The Analysis of Variance.

Cloning and characterization of the

Variation in DNA content has been largely ignored as a factor in evolution, particularly following the advent of sequence-based approaches to genomic analysis. The significant genome size diversity among organisms (more than 200 000-fold among eukaryotes) bears no relationship to organismal complexity and both the origins and reasons for the clearly non-random distribution of this variation remain unclear. Several theories have been proposed to explain this ‘C-value enigma’ (heretofore known as the ‘C-value paradox’), each of which can be described as either a ‘mutation pressure’ or ‘optimal DNA’ theory. Mutation pressure theories consider the large portion of non-coding DNA in eukaryotic genomes as either ‘junk’ or ‘selfish’ DNA and are important primarily in considerations of the origin of secondary DNA. Optimal DNA theories differ from mutation pressure theories by emphasizing the strong link between DNA content and cell and nuclear volumes. While mutation pressure theories generally explain this association with cell size as coincidental, the nucleoskeletal theory proposes a coevolutionary interaction between nuclear and cell volume, with DNA content adjusted adaptively following shifts in cell size. Each of these approaches to the C-value enigma is problematic for a variety of reasons and the preponderance of the available evidence instead favours the nucleotypic theory which postulates a causal link between bulk DNA amount and cell volume. Under this view, variation in DNA content is under direct selection via its impacts on cellular and organismal parameters. Until now, no satisfactory mechanism has been presented to explain this nucleotypic effect. However, recent advances in the study of cell cycle regulation suggest a possible ‘gene–nucleus interaction model’ which may account for it. The present article provides a detailed review of the debate surrounding the C-value enigma, the various theories proposed to explain it, and the evidence in favour of a causal connection between DNA content and cell size. In addition, a new model of nucleotypic influence is developed, along with suggestions for further empirical investigation. Finally, some evolutionary implications of genome size diversity are considered, and a broadening of the traditional ‘biological hierarchy’ is recommended.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.2000.tb00059.x

Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma.

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.

Maize HapMap2 identifies extant variation from a genome in flux

All else being equal, polyploids are expected to have larger C-values (amount of DNA in the unreplicated gametic nucleus) than their diploid progenitors, increasing in direct proportion with ploidy. This expectation is observed in some polyploid series, especially those newly formed, but there are examples suggesting that C-values in particular polyploids are less than expected. The availability of the Angiosperm DNA C-values database (http:// www.rbgkew.org.uk/cvavhomepage.html) has allowed this question to be addressed across a broad range of angiosperms and has revealed striking results deviating from expectation: (i) mean 1C DNA amount did not increase in direct proportion with ploidy, and (ii) mean DNA amount per basic genome (calculated by dividing the 2C value by ploidy) tended to decrease with increasing ploidy. These results suggest that loss of DNA following polyploid formation, or genome downsizing, may be a widespread phenomenon of considerable biological significance. Recent advances in our understanding of the molecular events that take place following polyploid formation together with new data on how DNA amounts can both increase and decrease provide some insights into how genome downsizing may take place. The nature of the evolutionary forces that may be driving DNA loss are also discussed.

Genome downsizing in polyploid plants

Cytological diploidization process is different in autopolyploid and allopolyploid species. Colchicine applied at the onset of meiosis suppresses the effect of pairing regulator genes resulting multivalents formation in bivalent-forming species. Colchicine treated maizes (4x = 2n = 20, AmAmBmBm) showed up to 5IV, suggesting pairing between chromosomes from genomes homoeologous Am and Bm. In untreated individuals of the alloautooctoploid Zea perennis (8x = 2n = 40, ApApAp´Ap´Bp1Bp1Bp2Bp2) the most frequent configuration was 5IV+10II (formed by A and B genomes, respectively). The colchicine treated Z. perennis show up to 10IV revealing higher affinity within genomes A and B, but any homology among them. These results suggest the presence of a paring regulator locus (PrZ) in maize and Z. perennis, whose expression is suppressed by colchicine. It could be postulated that in Z. perennis, PrZ would affect independently the genomes A and B, being relevant the threshold of homology, the fidelity of pairing in each genomes and the ploidy level. Cytological analysis of the treated hexaploid hybrids (6x = 2n = 30), with Z. perennis as a parental, strongly suggests that PrZ is less effective in only one doses. This conclusion was reinforced by the homoeologous pairing observed in untreated dihaploid maizes, which showed up to 5II. Meiotic behaviour of individuals treated with different doses of colchicine allowed to postulate that PrZ affect the homoeologous association by controlling entire genomes (Am or Bm) rather than individual chromosomes. Based on cytological and statistical results it is possible to propose that the cytological diploidization in Zea species occurs by restriction of pairing between homoeologous chromosomes or by genetical divergence of the homoeologous chromosomes, as was observed in untreated Z. mays ssp. parviglumis. These are independent but complementary systems and could be acting jointly in the same nucleus.

/pdf/cytological-diploidization-of-paleopolyploid-genus-zea-2xxxdun5i0.pdf

Cytological diploidization of paleopolyploid genus Zea: Divergence between homoeologous chromosomes or activity of pairing regulator genes?

Behaviour of ring bivalents in holokinetic systems

Senecio is the largest genus in the Asteraceae family growing in all environments around the world. It displays taxonomic and systematical difficulties. Cytogenetic knowledge of this genus is ancient, scarce and mainly restricted to chromosome number records. In this study we analyzed chromosome number, meiotic configuration, bivalent morphology, meiotic behavior and pollen grain stainability on 100 accessions of 27 different polyploid Senecio L. sect Senecio entities. Median, standard deviation and mode were calculated for number and position of chiasmata and meiotic recombination was statistically evaluated. Although high frequency of multivalents and associated meiotic irregularities are expected in high polyploids, bivalents predominance and, consequently, regular meiosis were observed, with normal sporogenesis and high pollen grain stainability. Depletion in the total chiasmata was significant only in some species but the terminal position was preferential in all the entities analyzed, indicating significant reduction in recombination. The regular meiosis observed suggest that intra and intergenomic reorganization process occur quickly and efficiently in this genus. Mechanisms of diploidization, common to all polyploids, are reinforced by the strong reduction in crossing-over rushing polyploids stabilization.

/pdf/deep-cytogenetics-analysis-reveals-meiotic-recombination-4k3v892z5a.pdf

Deep cytogenetics analysis reveals meiotic recombination depletion in species of Senecio (Asteraceae)

Bromus setifolius var. pictus (Hook) Skottsb., B. setifolius var. setifolius Presl. and B. setifolius var. brevifolius Ness are three native Patagonian taxa in the section Pnigma Dumort of the genus Bromus L. AFLP and RAPD analysis, in conjunction with genetic distance measurements and statistical techniques, revealed variation within this group and indicated that B. setifolius var. brevifolius was closely related to B. setifolius var. pictus, with both taxa being more distantly related to B. setifolius var. setifolius. Cytogenetic analysis confirmed the chromosomal number of B. setifolius var. pictus (2n = 70) and B. setifolius var. setifolius (2n = 28) and showed for the first time that B. setifolius var. brevifolius had 2n = 70. The combination of molecular genetic and cytogenetic evidence supported a species status for two of the three taxa and suggested hypotheses for the evolutionary origin of these complex taxa. Species status was also indicated for B. setifolius var. setifolius. Based on these findings, we suggest that B. setifolius var. pictus be referred to as B. pictus Hook var. pictus, and B. setifolius var brevifolius as B. pictus Hook var brevifolius. The correlation between AFLP diversity and variation in ecological parameters suggested that this marker system could be used to assess breeding progress and to monitor the domestication of Patagonian Bromus species for agronomic use.

/pdf/use-of-aflp-and-rapd-molecular-genetic-markers-and-jgvb3jpqcc.pdf

Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex.

The karyotypes and chromosome pairing of three populations (Argentina, Hungary and Libya) and two cultivars (Budakalasie-Hungary- and Hrubicki-Poland-) of Coriandrum sativum L (Umbelliferae) (2n=22) were studied. Slight differences were found between the karyotype formulae as well as the total chromosome length and volume among several of the plants investigated. A microsatellite in the short arm of a st chromosome (the largest one) and a maximum number of two nucleoli per cell were observed in the five populations. The results show the existence of polymorphism for C-banding pattern. Chromosome pairing studies showed important inter-population differences in the frequency of closed bivalents and chiasmata.

Lidia Poggio

Papers

Cytological diploidization of paleopolyploid genus Zea: Divergence between homoeologous chromosomes or activity of pairing regulator genes?

Behaviour of ring bivalents in holokinetic systems

Deep cytogenetics analysis reveals meiotic recombination depletion in species of Senecio (Asteraceae)

Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex.

The Chromosomes of Coriandrum sativum L