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

Cytogenetic evidence indicates that Zea, which comprises maize (Z. mays ssp. mays) and its wild relatives, is an allopolyploid genus. Our research group has carried out numerous cytogenetic studies on Zea species, mainly focused on native Argentinian and Bolivian maize landraces. We found a wide inter- and intraspecific genome size variation in the genus, with mean 2C-values ranging between 4.20 and 11.36 pg. For the maize landraces studied here, it varied between 4.20 and 6.75 pg. The objectives of this work are to analyze the causes of genome size variation and to discuss their adaptive value in Zea. This variation is mainly attributed to differences in the heterochromatin located in the knobs and to the amount of interspersed DNA from retrotransposons. Polymorphisms in presence or absence of B-chromosomes (Bs) and the population frequency of Bs are also a source of genome size variation, with doses ranging between one and eight in the landraces analyzed here. Correlation analysis revealed that the percentage of heterochromatin is positively correlated with genome size. In addition, populations cultivated at higher altitudes, which are known to be precocious, have smaller genome sizes than do those growing at lower altitudes. This information, together with the positive correlation observed between the length of the vegetative cycle and the percentage of heterochromatin, led us to propose that it has an adaptive role. On the other hand, the negative relationship found between Bs and heterochromatic knobs allowed us to propose the existence of an intragenomic conflict between these elements. We hypothesize that an optimal nucleotype may have resulted from such intranuclear conflict, where genome adjustments led to a suitable length of the vegetative cycle for maize landraces growing across altitudinal clines.

Key words: B chromosomes, heterochromatin, intragenomic conflict, knobs, maize landraces

Causes and consequences of dna content variation in zea

Abstract Morphological and phenological variability of Guaraní maize germplasm from Northeastern Argentina (NEA) are potential sources of genetic resources, constituting valuable repositories of alleles associated with tolerance and resistance to biotic and abiotic stresses. Here, we studied the morphological and phenological variability in maize populations of 14 Guaraní landraces from NEA and analysed the relationship among them. These landraces were characterised according to the endosperm consistency of grain as Popcorn (Pc), Floury (F) and Floury with corneal periphery (F-Pc). There were inter-population differences in phenological characters as time from germination to tassel emergence, from germination to spike emergence and from germination to anthesis (length of vegetative cycle -LVC). The morphological and phenological data here reported were used to carry out a cluster analysis, in which the F and Pc populations appeared as two separate groups and the F-Pc populations were included in the F group. Thus, the well-defined F (including F-Pc) and Pc genetic pools should be prioritised within the framework of breeding plans as well as ex situ and in situ conservation programs. For these purposes it is essential the morphological, phenological and genetic characterisation the maize Guaraní landraces.

/pdf/morphological-and-phenological-variability-of-guarani-maize-1ru255h6.pdf

Morphological and phenological variability of Guaraní maize germplasm from Northeastern Argentina (NEA)

The new name, subseries Alcabrerae M. G. Lopez, A. F. Wulff & Xifreda for Senecio L. ser. Corymbosi (Cabrera) Cabrera, is here proposed to replace Senecio subsect. Amplectentes Cabrera. Although the name Amplectentes was published at different subgeneric ranks within the genus Senecio (Asteraceae, Senecioneae), the use of the same epithet is considered homonymy according to the International Code of Botanical Nomenclature, Article 53.4 and Article 21, Note 1. Additionally, S. saucensis Cabrera, one of the five species belonging to Senecio subser. Alcabrerae, is synonymized with S. toroanus Cabrera, formerly assigned to Senecio ser. Hualtatini DC., and S. toroanus is transferred to subseries Alcabrerae. The micromorphology of the cypselae for both species is provided, in support of the synonymy.

Lidia Poggio

Papers

Causes and consequences of dna content variation in zea

Morphological and phenological variability of Guaraní maize germplasm from Northeastern Argentina (NEA)

Nomenclatural and Taxonomic Novelties in Senecio ser. Corymbosi (Asteraceae, Senecioneae) from Southern South America