Karyotypic diversification in Hypostomus Lacépède, 1803 (Siluriformes, Loricariidae): biogeographical and phylogenetic perspectives

Hypostomus is a species-rich genus of fish with unclear systematics and phylogenetic relationships. Ten species of Hypostomus (H. albopunctatus, H. ancistroides, H. cochliodon, H. commersoni, H. faveolus, H. hermanni, H. aff. paulinus, H. regani, H. strigaticeps and H. topavae) were cytogenetically analyzed through Giemsa staining and silver nitrate impregnation, and the obtained data were correlated to the available biogeographical and phylogenetic analyses for the genus. Although the silver stained nucleolar organizer regions (AgNORs) were found to vary significantly among the species, the diploid numbers could be correlated to the distribution of the species on northern and southern South America river basins. Species with the lower diploid numbers (2n = 64) were associated to northern hydrographic basins and showed a single AgNORs bearing pair. Diploid numbers of 66–68 chromosomes and of 70–84 chromosomes were correlated to two major clades within Hypostomus and southern hydrographic basins, and showed AgNORs varying on number and position. Our results show that cytogenetic data can be correlated to the phylogeny and biogeography of the genus, helping to clarify its complex evolutionary history.     

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.     

Evolutionary and biogeographical approach on Australoheros angiru (Cichlidae) from lagoons in a dividing plateau between the basins of the Iguassu River and the Uruguay River,Brazil

Australoheros is represented by species of Cichlidae spread over different Brazilian river systems. Individuals of Australoheros angiru were collected in isolated lagoons at 950 m of altitude in a dividing plateau between the basins of the Iguassu River and the Uruguay River, located in the São Lourenço do Oeste region (Santa Catarina State), and subject to basic and molecular cytogenetic analyzes. Moreover, a review about the occurrence and collections sites of A. angiru was used to the clarification of biogeographical issues of Australoheros and other species of fish that are common between the basins of the Uruguay River and Iguassu River. The analysis by conventional staining with Giemsa found a diploid number of 48 chromosomes (18 submetacentric + 30 subtelocentric/acrocentric) for males and females, without sex chromosome differentiation. The nucleolar organizing regions identified by silver impregnation and by fluorescence in situ hybridization with 18S rDNA probes showed to be simple, located on the end of the short arm of subtelocentric chromosome pair 15. Heterochromatin was observed in the centromeric region of most of the chromosomes of the complement, in addition to coincide with the nucleolar organizing regions. The data presented in this study are the first reports on the location of sites of 5S rDNA for Australoheros, being located in interstitial position on the long arm of subtelocentric chromosome pair 11. The basic and molecular cytogenetic data presented here contribute to the better understanding of chromosomal evolution of Cichlidae, act as interesting tools for taxonomy and phylogeny of the group, in addition to help in understanding the dispersion of A. angiru between the two hydrographic basins.     

Genomic prediction applied to high-biomass sorghum for bioenergy production

The increasing cost of energy and finite oil and gas reserves have created a need to develop alternative fuels from renewable sources. Due to its abiotic stress tolerance and annual cultivation, high-biomass sorghum (Sorghum bicolor L. Moench) shows potential as a bioenergy crop. Genomic selection is a useful tool for accelerating genetic gains and could restructure plant breeding programs by enabling early selection and reducing breeding cycle duration. This work aimed at predicting breeding values via genomic selection models for 200 sorghum genotypes comprising landrace accessions and breeding lines from biomass and saccharine groups. These genotypes were divided into two sub-panels, according to breeding purpose. We evaluated the following phenotypic biomass traits: days to flowering, plant height, fresh and dry matter yield, and fiber, cellulose, hemicellulose, and lignin proportions. Genotyping by sequencing yielded more than 258,000 single-nucleotide polymorphism markers, which revealed population structure between subpanels. We then fitted and compared genomic selection models BayesA, BayesB, BayesCπ, BayesLasso, Bayes Ridge Regression and random regression best linear unbiased predictor. The resulting predictive abilities varied little between the different models, but substantially between traits. Different scenarios of prediction showed the potential of using genomic selection results between sub-panels and years, although the genotype by environment interaction negatively affected accuracies. Functional enrichment analyses performed with the marker-predicted effects suggested several interesting associations, with potential for revealing biological processes relevant to the studied quantitative traits. This work shows that genomic selection can be successfully applied in biomass sorghum breeding programs.     

Phylogeographic evidence for two species of muriqui (genus Brachyteles)

The taxonomy of muriquis, the largest extant primates in the New World, is controversial. While some specialists argue for a monotypic genus (Brachyteles arachnoides), others favor a two‐species classification, splitting northern muriquis (Brachyteles hypoxanthus) from southern muriquis (B. arachnoides). This uncertainty affects how we study the differences between these highly endangered and charismatic primates, as well as the design of more effective conservation programs. To address this issue, between 2003 and 2017 we collected over 230 muriqui fecal samples across the genus’ distribution in the Brazilian Atlantic Forest, extracted DNA from these samples, and sequenced 423 base pairs of the mitochondrial DNA (mtDNA) control region. Phylogenetic and species delimitation analyses of our sequence dataset robustly support two reciprocally monophyletic groups corresponding to northern and southern muriquis separated by an average 12.7% genetic distance. The phylogeographic break between these lineages seems to be associated with the Paraíba do Sul River and coincides with the transition between the north and south Atlantic Forest biogeographic zones. Published divergence estimates from whole mitochondrial genomes and nuclear loci date the split between northern and southern muriquis to the Early Pleistocene (ca. 2.0 mya), and our new mtDNA dataset places the coalescence time for each of these two clades near the last interglacial (ca. 120–80 kya). Our results, together with both phenotypic and ecological differences, support recognizing northern and southern muriquis as sister species that should be managed as distinct evolutionarily significant units. Given that only a few thousand muriquis remain in nature, it is imperative that conservation strategies are tailored to protect both species from extinction.     

Reconstruction of the Doradinae (Siluriformes-Doradidae) ancestral diploid number and NOR pattern reveals new insights about the karyotypic diversification of the Neotropical thorny catfishes

Doradinae (Siluriformes: Doradidae) is the most species-rich subfamily among thorny catfishes, encompassing over 77 valid species, found mainly in Amazon and Platina hydrographic basins. Here, we analyzed seven Doradinae species using combined methods (e.g., cytogenetic tools and Mesquite ancestral reconstruction software) in order to scrutinize the processes that mediated the karyotype diversification in this subfamily. Our ancestral reconstruction recovered that 2n=58 chromosomes and simple nucleolar organizer regions (NOR) are ancestral features only for Wertheimerinae and the most clades of Doradinae. Some exceptions were found in Trachydoras paraguayensis (2n=56), Trachydoras steindachneri (2n=60), Ossancora punctata (2n=66) and Platydoras hancockii whose karyotypes showed a multiple NOR system. The large thorny catfishes, such as Pterodoras granulosus, Oxydoras niger and Centrodoras brachiatus share several karyotype features, with subtle variations only regarding their heterochromatin distribution. On the other hand, a remarkable karyotypic variability has been reported in the fimbriate barbells thorny catfishes. These two contrasting karyoevolution trajectories emerged from a complex interaction between chromosome rearrangements (e.g., inversions and Robertsonian translocations) and mechanisms of heterochromatin dispersion. Moreover, we believe that biological features, such as microhabitats preferences, populational size, low vagility and migratory behavior played a key role during the origin and maintenance of chromosome diversity in Doradinae subfamily.     

Physical mapping of 5S rDNA in two species of Knifefishes: Gymnotus pantanal and Gymnotus paraguensis (Gymnotiformes)

Physical mapping of 5S rDNA in 2 species of knifefishes, Gymnotuspantanal and G. paraguensis (Gymnotiformes), was performed using fluorescence in situ hybridization with a 5S rDNA probe. The 5S rDNA PCR product from the genomes of both species was also sequenced and aligned to determine non-transcribed spacer sequences (NTS). Both species under study had different patterns of 5S rDNA gene cluster distribution. While in the karyotype of G. pantanal two 5S rDNA-bearing pairs were observed, the karyotype of G. paraguensis possessed as many as 19 such pairs. Such multiplication of 5S rDNA gene clusters might be caused by the involvement of transposable elements because the NTS of G. paraguensis was 400 bp long with high identity (90%) with a mobile transposable element called Tc1-like transposon, described from the cyprinid fish Labeo rohita.     

Repetitive DNA and meiotic behavior of sex chromosomes in Gymnotus pantanal (Gymnotiformes, Gymnotidae)

Neotropical fishes have a low rate of chromosome differentiation between sexes. The present study characterizes the first meiotic analysis of sex chromosomes in the order Gymnotiformes. Gymnotus pantanal - females had 40 chromosomes (14m/sm, 26st/a) and males had 39 chromosomes (15m/sm, 24st/a), with a fundamental number of 54 - showed a multiple sexual determination chromosome system of the type X(1)X(1)X(2)X(2)/X(1)X(2)Y. The heterochromatin is restricted to centromeres of all chromosomes of the karyotype. The meiotic behavior of sex chromosomes involved in this system in males is from a trivalent totally pared in the pachytene stage, with a high degree of similarity. The cells of metaphase II exhibit 19 and 20 chromosomes, normal disjunction of sex chromosomes and the formation of balanced gametes with 18 + Y and 18 + X(1)X(2) chromosomes, respectively. The small amount of heterochromatin and repetitive DNA involved in this system and the high degree of chromosome similarity indicated a recent origin of the X(1)X(1)X(2)X(2)/X(1)X(2)Y system in G. pantanal and suggests the existence of a simple ancestral system with morphologically undifferentiated chromosomes.     

Chromosomal markers in Parodontidae: an analysis of new and reviewed data with phylogenetic inferences

The taxonomy of the family Parodontidae is confused, with many open questions regarding the most appropriate generic groupings. Studies on the organization, structure, composition, and in situ location of chromosomal features have led to consistent advances in the understanding of genome evolution. Among the species of Parodontidae, the consistent chromosomal divergences can be helpful in taxonomic classification, such as heteromorphic chromosome sex, karyotypic formulae, and number/location of the repetitive DNAs. Molecular analysis of repetitive sequences of satellite DNA and their physical mapping in the chromosomes of different species in a single group may be used to infer evolutionary divergence and cladistic grouping. In the present study, rDNA and the satellite DNA pPh2004 were mapped by fluorescent in situ hybridization on the chromosomes of some species of Parodontidae. These results were analyzed and reviewed together with other chromosomal markers and previously published data, to formulate inferences about the diversification of the genomes and propose a clustering of some Parodontidae species. This analysis indicated that the species Apareiodon affinis, Parodon moreirai, Parodon hilarii, Parodon nasus, and Parodon pongoensis have an apomorphic state for satellite DNA pPh2004 in Parodontidae in relation to previously studied species of Apareiodon.