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

Phenetic relationships among II species belonging to the genus Berberis from 46 populations of NW Patagonia Argentina, were studied using numerical techniques. The species are B. bidentata Lechl., B. buxifolia Lam., B. cabrerae Job, B. chillanensis Sprag. ex Sandwith, B. darwinii Hook., B. empetrifolia Lam., B. heterophylla Juss., B. linearifolia Phil., B. montana Gay, B. parodii Job and B. serrato-dentata Lechl. Fifty four morphological characters were defined (24 vegetative and 30 reproductive). Forty six populations (with a total of 288 individuals) were analyzed. Two main groups were distinguished from the phenogram. One consists of the populations of 10spiny species; the other one is only formed by populations of B. serrato-dentata (without - or rarely / with scarce little weak - spines). Numerical analysis allowed to differentiate the species studied and each of the populations within a same species. This may be related to microambiental agents conditioning the phenotype. The results here obtained agree fairly well with the interespecific relationships previously published in the genus Berberis .

Relaciones fenéticas entre las especies de Berberis (Berberidaceae) del noroeste de la región patagónica

Estudios cromosómicos en Bulnesia, Pintoa, Porlieria, Plectrocarpa y Sericodes (Zygophyllaceae)

In Argentina there are two different centers of maize diversity, the Northeastern (NEA) and the Northwestern (NWA) regions of the country. In NEA, morphological studies identified 15 landraces cultivated by the Guarani communities in Misiones Province. In the present study we analyzed the karyotype diversity of 20 populations of Guarani maize landraces through classical and molecular cytogenetic analyses. Our results demonstrate significant intra and inter-populational variation in the percentage, number, size, chromosome position and frequencies of the heterochromatic blocks, which are called knobs. Knob sequence analysis (180-bp and TR-1) did not show significant differences among Guarani populations. B chromosomes were not detected, and abnormal 10 (AB10) chromosomes were found with low frequency (0.1≥f ≤0.40) in six populations. Our results allowed karyotypic characterization of each analyzed population, defining for the first time the chromosomal constitution of maize germplasm from NEA. The multivariate analysis (PCoA and UPGMA) of karyotype parameters allowed the distinction between two populations groups: the Popcorn and the Floury maize populations. These results are in agreement with previously published microsatellite and morphological/phenological studies. Finally, we compared our karyotype results with those previously reported for NWA and Central Region of South America maize. Our data suggest that there are important differences between maize from NEA and NWA at the karyotype level, supporting the hypothesis that there are two pathways of input of South America maize. Our results also confirm the existence of two centers of diversification of Argentinian native maize, NWA and NEA. This work contributes new knowledge about maize diversity, which is relevant for future plans to improve commercial maize, and for conservation of agrobiodiversity.

Exploring karyotype diversity of Argentinian Guaraní maize landraces: Relationship among South American maize.

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis ('yerba mate') and Ilex dumosa ('yerba senorita') is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa. © NIAB 2014.

Quantitative and qualitative genomic characterization of cultivated Ilex L. species

We studied three different tricepiros: (Don Santiago x Don Noe), (Cume x Horovitz) and (Cume x Don Noe). The tricepiro (Don Santiago x Don Noe) was obtained by crossing the triticale Don Santiago INTA (AABBRR, 2n = 6x = 42) with the trigopiro Don Noe INTA (AABBDDJJ, 2n = 8x = 56). The number of chromosomes for the F1 was 2n = 49, the most frequent meiotic configuration being 14 bivalents and 21 univalents. The univalents were situated in the periphery of the equatorial plane, whereas the bivalents were located in the central zone. The chromatids in some of the univalents split when bivalents underwent reductional division in anaphase I. There were few laggard chromosomes or chromatids at this phase. The number of chromosomes (2n = 48-58) was high and variable, and the number of bivalents per cell (18-23) also high in F3 individuals. In all F8 tricepiros (Don Santiago x Don Noe), F12 tricepiros (Cume x Horovitz) and F12 tricepiros (Cume x Don Noe), the number of chromosomes (2n = 42) was the same, these retaining the rye genome, as demonstrated by GISH and FISH. These new synthesized allopolyploids constitute interesting models for investigating the evolutionary changes responsible for diploidization, and the chromosomal and genomic re-ordering that cannot be revealed in natural allopolyploids.

/pdf/cytological-analysis-of-hybrids-among-triticales-and-296asei9y6.pdf

Lidia Poggio

Papers

Relaciones fenéticas entre las especies de Berberis (Berberidaceae) del noroeste de la región patagónica

Estudios cromosómicos en Bulnesia, Pintoa, Porlieria, Plectrocarpa y Sericodes (Zygophyllaceae)

Exploring karyotype diversity of Argentinian Guaraní maize landraces: Relationship among South American maize.

Quantitative and qualitative genomic characterization of cultivated Ilex L. species

Cytological analysis of hybrids among triticales and trigopiros