Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View

Switch them off or not: selective rRNA gene repression in grasses

Nucleolar dominance (ND) is selective epigenetic silencing of 35-48S rDNA loci. In allopolyploids, it is frequently manifested at the cytogenetic level by the inactivation of nucleolar organiser region(s) (NORs) inherited from one or several evolutionary ancestors. Grasses are ecologically and economically one of the most important land plant groups, which have frequently evolved through hybridisation and polyploidisation events. Here we review common and unique features of ND phenomena in this monocot family from cytogenetic, molecular, and genomic perspectives. We highlight recent advances achieved by using an allotetraploid model grass, Brachypodium hybridum, where ND commonly occurs at a population level, and we cover modern genomic approaches that decipher structural features of core arrays of NORs.

Allium cytogenetics: a critical review on the Indian taxa

The genus Allium Linnaeus, 1753 (tribe Allieae) contains about 800 species worldwide of which almost 38 species are reported in India, including the globally important crops (onion, garlic, leek, shallot) and many wild species. A satisfactory chromosomal catalogue of Allium species is missing which has been considered in the review for the species occurring in India. The most prominent base number is x=8, with few records of x=7, 10, 11. The genome size has sufficient clues for divergence, ranging from 7.8 pg/1C to 30.0 pg/1C in diploid and 15.16 pg/1C to 41.78 pg/1C in polyploid species. Although the karyotypes are seemingly dominated by metacentrics, substantial variation in nucleolus organizing regions (NORs) is noteworthy. The chromosomal rearrangement between A.cepa Linnaeus, 1753 and its allied species has paved way to appreciate genomic evolution within Allium. The presence of a unique telomere sequence and its conservation in Allium sets this genus apart from all other Amaryllids and supports monophyletic origin. Any cytogenetic investigation regarding NOR variability, telomere sequence and genome size in the Indian species becomes the most promising field to decipher chromosome evolution against the background of species diversity and evolution, especially in the Indian subcontinent.

Investigating the Origin and Evolution of Polyploid Trifolium medium L. Karyotype by Comparative Cytogenomic Methods

Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though allopolyploid origin has previously been suggested, little has in fact been known about the T. medium karyotype and its origin. We researched T. medium and related karyotypes using comparative cytogenomic methods, such as fluorescent in situ hybridization (FISH) and RepeatExplorer cluster analysis. The results indicate an exceptional karyotype diversity regarding numbers and mutual positions of 5S and 26S rDNA loci and centromeric repeats in populations of T. medium ecotypes and varieties. The observed variability among T. medium ecotypes and varieties suggests current karyotype instability that can be attributed to ever-ongoing battle between satellite DNA together with genomic changes and rearrangements enhanced by post-hybridization events. Comparative cytogenomic analyses of a T. medium hexaploid variety and diploid relatives revealed stable karyotypes with a possible case of chromosomal rearrangement. Moreover, the results provided evidence of T. medium having autopolyploid origin.

Analysis of Nuclear DNA Content and Karyotype of Phaseolus vulgaris L

The common bean (Phaseolus vulgaris L.), whose annual production is 26 million tons worldwide, is one of the main sources of protein and is known as one of the most important food sources. In this study, the karyotype variations and the genome size of four common bean genotypes in Turkey were investigated to determine whether the geographic variables in these regions affected the genome size and the karyotype parameters. In addition, it is known that as that the cytological and chromosomal parameters change under the influence of the climatic conditions of each region, appropriate and stable cytological methods for each plant facilitate and enable the determination of the chromosomal structure and the identification of specific chromosomes in the genotypes of the relevant region. Correct and valuable information such as this enables breeders and researchers to determine the correct shape and actual size of chromosomes. The genome size of the genotypes was measured with a flow cytometer, and chromosome analyses were performed with the squash method. For each genotype, the karyotype parameters, such as the number of somatic chromosomes, the Mean Total Chromosome Length (MTCL), the Mean Centromere Index (MCI), and the Mean Arm Ratio (MAR), were measured. The results showed that the highest and the lowest amounts of DNA per nucleus (3.28 pg and 1.49 pg) were observed in the Bitlis and Elaziğ genotypes. In addition, all genotype chromosome numbers were counted to be 2n = 2x = 22. The Mean Total Chromosome Length varied from 15.65 µm in Elaziğ to 34.24 µm in the Bitlis genotype. The Mean Chromosome Length ranged between 1.42 µm and 3.11 µm in the Elaziğ and Bitlis genotypes. The Hakkari and Van genotypes consist of eleven metacentric chromosomes, while the Bitlis and Elaziğ genotypes consist of ten metacentric chromosomes and one sub-metacentric chromosome. However, the Mean Centromere Index and Arm Ratio differed considerably among the genotypes. The highest (46.88) and the lowest (43.18) values of the Mean Centromere Index were observed in the Hakkari and Elaziğ genotypes, respectively. On the other hand, the lowest (1.15) and the highest (1.36) values of the Mean Arm Ratio were obtained in the Bitlis and Elaziğ genotypes, respectively. Eventually, intraspecies variations in genome size and chromosomal parameters were observed, and it was determined that the changes in nuclear DNA content and different chromosomal parameters among the four Phaseolus genotypes from four different regions of Turkey indicate the effect of climate change in the regions on these parameters. Such information in these areas can be used as useful information for the improvement of this plant and breeding programs.

The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae)

The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.

Centromere-Specific Single-Copy Sequences of Secale Species

Single-copy FISH analysis is a useful tool to physically locate a given sequence on chromosome. Centromeric single-copy sequences can be used to locate the position of centromere and disclose the subtle differences among different centromeres. Nine centromeric single-copy sequences 1R1, 3R1, 4R1, 4R2, 5R1, 5R2, 6R2, 6R3, and 7R1 were cloned from Kustro (Secale cereale L.). FISH analysis using these sequences as probes indicated that the signals of 1R1, 3R1, 4R1, 4R2, 5R1, 5R2, 6R1, 6R2, and 7R1 were located in the centromeric regions of rye 1R, 3R, 4R, 4R, 5R, 5R, 6R, 6R, and 7R chromosomes, respectively. In addition, for each of the centromeric single-copy sequences, high sequence similarity was observed among different Secale species. Combined with rye genomic sequence, single-copy FISH analysis indicated that the 1BL.1RS translocations in wheat cultivar CN17 and wheat line 20T363-4 contained the centromeric segment of 1R chromosome from 349,498,361 to 349,501,266 bp, and the 1BL.1RS translocations in the other two wheat cultivars did not contain this segment. The nine sequences are useful in determining the centromere location on rye chromosomes, and they have the potential to disclose the accurate structural differences of centromeres among the wheat-rye centric fusion translocation chromosomes; therefore, more centromeric single-copy sequences are needed.