In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.

Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.

Breeding Jatropha curcas by genomic selection: A pilot assessment of the accuracy of predictive models.

Genomic wide selection is a promising approach for improving the selection accuracy in plant breeding, particularly in species with long life cycles, such as Jatropha. Therefore, the objectives of this study were to estimate the genetic parameters for grain yield (GY) and the weight of 100 seeds (W100S) using restricted maximum likelihood (REML); to compare the performance of GWS methods to predict GY and W100S; and to estimate how many markers are needed to train the GWS model to obtain the maximum accuracy. Eight GWS models were compared in terms of predictive ability. The impact that the marker density had on the predictive ability was investigated using a varying number of markers, from 2 to 1,248. Because the genetic variance between evaluated genotypes was significant, it was possible to obtain selection gain. All of the GWS methods tested in this study can be used to predict GY and W100S in Jatropha. A training model fitted using 1,000 and 800 markers is sufficient to capture the maximum genetic variance and, consequently, maximum prediction ability of GY and W100S, respectively. This study demonstrated the applicability of genome-wide prediction to identify useful genetic sources of GY and W100S for Jatropha breeding. Further research is needed to confirm the applicability of the proposed approach to other complex traits.

Parâmetros genéticos e diversidade em progênies de Macaúba com base em características morfológicas e fisiológicas / Genetic parameters and diversity in progenies from Macaw Palm based on morphological and physiological traits

A obtenção de estimativas confiáveis de parâmetros genéticos, incluindo dados relacionados à variabilidade das populações sob melhoramento, é essencial para se elucidar a estrutura genética das populações e para se inferir sobre sua variabilidade genética e seu potencial de melhoramento. Nesse sentido, este trabalho teve por objetivo estimar parâmetros genéticos e a diversidade em progênies de Macaúba com base em características morfológicas e fisiológicas. Para o estudo, foram avaliadas características morfológicas e fisiológicas em 15 progênies de macaúba, em delineamento em blocos ao acaso com 5 repetições e 3 plantas por parcela, no espaçamento de 5x5m. Não houve variabilidade para a maioria das características fisiológicas no conjunto de progênies avaliadas. Porém, verificou-se variabilidade genética para os caracteres morfológicos avaliados. As famílias de macaúba agruparam-se em três grupos distintos quanto à diversidade genética, sendo a família CPAC-03 a mais divergente em relação às demais. A eficiência no uso da água e o comprimento de raquis foram as características que mais contribuíram para a dissimilaridade das famílias de macaúba.

Obtaining reliable estimates of genetic parameters, including data related to the existing level of variability in breeding populations is essential to elucidate the genetic structure of populations and to infer their genetic variability and potential for improvement. Therefore, this study aimed to estimate genetic parameters and diversity in progenies from Macaw Palm based on morphological and physiological traits. For that, morphological and physiological traits were evaluated in 15 macaw palm progenies (established following a random block design with 5 repetitions and 3 plants per plot - 5x5m spacing). No significant genetic variability was observed for physiological traits in the evaluated progenies. However, for the morphological traits, the existence of genetic variability was evidenced. The macaw palm families were grouped into three distinct groups based on its genetic dissimilarity, being CPAC-03, the most divergent progeny to the others. The water use efficiency and the leaflet length were the traits that contributed most to the dissimilarity of the families.

Perennial plants for biofuel production: bridging genomics and field research.

Development of dedicated perennial crops has been indicated as a strategic action to meet the growing demand for biofuels. Breeding of perennial crops,however, is often time- and resource-consuming. As genomics offers a platform from which to learn more about the relationships of genes and phenotypes,its operational use in the context of breeding programs through strategies such as genomic selection promises to foster the development of perennial crops dedicated to biodiesel production by increasing the efficiency of breeding programs and by shortening the length of the breeding cycles.

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank.

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.

Estimates of genetic parameters for physic nut traits based in the germplasm two years evaluation / Estimativa de parâmetros genéticos de caracteres de pinhão-manso em dois anos de avaliação do banco de germoplasma

In spite of increasingly widespread interest in planting physic nut, breeding efforts are still in its infancy. In that context, an important resource recently established aiming future breeding efforts was the assembly of a germplasm bank with near 200 accessions. The objective of this study was to estimate genetic parameters, repeatibility coefficients and genetic correlation between seven traits, measured in 110 accessions (half sib families) of this germplasm bank in different stages of development. The results show that higher relative values of additive variance were only found for yield and height, and the existence of low environmental variation (either of temporary or permanent nature) among plots within blocks. Given the high repeatibility values found for all traits, on average three measurements are necessary to predict, accurately and efficiently, the true breeding value of an individual. Based on the results of genetic correlations, breeding effort should initially be use track trees with increased stem diameter, elevated number of branches and canopy volume so as to increase the chances of finding an exceptionally highly productive tree.

Apesar do crescente interesse no plantio do pinhão manso, os esforços de melhoramento ainda estão em seu início. Nesse contexto, um importante recurso recentemente estabelecido visando a futuros trabalhos de melhoramento foi a montagem de um banco de germoplasma com cerca de 200 acessos. O objetivo deste estudo foi estimar parâmetros genéticos, coeficientes de repetibilidade e correlações genéticas entre sete características, mensuradas em 110 acessos (famílias de meios-irmãos) desse banco de germoplasma em diferentes estágios de desenvolvimento. Os resultados demonstram que valores elevados de variância genética aditiva foram encontrados apenas para produção e altura e a existência de baixa variação ambiental (tanto de natureza temporária quanto permanente) entre parcelas dentro de blocos. Dado os altos valores de repetibilidade encontrados para todas as características, em média três mensurações são necessárias para se predizer, acurada e eficientemente, o real valor de melhoramento de um indivíduo. Baseado nos resultados de correlações genéticas, esforços de melhoramento devem inicialmente ser usados para se identificar árvores de elevado diâmetro de caule, elevado número de ramos e volume de copa, de modo a aumentar as chances de se encontrar árvores excepcionalmente produtivas.

Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species.

As high-throughput genomic tools, such as the DNA microarray platform, have lead to the development of novel genotyping procedures, such as Diversity Arrays Technology (DArT) and Single Nucleotide Polymorphisms (SNPs), it is likely that, in the future, high density linkage maps will be constructed from both dominant and co-dominant markers. Recently, a strictly genetic approach was described for estimating recombination frequency (r) between co-dominant markers in full-sib families. The complete set of maximum likelihood estimators for r in full-sib families was almost obtained, but unfortunately, one particular configuration involving dominant markers, segregating in a 3:1 ratio and co-dominant markers, was not considered. Here we add nine further estimators to the previously published set, thereby making it possible to cover all combinations of molecular markers with two to four alleles (without epistasis) in a full-sib family. This includes segregation in one or both parents, dominance and all linkage phase configurations.

Genetic control of Eucalyptus urophylla and E. grandis resistance to canker caused by Chrysoporthe cubensis.

Chrysophorte cubensis induced canker occurs in nearly all tropical and subtropical regions where eucalypts are planted, causing losses in both wood quality and volume productivity, especially so in the warmer and more humid regions of Brazil. The wide inter and intra-specific genetic variability of resistance to canker among Eucalyptus species facilitates the selection of resistant plants. In this study, we evaluated resistance to this pathogen in five Eucalyptus grandis (G) and 15 E. urophylla (U) trees, as well as in 495 individuals from 27 progenies derived from crosses between the trees. In the field, six-months-old test seedlings were inoculated with C. cubensis. Lesion length in the xylem and bark was measured eight months later. The results demonstrated that xylem lesions could preferentially be used for the selection of resistant clones. Eight trees (7 U and 1 G) were susceptible, and the remainder (8 U and 4 G) resistant. Individual narrow and broad sense heritability estimates were 17 and 81%, respectively, thereby suggesting that canker resistance is quantitative and highly dependent on dominance and epistasis.

Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species

As high-throughput genomic tools, such as the DNA microarray platform, have lead to the development of novel genotyping procedures, such as Diversity Arrays Technology (DArT) and Single Nucleotide Polymorphisms (SNPs), it is likely that, in the future, high density linkage maps will be constructed from both dominant and co-dominant markers. Recently, a strictly genetic approach was described for estimating recombination frequency (r) between co-dominant markers in full-sib families. The complete set of maximum likelihood estimators for r in full-sib families was almost obtained, but unfortunately, one particular configuration involving dominant markers, segregating in a 3:1 ratio and co-dominant markers, was not considered. Here we add nine further estimators to the previously published set, thereby making it possible to cover all combinations of molecular markers with two to four alleles (without epistasis) in a full-sib family. This includes segregation in one or both parents, dominance and all linkage phase configurations.

Genetic control of Eucalyptus urophylla and E. grandis resistance to canker caused by Chrysoporthe cubensis

Chrysophorte cubensis induced canker occurs in nearly all tropical and subtropical regions where eucalypts are planted, causing losses in both wood quality and volume productivity, especially so in the warmer and more humid regions of Brazil. The wide inter and intra-specific genetic variability of resistance to canker among Eucalyptus species facilitates the selection of resistant plants. In this study, we evaluated resistance to this pathogen in five Eucalyptus grandis (G) and 15 E. urophylla (U) trees, as well as in 495 individuals from 27 progenies derived from crosses between the trees. In the field, six-months-old test seedlings were inoculated with C. cubensis. Lesion length in the xylem and bark was measured eight months later. The results demonstrated that xylem lesions could preferentially be used for the selection of resistant clones. Eight trees (7 U and 1 G) were susceptible, and the remainder (8 U and 4 G) resistant. Individual narrow and broad sense heritability estimates were 17 and 81 percent, respectively, thereby suggesting that canker resistance is quantitative and highly dependent on dominance and epistasis.

Pólen 2n e mecanismos meióticos de formação em Solanum commersonii ssp / 2n pollen and meiotic mechanisms of Formation in Solanum commersonii ssp

Solanum commersonii subsp. commersonii Dun. e Solanum commersonii subsp. malmeanum Bitt. (2n=2x=24 - 1EBN) não podem ser diretamente cruzadas com a batata cultivada de S. tuberosum subsp. tuberosum L. (2n=4x=48 -4 EBN) em razão da barreira da ploidia e do número de equilíbrio do endosperma (EBN). No entanto, a produção de pólen não reduzido por S. commersonii ssp. (2x=2n=24 - 1EBN), permite o cruzamento desta com dihaplóides de batata e com as espécies diplóides S. phureja Juz. & Bukasov. e S. chacoense Bitt., que possuem 2 EBN. Conduziu-se este trabalho, com o objetivo de determinar o mecanismo meiótico e a freqüência dos grãos de pólen não reduzidos em cinco clones de Solanum commersonii ssp. Foram avaliados três clones de S. commersonii subsp. commersonii (SCC) e dois de S. commersonii subsp. malmeanum (SCM). Nas avaliações, duzentos grãos de pólen viáveis foram corados (carmim acético 2%) e mensurados, sendo considerados não reduzidos aqueles com o diâmetro igual ou superior a 25 µm. O clone Solanum commersonii subsp. commersonii Dun. (SCC 100) produz 26.1% de polen não reduzido, por fusos fundidos e fusos paralelos, o qual pode ser utilizado em programas de melhoramento.

Solanum commersonii subsp. commersonii Dun. and Solanum commersonii subsp. malmeanum Bitt. (2n=2x=24 -1EBN) cannot be directly crossed with the cultivated Solanum tuberosum subsp. Tuberosum L. (2n=4x=48 - 4EBN) species due to ploidy barriers and endosperm balance number (EBN). However, non-reduced pollen production by the wild species S. commersonii ssp. (2x=2n=24 -1EBN), allows the crossing of these species with dihaploids of potato and with the diploids species, S. phureja Juz. & Bukasov. and S. chacoense Bitt., all with 2EBN. The aim of this work was to determine the meiotic mechanism and frequency of non-reduced pollen production of five clones of S. commersonii ssp. Three different clones of S. commersonii subsp. commersonii Dun. (SCC) and two of S. commersonii subsp. malmeanum Bitt. (SCM) were evaluated. In the evaluation, two hundred viable pollen grains were stained (2% acetic carmin) and measured. The pollen grains measuring 25 µm in diameter or more were considered nonreduced. The clone Solanum commersonii subsp. commersonii Dun. (SCC 100) produces 26.1% of non-reduced pollen grains caused by parallel spindles and fusion spindles, which may be used in breeding program.