Prianda Rios Laborda

Tropical maize germplasm: what can we say about its genetic diversity in the light of molecular markers?

Knowledge about genetic variability of a crop allows for more efficient and effective use of resources in plant improvement programs. The genetic variation within temperate maize has been studied extensively, but the levels and patterns of diversity in tropical maize are still not well understood. Brazilian maize germplasm represents a very important pool of genetic diversity due to many past introductions of exotic material. To improve our knowledge of the genetic diversity in tropical maize inbred lines, we fingerprinted 85 lines with 569 AFLP bands and 50 microsatellite loci. These markers revealed substantial variability among lines, with high rates of polymorphism. Cluster analysis was used to identify groups of related lines. Well-defined groups were not observed, indicating that the tropical maize studied is not as well organized as temperate maize. Three types of genetic distance measurements were applied (Jaccard’s coefficient, Modified Rogers’ distance and molecular coefficient of coancestry), and the values obtained with all of them indicated that the genetic similarities were small among the lines. The different coefficients did not substantially affect the results of cluster analysis, but marker types had a large effect on genetic similarity estimates. Regardless of genetic similarity coefficient used, estimates based on AFLPs were poorly correlated with those based on SSRs. Analyses using AFLP and SSR data together do not seem to be the most efficient manner of assessing variability in highly diverse materials because the result was similar to using AFLPs alone. It was seen that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.

Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse.

Profiling the transcriptome that underlies biomass degradation by the fungus Trichoderma harzianum allows the identification of gene sequences with potential application in enzymatic hydrolysis processing. In the present study, the transcriptome of T. harzianum IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities. This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass. An additional analysis of expression levels identified a set of carbohydrate-active enzymes that are upregulated under different conditions. The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

Correlação da heterose de híbridos de milho com divergência genética entre linhagens

The objective of this work was to evaluate grain yield of maize single cross hybrids obtained from diallel crosses among contrasting lines, to estimate the combining ability of the lines, and finally to confirm if the genetic diversity among those lines assessed by molecular markers is correlated with single cross hybrids heterosis. The 36 single cross hybrids resulting from partial diallel and 12 parental lines were evaluated in Campinas in randomized block design, with three replicates and two control lines checks. General combining ability of the lines was estimated according to Griffing model 4. Correlations among matrices were estimated through Mantel statistics, considering heterosis, yield and specific combining ability with genetic divergence assessed by AFLP and SSR. The hybrids PM518 x L111 exhibited an outstanding yield and the lines PM518, IP4035 and L111 showed positive general combining ability. The estimate heterosis ranged from 927 to 6,698 kg ha -1 . A positive and significant correlation was observed in parental lines between heterosis and genetic diversity assessed by AFLP and SSR. The genetic divergence, however, was not enough to determine the specific combining ability and the hybrids yield.The objective of this work was to evaluate grain yield of maize single cross hybrids obtained from diallel crosses among contrasting lines, to estimate the combining ability of the lines, and finally to confirm if the genetic diversity among those lines assessed by molecular markers is correlated with single cross hybrids heterosis. The 36 single cross hybrids resulting from partial diallel and 12 parental lines were evaluated in Campinas in randomized block design, with three replicates and two control lines checks. General combining ability of the lines was estimated according to Griffing model 4. Correlations among matrices were estimated through Mantel statistics, considering heterosis, yield and specific combining ability with genetic divergence assessed by AFLP and SSR. The hybrids PM518 x L111 exhibited an outstanding yield and the lines PM518, IP4035 and L111 showed positive general combining ability. The estimate heterosis ranged from 927 to 6,698 kg ha. A positive and significant correlation was observed in parental lines between heterosis and genetic diversity assessed by AFLP and SSR. The genetic divergence, however, was not enough to determine the specific combining ability and the hybrids yield.

Development of microsatellite markers for Brachiaria humidicola (Rendle) Schweick

We describe the first panel of nuclear simple sequence repeats (SSRs) loci for Brachiaria humidicola (Rendle) Schweick., a warmseason grass with facultative apomixis, variation in ploidy levels (6X–9X), and important forage grass species in the Tropics. Of 38 pairs of primers obtained by using an enriched-library methodology, 27 revealed polymorphism in 58 accessions of the Germplasm Collection of B. humidicola held at Embrapa Beef Cattle, Brazil. Eleven loci amplified in B. dictyoneura, a closely related species with unclear taxonomic boundaries with B. humidicola. Transferability to other three Brachiaria species was also evaluated. The developed microsatellites are potentially useful for genetic studies of B. humidicola, as well as phylogenetic evaluations, conservation and breeding applications.

Capacidade combinatória, divergência genética entre linhagens de milho e correlação com heterose

The objectives of this research were to evaluate single cross hybrids of maize (Zea mays L.) obtained from partial diallel crosses among contrasting inbred lines, to estimate the combining ability of the lines and to verify whether the genetic diversity among those lines assessed by moleculars markers is correlated with single cross hybrid heterosis Thirty-six single-crosses resulting from partial diallel and the 12 parental lines were evaluated in Campinas, State of Sao Paulo, in randomized block design, with tree replicates and two commercial checks. The following traits were evaluated: plant and ear height, ear weight and grain weight. Individual variance analysis of hybrids were performed, and the averages were compared by Tukey test (P<0.05). General combining ability of the lines was obtained according to Geraldi e Miranda Filho. Correlations among matrices were estimated through Mantel statistics, considering heterosis, yield and specific combining ability with genetic divergence assessed by AFLP and SSR. The hybrid PM624 x IP398 exhibited outstanding yield capacity and the lines VER266 and L105 showed positive GCA for grain yield. Estimate heterosis ranged from -559 to 6.320 kg ha-1. No significant correlation was observed between heterosis, specific combination ability or grain yield with genetic distance assessed by AFLP and SSR. Therefore, no prediction of hybrids performance could be made on the basis of the genetic divergence of the parent lines.

Identification of oxidoreductases from the petroleum Bacillus safensis strain

Highlights • A bacterium responsible for degradation of the petroleum aromatic fractions was isolated.• The bacterium was identified as Bacillus safensis.• Enzymatic assays revealed the presence of two oxidoreductases.• The B. safensis strain can be used for bioremediation of petroleum-polluted environment.

Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line

Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA.

Genome Sequence of Bacillus safensis CFA06, Isolated from Biodegraded Petroleum in Brazil

ABSTRACT Bacillus safensis is a microorganism recognized for its biotechnological and industrial potential due to its interesting enzymatic portfolio. Here, as a means of gathering information about the importance of this species in oil biodegradation, we report a draft genome sequence of a strain isolated from petroleum.

Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret

Acca sellowiana has commercial potential due to the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on its genetic conservation, characterization and breeding.

Isolation and characterization of polymorphic microsatellites for the natural populations of barker frog Physalaemus cuvieri

Ten polymorphic microsatellite loci were isolated for Physalaemus cuvieri from a GA—CA enriched library. In 160 P. cuvieri individuals, the number of alleles per locus ranged to 2–9 and the expected heterozygosity ranged from 0.30 to 0.85. The primers were successfully cross-amplified in the congeneric species P. albonotatus, P. ephippifer and Physalaemus cf. cuvieri, suggesting that these loci are potentially useful for studies on population genetic structure of Physalaemus sp.