Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions

Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant breeding. Two data sets were used to compare the prediction abilities of multienvironment G×E genomic models and two kernel methods. Specifically, a linear kernel, or GB (genomic best linear unbiased predictor [GBLUP]), and a nonlinear kernel, or Gaussian kernel (GK), were used to compare the prediction accuracies (PAs) of four genomic prediction models: 1) a single-environment, main genotypic effect model (SM); 2) a multienvironment, main genotypic effect model (MM); 3) a multienvironment, single-variance G×E deviation model (MDs); and 4) a multienvironment, environment-specific variance G×E deviation model (MDe). We evaluated the utility of genomic selection (GS) for 435 individual rubber trees at two sites and genotyped the individuals via genotyping-by-sequencing (GBS) of single-nucleotide polymorphisms (SNPs). Prediction models were used to estimate stem circumference (SC) during the first 4 years of tree development in conjunction with a broad-sense heritability (H2) of 0.60. Applying the model (SM, MM, MDs, and MDe) and kernel method (GB and GK) combinations to the rubber tree data revealed that the multienvironment models were superior to the single-environment genomic models, regardless of the kernel (GB or GK) used, suggesting that introducing interactions between markers and environmental conditions increases the proportion of variance explained by the model and, more importantly, the PA. Compared with the classic breeding method (CBM), methods in which GS is incorporated resulted in a 5-fold increase in response to selection for SC with multienvironment GS (MM, MDe, or MDs). Furthermore, GS resulted in a more balanced selection response for SC and contributed to a reduction in selection time when used in conjunction with traditional genetic breeding programs. Given the rapid advances in genotyping methods and their declining costs and given the overall costs of large-scale progeny testing and shortened breeding cycles, we expect GS to be implemented in rubber tree breeding programs

Mineral nutrients in the shoot biomass of soil cover crops

O objetivo deste trabalho foi estimar as quantidades de nutrientes reciclados por cinco espécies vegetais utilizadas como culturas de cobertura do solo e que podem retornar ao solo pela mineralização da biomassa. Foram coletadas de vários experimentos amostras da matéria verde de aveia-preta (Avena strigosa Schreb), mucuna-preta (Stizolobium aterrimum Piper & Tracy), guandu (Cajanus cajan (L.) Millsp), tremoço (Lupinus albus L. e L. angustifolius L.) e ervilhaca (Vicia sativa L.). Foi estimado o rendimento de matéria seca e determinados os teores de N, P, K, Ca, Mg, Mn, Zn, Cu, e, a partir dessas concentrações, foram calculadas a média observada, a média estimada e o intervalo de confiança a 95% para cada nutriente dentro de cada classe de rendimento de matéria seca, em cada espécie vegetal. Os dados foram tabulados dentro de intervalos de classe de rendimento de matéria seca e apresentadas as quantidades estimadas de nutrientes minerais. Foram ajustadas equações para estimar as quantidades desses nutrientes. A aveia-preta e a ervilhaca reciclam grande quantidade de K, e a ervilhaca, a mucuna-preta, o tremoço e o guandu reciclam grande quantidade de N. Todas as espécies reciclam quantidades apreciáveis de Ca, Mg e micronutrientes, porém baixas quantidades de P. A rotação de culturas é um meio de implementar com sucesso o aumento das áreas de lavoura em semeadura direta.The objective of this work was to estimate the quantity of nutrients recycled by five species of cover crops and returned to the soil after the mineralization of the biomass. Fresh samples of several experiments of black oats (Avena strigosa Schreb), black mucuna (Stizolobium aterrimum Piper & Tracy), pigeon pea (Cajanus cajan (L.) Millsp), lupin (Lupinus albus L. and L. angustifolius L.) and common vetch (Vicia sativa L.) were taken to estimate dry matter yield and determine the content of N, P, K, Ca, Mg, Mn, Zn, and Cu. From the dry matter yield, nutrient content were analyzed, and the estimated and observed mean, and a confidence limit at the 95% level, for each nutrient, in each class of dry matter yield and in each cover crop species were calculated. The data were tabulated with the corresponding dry matter class intervals and estimated quantity of nutrients. Equations were adjusted to estimate the quantity of nutrients in relation to dry matter yield. Black oats and common vetch, are good for recycling K, and common vetch, black mucuna, lupin and pigeon pea recycled large amounts of N. All species recycled large amounts of Ca, Mg and micronutrients, but small amounts of P. Crop rotation is a way of successfully increasing field areas under no-tillage

Efeito da poda apical nos atributos morfofisiológicos do porta-enxerto clonal de seringueira GT1

The rubber tree rootstocks require a period in nursery to reach the grafting stage, and it is necessary the application of practices to optimize the time of seedling formations. The objective of this work was to evaluate the effect of apical pruning on the morphophysiological attributes of the GT1 rubber tree rootstocks. The experiment was performed from May 2014 to May 2015 and the treatments consisted in T1: without apical pruning; T2: apical pruning performed once after the third mature leaf release; T3: apical pruning performed monthly after the third mature leaf release; T4: apical pruning performed once after the fourth mature leaf release; T5: apical pruning performed monthly after the fourth mature leaf release; T6: apical pruning performed once after the fifth mature leaf release and T7: apical pruning performed monthly after the fifth mature leaf release. Measurements were performed monthly, measuring the diameter and height of the plants, from 90 to 360 DAT (days after planting transfer). At 360 DAT were evaluated: dry mass of root, stem, leaves and total dry mass; number of leaflets; length of the pivoting root; volume of the root system; leaf area and mineral element content in leaves. The apical pruning influenced stem diameter, height, dry stem mass, dry leaf mass and leaf area of plants. Plants submitted to apical pruning showed dry root mass, total dry mass, root length, root volume and number of leaflets similar to those not budded. The treatments with monthly apical pruning showed a higher concentration of mineral elements in the leaves. The apical pruning performed monthly after the fourth mature leaf release allowed the development in diameter of the rootstocks of the rubber tree in a period similar to the plants not blossomed, but ally to a smaller height, which facilitates the cultural treatments.Os porta-enxertos de seringueira requerem um período em viveiro para atingir o estádio de enxertia, sendo necessária a aplicação de práticas para otimizar o tempo de formação das mudas. O objetivo do trabalho foi avaliar o efeito da poda apical nos atributos morfofisiológicos dos porta-enxertos de seringueira GT1. O experimento foi realizado no período de maio de 2014 a maio de 2015 e os tratamentos consistiram em T1: sem poda apical; T2: poda apical realizada uma vez após o terceiro lançamento foliar maduro; T3: poda apical realizada mensalmente após o terceiro lançamento foliar maduro; T4: poda apical realizada uma vez após o quarto lançamento foliar maduro; T5: poda apical realizada mensalmente após o quarto lançamento foliar maduro; T6: poda apical realizada uma vez após o quinto lançamento foliar maduro e T7: poda apical realizada mensalmente após o quinto lançamento foliar maduro. As mensurações foram realizadas mensalmente, medindo-se o diâmetro e a altura das plantas, de 90 até 360 DAT (dias após o transplantio). Aos 360 DAT foram avaliados: massa seca de raiz, caule, folhas e massa seca total; número de folíolos; comprimento da raiz pivotante; volume do sistema radicular; área foliar e teores de elementos minerais nas folhas. A poda apical influenciou no diâmetro do caule, da altura, da massa seca de caule, da massa seca foliar e da área foliar das plantas. Plantas submetidas às podas apicais apresentaram a massa seca de raiz, a massa seca total, o comprimento de raiz, o volume de raiz e o número de folíolos semelhantes às não despontadas. Os tratamentos com poda apical realizada mensalmente apresentaram maior concentração de elementos minerais nas folhas. A poda apical realizada mensalmente após o quarto lançamento foliar maduro possibilitou o desenvolvimento em diâmetro dos porta-enxertos de seringueira em período semelhante às plantas não despontadas, porém aliado a uma menor altura, que facilita os tratos culturais

De Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways.

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.9e10266

Analysis of capture-recapture experiments through log-linear models

Neste trabalho abordamos a análise de experimento de captura-recaptura usando modelos log-lineares. Para muitos modelos uma equivalente exata pode ser demonstrada entre os parâmetros do modelo log-linear e os parâmetros biológicos usuais tal que as estimativas destes são também estimativas de máxima verossimilhança. Os modelos para populações fechadas onde equivalência exata pode ser estabelecida são Mo, Mt, Mb e Mtb de Otis et al. (1978). Para população aberta exata equivalência é disponível com o modelo Jolly-Seber, ou qualquer submodelo obtido pela omissão de nascimento ou morte, ou ainda, especificando probabilidade de captura constante sobre todas, ou qualquer subconjunto de amostras. Um problema no SAS que produz as histórias de captura com respectivas contagens observadas e outro no GLIM que possibilita uma completa análise dos dados sob o modelo Jolly-Seber ou qualquer derivação deste, são apresentados. É discutida a aplicação desta metodologia num conjunto de dados reais de recaptura de jacaré (Caiman crocrodilus Yacare) obtidos no Pantanal da Nhecolândia, Mato Grosso do Sul, com os resultados mostrando que parâmetros de heterogeneidade nas probabilidades de captura dos animais e parâmetros de dependência de armadilha estão em operação na população estudada. Além disso, verificou-se que a densidade estimada para o ano de 1990 é de 50 animais/km2 valor igual ao encontrado por MOURÃO et al. (1994) utilizando o método de levantamento aéreo.In this research we approached the analysis of capture-recapture experiments using log-linear models. For many models an exact equivalence can be shown between the parameters of the log-linear model and the usual biological parameters, in such a way that estimatives of them are also maximum likelihood estimatives. Models for closed populations in which an exact equivalencecan be established are Mo, Mt, Mb e Mtb from OTIS et al. (1978). For open populations, exact equivalence is available with the Jolly-Seber model, or submodels obtained by omission of birth, death, or even specifying constant probability of capture over all or any subset of samples. A SAS program, which generates the histories of capture with their respective observed countings and another with GLIM which makes possible a complete analysis of the data based on Jolly-Seber model or any derivation of this, are shown. Aplication of this methodology is discussed on a set of real data on recapture of alligator (Caiman crocodilus yacare) observed at Pantanal de Nhecolândia (Nhecolândia swamp), in the state of Mato Grosso do Sul, Brazil, with results showing that heterogeneity parameters on the probabilities of animal capture and parameters of trap-hapiness were in operation in the target population. On the other hand it was estimated the animal density for the year of 1990 that was 50 animal per squared kilometer the same value as the one found by MOURÃO et al. (1994) utilizing aerial survey

Analysis of capture-recapture experiments through log-linear models

Neste trabalho abordamos a análise de experimento de captura-recaptura usando modelos log-lineares. Para muitos modelos uma equivalente exata pode ser demonstrada entre os parâmetros do modelo log-linear e os parâmetros biológicos usuais tal que as estimativas destes são também estimativas de máxima verossimilhança. Os modelos para populações fechadas onde equivalência exata pode ser estabelecida são Mo, Mt, Mb e Mtb de Otis et al. (1978). Para população aberta exata equivalência é disponível com o modelo Jolly-Seber, ou qualquer submodelo obtido pela omissão de nascimento ou morte, ou ainda, especificando probabilidade de captura constante sobre todas, ou qualquer subconjunto de amostras. Um problema no SAS que produz as histórias de captura com respectivas contagens observadas e outro no GLIM que possibilita uma completa análise dos dados sob o modelo Jolly-Seber ou qualquer derivação deste, são apresentados. É discutida a aplicação desta metodologia num conjunto de dados reais de recaptura de jacaré (Caiman crocrodilus Yacare) obtidos no Pantanal da Nhecolândia, Mato Grosso do Sul, com os resultados mostrando que parâmetros de heterogeneidade nas probabilidades de captura dos animais e parâmetros de dependência de armadilha estão em operação na população estudada. Além disso, verificou-se que a densidade estimada para o ano de 1990 é de 50 animais/km2 valor igual ao encontrado por MOURÃO et al. (1994) utilizando o método de levantamento aéreo.In this research we approached the analysis of capture-recapture experiments using log-linear models. For many models an exact equivalence can be shown between the parameters of the log-linear model and the usual biological parameters, in such a way that estimatives of them are also maximum likelihood estimatives. Models for closed populations in which an exact equivalencecan be established are Mo, Mt, Mb e Mtb from OTIS et al. (1978). For open populations, exact equivalence is available with the Jolly-Seber model, or submodels obtained by omission of birth, death, or even specifying constant probability of capture over all or any subset of samples. A SAS program, which generates the histories of capture with their respective observed countings and another with GLIM which makes possible a complete analysis of the data based on Jolly-Seber model or any derivation of this, are shown. Aplication of this methodology is discussed on a set of real data on recapture of alligator (Caiman crocodilus yacare) observed at Pantanal de Nhecolândia (Nhecolândia swamp), in the state of Mato Grosso do Sul, Brazil, with results showing that heterogeneity parameters on the probabilities of animal capture and parameters of trap-hapiness were in operation in the target population. On the other hand it was estimated the animal density for the year of 1990 that was 50 animal per squared kilometer the same value as the one found by MOURÃO et al. (1994) utilizing aerial survey

sumario v2n3.pmd

ABSTRACT The frequency of meiotic abnormalities among single-, double-and three-way cross experimental hybrids and their parental inbred lines is studied. Among the sixteen inbred lines examined, fifteen originated from populations developed at the National Center of Research in Maize and Sorghum (CNPMS/Embrapa) and one from a population developed at ESALQ (Faculty of Agriculture Luiz de Queiroz of the University of São Paulo). Previous analyses of homozygous and heterozygous maize genotypes from CNPMS populations demonstrated high meiotic instability. The present investigation aims at analyzing the meiotic behavior of different inbred lines obtained from CNPMS populations by another breeding enterprise to verify the presence of the same abnormalities and determine whether the abnormalities might compromise productivity. Analyses showed the presence of some abnormalities described previously, albeit at a lower frequency. The most common abnormalities in homozygous and heterozygous genotypes from CNPMS populations were related to irregular chromosome segregation and to chromosome stickiness. An inbred line from the ESALQ population showed only abnormalities related to irregular chromosome segregation caused by the presence of univalent chromosomes. The Pearson correlation procedure indicated high negative correlation between meiotic abnormalities and productivity