A Bayesian approach for constructing genetic maps when markers are miscoded

The advent of molecular markers has created opportunities for a better understanding of quantitative inheritance and for developing novel strategies for genetic improvement of agricultural species, using information on quantitative trait loci (QTL). A QTL analysis relies on accurate genetic marker maps. At present, most statistical methods used for map construction ignore the fact that molecular data may be read with error. Often, however, there is ambiguity about some marker genotypes. A Bayesian MCMC approach for inferences about a genetic marker map when random miscoding of genotypes occurs is presented, and simulated and real data sets are analyzed. The results suggest that unless there is strong reason to believe that genotypes are ascertained without error, the proposed approach provides more reliable inference on the genetic map.

Cytogenetic studies in Diplopoda

The Diplopoda have received little attention from cytogeneticists owing mostly to technical difficulties in obtaining mitotic chromosomes, restricting the studies to meiosis and eventual spermatogonial metaphases, which limits the use of modern cytogenetical techniques. A literature search shows that only about 0.1% of all known species have been cytogenetically studied. There are 80,000 species estimated for this group, making it the 3rd. larger class in Arthropoda, after Insecta and Arachnida. The diploid chromosomal number in diplopods varies from 2n=8 to 2n=30 and the sex determination mechanism commonly found is XY/XX. In meiotic prophase, the bouquet formation and the diffuse state in pachytene are typical events. The few works performed on Brazilian fauna add up to 16 species, out of an estimated number of 2000 to 3000 species. The present review reports all the species of diplopods that have been cytogenetically studied so far, each with its chromosome number and sex determination system.

First cytogenetic description of the species Rhamdella microcephala (Pisces, Hepapteridae)

Cytogenetic studies were carried out on Rhamdella microcephala collected from the headwaters of the Machado river, a tributary of the Sapucaí river, Minas Gerais, Brazil. Sixteen specimens exhibited 2n=56 chromosomes, with 18 metacentrics, 30 submetacentrics and 8 subtelocentric-acrocentrics (FN=84). The nucleolar organizing regions (NORs) were identified in the interstitial position on the long arm of a submetacentric pair (pair 12). Chromomycin A3 staining evidenced only the NOR-bearing segments. Positive C-band segments were identified in a pericentromeric position in most of the chromosomes and the NOR-bearing segments were also C-band positive. Some aspects related to the chromosomal characteristics of Rhamdella microcephala are discussed.

Morphologic and Cytogenetic Description of the Small Red Brocket (Mazama bororo Duarte, 1996) in Brazil

We evaluated morphological and cytogenetic data for three animals similar to the species of deer previously described as the Small Red Brocket (Mazama bororo Duarte, 1996). We compared these animals with five M. americana, five M. nana and three hybrids between M. americana and M. nana. The M. bororo chromosomes can be standardized as follows : 8 group A chromosomes (large bi-armed) ; 2 group C chromosomes (small bi-armed) ; 4 group D chromosomes (large acrocentric) ; and 18 group E chromosomes (small acrocentric). There were great differences between this karyotype and those of M. nana and M. americana. With respect to external morphology, the animals in the present study had some similarities to M. americana and M. nana and great similarities with their hybrids. Most of the body measurements of M. bororo were significantly different from those of M. americana and M. nana, but similar to those of the hybrids. Mazama bororo is distributed in the last remnants of the Atlantic forest, extending from the southeastern part of the State of São Paulo to the northeastern part of the State of Paraná, Brazil. The rapid destruction of the Atlantic Forest requires urgent conservation measures for the species.

Cytogenetic study of holocentric chromosomes in three species of triatomines (Heteroptera, Reduvidae)

In the present work, spermatogenesis was analyzed in 3 species of the genus Triatoma (T. platensis, T. proctata, T. tibiamaculata). Lacto-acetic orcein staining was used in order to investigate chromosomal meiotic behavior of these species. It allowed the identification of the T. tibiamaculata karyotype (20, X 1X 2Y), the observation that in T. protacta doesn't occur late migration of sexual chromosomes and corroborated knowledgments about holocentric chromosome nature.

Cytogenetic analysis of A-, B-chromosomes and ZZ/ZW sex chromosomes of Characidium gomesi (Teleostei, Characiformes, Crenuchidae)

Different cytogenetic techniques were used to analyze the chromosomes of Characidium gomesi with the main objective of comparing the base composition of ZZ/ZW sex-chromosomes, B-chromosomes and the heterochromatin of A-chromosomes. The results of digestion of chromosomes with AluI restriction endonuclease (RE), silver and CMA3 staining, C-banding and fluorescence in situ hybridization (FISH) with the 18S rDNA probe suggested the existence of compositional differences between the heterochromatin of ZZ/ZW sex-chromosomes, A- and B-chromosomes, and indicated the presence of different numbers and morphology of B-chromosomes in the samples of this population.

Cytogenetic analysis of species of the genera Acestrorhynchus, Oligosarcus and Rhaphiodon (Teleostei: Characiformes)

In the present study the karyotypes and the number and position of nucleolus organizer regions (NORs) of four species of Characiformes are described. The analyses showed that Acestrorhynchus lacustris had 2n=50 chromosomes (8M+34SM+6ST+2A), Oligosarcus longirostris had 2n=50 chromosomes (2M+20SM+10ST+18A), Oligosarcus cf. paranensis from Keller and Mourão rivers had 2n=50 chromosomes (2M+26SM+8ST+14A), and Rhaphiodon vulpinus had 2n=54 chromosomes (32M+12SM+8ST+2A). The number of NOR-bearing chromosome pairs ranged from one to three among the species studied. The results available show that there is no variation in the diploid number within the genera analyzed. However, clear differences related to the karyotypic formulae and the number and position of Ag-NORs were found even in the comparison between populations. The possible relationships between the genera analyzed and other Characiformes are discussed.

Cytogenetic analyses of Pseudopimelodus mangurus (Teleostei: Siluriformes: Pseudopimelodidae)

The cytogenetic analyses showed that Pseudopimelodns mangurus has a diploid number of 2n=54 chromosomes (6M, 26SM, 12ST and 10A), single Ag-NORs on the short arm of a middle-sized ST pair, identified as pair 19, and a very small amount of C-band positive segments in two chromosome pairs. The Ag-NORs are C-band positive. The staining of the chromosomes of P. mangurus with CMA 3 reveled the occurrence of bright signals corresponding to the Ag-NORs segments, to the C-band positive segments and also to some C-band negative segments. The occurrence of a diploid number of 2n=54 in all species of the family Pseudopimelodidae and its absence among representatives of Pimelodidae and Heptapteridae, two related families previously considered, reinforces the hypothesis that Pseudopimelodidae is a monophyletic group. © 2004 The Japan Mendel Society.

Comparative cytogenetic studies in species of the subfamily Callichthyinae (Teleostei: Siluriformes: Callichthyidae)

In the present study, the karyotype of three species (nine populations) of the Callichthyinae subfamily were investigated with the objective of better understanding the pattern of relationship among the genera that compose the subfamily. Among the four populations of Callichthys callichthys studied, two showed 2n=56 chromosomes and two 2n=58 chromosomes. Up to eight additional microchromosomes were observed in the sample from Marilia. The three populations of Hoplosternum littorale displayed the same number of chromosomes, 2n=60, and karyotypic constitution, 6M+2SM+52A. The two populations of Megalechis personata showed 2n=62 chromosomes and similar karyotypic formulae, 8M+54A and 6M+2SM+54A. Terminal Ag-NORs were found in one chromosome pair of C. callichthys, H. littorale, and M. personata from Itiquira, and in two pairs in M. personata from Rio Branco. The populations of C. callichthys showed C-band positive segments in centromeric and pericentromeric position and the populations of H. littorale and M. personata exhibited C-band positive segments in centromeric and/or interstitial position. Contrarily to the extensive chromosome rearrangements verified in the Corydoradinae subfamily, in the Callichthyinae subfamily a small number of changes seems to have occurred in its karyotypic evolution.

Cytogenetic study on three species of the genus Triatoma (Heteroptera: Reduviidae) with emphasis on nucleolar organizer regions

The use of banding techniques allows the recognition of chromosomal pairs and karyotypical arrangements. However, its application in Heteroptera holocentric chromosomes is limited. Thus, little is known about their structure, specially their Nucleolar Organizer Regions (NORs). A comparative analysis of the nucleolar characteristics present during spermatogenesis in Triatoma platensis, Triatoma protacta and Triatoma tibiamaculata seems to indicate that in this group of insects nucleolar fragmentation occurs after prophase I. The study of chromosomal structure of these triatomines indicates that NORs are located at some telomeric and interstitial autosome regions and at sexual chromosomes (X/X1X2).

Comparative cytogenetics of nine species of Hypoptopomatinae (Teleostei: Siluriformes: Loricariidae): The importance of structural rearrangements in chromosome evolution

Fishes of the subfamily Hypoptopomatinae are very common and found in the lowlands of cis-Andean South America from Venezuela to the north of Argentina. With the main objective of contributing for a better understanding of the importance of chromosome rearrangements in the loricariid evolution, cytogenetic analyses were conducted in nine species of Hypoptopomatinae. The results showed a marked gross karyotypic conservation with the presence of 2n=54 chromosomes in all species analyzed. The main differences were found in the karyotypic formulae level. Most species had a single interstitial Ag-NORs, however terminal Ag-NORs were observed in three species. One species exhibited two Ag-NOR-bearing chromosome pairs. The distribution of C-band positive segments was species specific but chromosome markers were observed among the species analyzed. The gross cytogenetic characteristics observed among the Hypoptopomatinae species are similar to those observed in other primitive Loricariidae species suggesting that small changes, mainly paracentric and pericentric inversion were the main events in the karyotypic evolution of this fish group.

Kappa-casein gene study with molecular markers in female buffaloes (Bubalus bubalis)

Caseins comprise make up about 80% of the total protein content of milk and present polymorphism with change in the amino acid sequence. Within this abundance of proteins, kappa-casein is noteworthy, since it has been associated with differences in milk yield, composition and processing. The objective of this study was to observe the existence of polymorphism in the kappa-casein gene in female buffaloes. For this purpose, blood samples from 115 female buffaloes, collected with vacutainer by needle punctionure of the jugular vein, were used. for genomic DNA extraction was done from blood samples. The PCR-RFLP and SSCP techniques demonstrated that the studied animals were monomorphic for the kappa-casein gene. Only allele B was observed in these animals, which was present in homozygosis. Therefore, it was not possible to quantify the gene action on milk yield and its constituents. The monomorphism observed in the population studied would allow the development of a method to identify mixtures of cow and buffalo milk in mozzarella cheese production, especially because, in cattle, the kappa-casein gene is polymorphic. Copyright by the Brazilian Society of Genetics.

Cytogenetic characterization of the silverside fish Odontesthes regia (Humboldt, 1833) (Teleostei: Atheriniformes: Atherinopsidae) from Iquique, Chile

This paper describes the karyotype of Odontesthes regia by means of Giemsa staining, C-banding, to reveal the distribution of the constitutive heterochromatin, and by Ag-staining and fluorescent in situ hybridization (FISH), to locate ribosomal genes (rDNA). The chromosome diploid modal count in the species was 2n = 48. The karyotype is composed of one submetacentric pair (pair 1), 16 subtelocentric pairs (pairs 2 to 17), and 7 acrocentric pairs (pairs 18 to 24). With the exception of pair 1 it was not possible to classify the homologous chromosomes accurately because differences in chromosome size were too slight between adjacent pairs. The distribution of C-banded heterochromatin allowed for a more accurate matching of the majority of chromosomes of the subtelocentric series. Silver staining of metaphase spreads allowed for the identification of Nucleolus Organizer Regions (Ag-NOR) on pair 1. FISH experiments showed that 18S rDNA sequences were located, as expected, in the same chromosome pair identified as the Ag-NOR-bearing one.

Genetic divergence in Eucalyptus spp. clones by molecular RAPD markers

The genetic divergence in 20 Eucalyptus spp. clones was evaluated by multivariate techniques based on 167 RAPD markers, of which 155 were polymorphic and 12 monomorphic. The measures of genetic distances were obtained by the arithmetic complement of the coefficients of Jaccard and of Sorenso-Nei and Li and evaluated by the hierarchical methods of Single Linkage clustering and Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Independent of the dissimilarity coefficient, the greatest divergence was found between clones 7 and 17 and the smallest between the clones 11 and 14. Clone clustering was little influenced by the applied procedure so that, adopting the same percentage of divergence, the UPGMA identified two groups less for the coefficient of Sorenso-Nei and Li. The clones evidenced considerable genetic divergence, which is partly associated to the origin of the study material. The clusters formed by the UPGMA clustering algorithm associated to the arithmetic complement of Jaccard were most consistent.

Transferability and use of microsatellite markers for the genetic analysis of the germplasm of some Arachis section species of the genus Arachis

The Arachis section is the most important of the nine sections of the genus Arachis because it includes the cultivated peanut, Arachis hypogaea. The genetic improvement of A. hypogaea using wild relatives is at an early stage of development in spite of their potential as sources of genes, including those for disease and pests resistance, that are not found in the A. hypogaea primary gene pool. Section Arachis species germplasm has been collected and maintained in gene banks and its use and effective conservation depends on our knowledge of the genetic variability contained in this material. Microsatellites are routinely used for the analysis of genetic variability because they are highly polymorphic and codominant. The objective of this study was to evaluate the transferability of microsatellite primers and the assay of genetic variability between and within the germplasm of some species of the Arachis section. Fourteen microsatellite loci developed for three different species of Arachis were analyzed and 11 (78%) were found to be polymorphic. All loci had transferability to all the species analyzed. The polymorphic loci were very informative, with expected heterozygosity per locus ranging from 0.70 to 0.94. In general, the germplasm analyzed showed wide genetic variation. © 2006 Sociedade Brasileira de Genética.