted to 28.3% of selfed progeny, almost exclusively through the female gamete.