Marker-Assisted Recurrent Selection for Pyramiding Leaf Rust and Coffee Berry Disease Resistance Alleles in Coffea arabica L.

In this study, marker-assisted recurrent selection was evaluated for pyramiding resistance gene alleles against coffee leaf rust (CLR) and coffee berry diseases (CBD) in Coffea arabica. A total of 144 genotypes corresponding to 12 hybrid populations from crosses between eight parent plants with desired morphological and agronomic traits were evaluated. Molecular data were used for cross-certification, diversity study and resistance allele marker-assisted selection (MAS) against the causal agent of coffee leaf rust (Hemileia vastatrix) and coffee berry disease (Colletotrichum kahawae). In addition, nine morphological and agronomic traits were evaluated to determine the components of variance, select superior hybrids, and estimate genetic gain. From the genotypes evaluated, 134 were confirmed as hybrids. The genetic diversity between and within populations was 75.5% and 24.5%, respectively, and the cluster analysis revealed three primary groups. Pyramiding of CLR and CBD resistance genes was conducted in 11 genotypes using MAS. A selection intensity of 30% resulted in a gain of over 50% compared to the original population. Selected hybrids with increased gain also showed greater genetic divergence in addition to the pyramided resistance alleles. The strategies used were, therefore, efficient to select superior coffee hybrids for recurrent selection programs and could be used as a source of resistance in various crosses.

Genetic parameters and selection gain in tropical wheat populations via Bayesian inference / Parâmetros genéticos e ganho de seleção em populações tropicais de trigo via inferência bayesiana

ABSTRACT: The development process of a new wheat cultivar requires time between obtaining the base population and selecting the most promising line. Estimating genetic parameters more accurately in early generations with a view to anticipating selection means important advances for wheat breeding programs. Thus, the present study estimated the genetic parameters of F2 populations of tropical wheat and the genetic gain from selection via the Bayesian approach. To this end, the authors assessed the grain yield per plot of 34 F2 populations of tropical wheat. The Bayesian approach provided an adequate fit to the model, estimating genetic parameters within the parametric space. Heritability (h2) was 0.51. Among those selected, 11 F2 populations performed better than the control cultivars, with genetic gain of 7.80%. The following populations were the most promising: TbioSossego/CD 1303, CD 1303/TbioPonteiro, BRS 254/CD 1303, Tbio Duque/Tbio Aton, and Tbio Aton/CD 1303. Bayesian inference can be used to significantly improve tropical wheat breeding programs.

RESUMO: O processo de desenvolvimento de uma nova cultivar de trigo requer tempo entre a obtenção da população base e a seleção da linhagem mais promissora. Estimar parâmetros genéticos com mais precisão nas primeiras gerações com vistas a antecipar a seleção significa avanços importantes para os programas de melhoramento de trigo. Assim, o presente estudo estima os parâmetros genéticos de populações F2 de trigo tropical e o ganho genético da seleção via abordagem Bayesiana. Para tanto, os autores avaliaram a produtividade de grãos por parcela de 34 populações F2 de trigo tropical. A abordagem Bayesiana proporcionou um ajuste adequado ao modelo, estimando parâmetros genéticos dentro do espaço paramétrico. A herdabilidade (h2) foi de 0,51. Dentre as selecionadas, 11 populações F2 obtiveram desempenho superior às cultivares controle, com ganho genético de seleção de 7,80%. As seguintes populações foram as mais promissoras: Tbio Sossego/CD 1303, CD 1303/Tbio Ponteiro, BRS 254/CD 1303, Tbio Duque/Tbio Aton e Tbio Aton/CD 1303. A inferência Bayesiana pode ser usada para melhorar significativamente programas de melhoramento de trigo tropical.

Genomic prediction through machine learning and neural networks for traits with epistasis.

Genomic wide selection (GWS) is one contributions of molecular genetics to breeding. Machine learning (ML) and artificial neural networks (ANN) methods are non-parameterized and can develop more accurate and parsimonious models for GWS analysis. Multivariate Adaptive Regression Splines (MARS) is considered one of the most flexible ML methods, automatically modeling nonlinearities and interactions of the predictor variables. This study aimed to evaluate and compare methods based on ANN, ML, including MARS, and G-BLUP through GWS. An F2 population formed by 1000 individuals and genotyped for 4010 SNP markers and twelve traits from a model considering epistatic effect, with QTL numbers ranging from eight to 480 and heritability ( h 2 ) of 0.3, 0.5 or 0.8 were simulated. Variation in heritability and number of QTL impacts the performance of methods. About quantitative traits (40, 80, 120, 240, and 480 QTLs) was observed highest R2 to Radial Base Network (RBF) and G-BLUP, followed by Random Forest (RF), Bagging (BA), and Boosting (BO). RF and BA also showed better results for traits to h 2 of 0.3 with R 2 values 16.51% and 16.30%, respectively, while MARS methods showed better results for oligogenic traits with R 2 values ranging from 39,12 % to 43,20 % in h 2 of 0.5 and from 59.92% to 78,56% in h 2 of 0.8. Non-additive MARS methods also showed high R2 for traits with high heritability and 240 QTLs or more. ANN and ML methods are powerful tools to predict genetic values in traits with epistatic effect, for different degrees of heritability and QTL numbers.

Short-term changes related to autotetraploidy in essential oil composition of Eucalyptus benthamii Maiden & Cambage and its applications in different bioassays.

Some forest trees have been polyploidized to improve their traits and to supply new germplasms for breeding programs. As trees have a long juvenile stage, the early characterization of the chromosome set doubling effects is crucial for previous selection. Thus, we aimed to characterize the chemical variability of essential oils from diploid and autotetraploid germplasms (autotetraploid A and B) of Eucalyptus benthamii, as well as to evaluate their larvicidal and allelopathic effects. Autotetraploid A showed a higher essential oil yield than diploid and autotetraploid B, which did not differ quantitatively. Aromadendrene, viridiflorol and α-pinene were the major compounds in the diploid essential oil. In contrast, compounds were present in autotetraploids, such as 1,8-cineole, limonene, α-terpineol, and α-terpinyl-acetate. Essential oils from the diploid at 50-200 ppm were twice as larvicidal than those from autotetraploids against Aedes aegypti larvae. Considering the phytotoxicity bioassays using Lactuca sativa, essential oils from both ploidy levels affected root growth. Moreover, the essential oils inhibited shoot growth at all concentrations tested (187.5; 375; 750; 1500; and 3000 ppm). Autotetraploid A and B had the same effect on shoot growth as glyphosate. The essential oils had no cytogenotoxic effect on root meristematic cells of L. sativa, whereas phytotoxic potential was identified mainly in shoot growth. This work demonstrated a dramatic change in secondary metabolism (terpene composition) related to an increase in the ploidy level in Eucalyptus germplasms. In addition, we report the novelty of the chemical composition of essential oils among germplasms and their potential use as larvicidal and post-emergence weed control agents.

High Throughput Field Phenotyping for Plant Height Using UAV-Based RGB Imagery in Wheat Breeding Lines: Feasibility and Validation.

Plant height (PH) is an essential trait in the screening of most crops. While in crops such as wheat, medium stature helps reduce lodging, tall plants are preferred to increase total above-ground biomass. PH is an easy trait to measure manually, although it can be labor-intense depending on the number of plots. There is an increasing demand for alternative approaches to estimate PH in a higher throughput mode. Crop surface models (CSMs) derived from dense point clouds generated via aerial imagery could be used to estimate PH. This study evaluates PH estimation at different phenological stages using plot-level information from aerial imaging-derived 3D CSM in wheat inbred lines during two consecutive years. Multi-temporal and high spatial resolution images were collected by fixed-wing (P l a t F W ) and multi-rotor (P l a t M R ) unmanned aerial vehicle (UAV) platforms over two wheat populations (50 and 150 lines). The PH was measured and compared at four growth stages (GS) using ground-truth measurements (PHground) and UAV-based estimates (PHaerial). The CSMs generated from the aerial imagery were validated using ground control points (GCPs) as fixed reference targets at different heights. The results show that PH estimations using P l a t F W were consistent with those obtained from P l a t M R , showing some slight differences due to image processing settings. The GCPs heights derived from CSM showed a high correlation and low error compared to their actual heights (R 2 ≥ 0.90, RMSE ≤ 4 cm). The coefficient of determination (R 2) between PHground and PHaerial at different GS ranged from 0.35 to 0.88, and the root mean square error (RMSE) from 0.39 to 4.02 cm for both platforms. In general, similar and higher heritability was obtained using PHaerial across different GS and years and ranged according to the variability, and environmental error of the PHground observed (0.06-0.97). Finally, we also observed high Spearman rank correlations (0.47-0.91) and R 2 (0.63-0.95) of PHaerial adjusted and predicted values against PHground values. This study provides an example of the use of UAV-based high-resolution RGB imagery to obtain time-series estimates of PH, scalable to tens-of-thousands of plots, and thus suitable to be applied in plant wheat breeding trials.

Half a century of studying adaptability and stability in maize and soybean in Brazil

The study of adaptability and stability underlies the cultivar recommendation process for all crops. There is a considerable number of statistical methods available for this purpose, but little is known about their actual adoption by the Brazilian scientific community. The objective of this study was to carry out a systematic review of the scientific literature on the adaptability and stability methods used in maize and soybean in Brazil from scientific articles published between 1970 and 2017 in Brazilian journals. Article searches were carried out in journals indexed through the SciELO database. The articles were classified according to the year of publication and the adaptability and stability methods used. We also evaluated the pattern of association between methods. We found 113 articles on adaptability and stability in maize and soybean, in which 21 methods were listed. The most commonly used method was the Eberhart and Russell methodology. The Cruz, Torres, and Vencovsky along with the AMMI methods were also widely used. The number of articles using most methods decreased in the current decade, except for the GGE Biplot, MHPRVG, and Centroid methods. In studies with more than one method, the methods were more likely to be used together with the Eberhart and Russell methodology. Adaptability and stability in maize and soybean have been widely studied over the last several decades in Brazil, although the number of publications on this subject has decreased over this time period.

Genetic diversity and heterotic grouping of sorghum lines using SNP markers

Sorghum breeding programs are based predominantly on developing homozygous lines to produce single cross hybrids, frequently with relatively narrow genetic bases. The adoption of complementary strategies, such as genetic diversity study, enables a broader vision of the genetic structure of the breeding germplasm. The purpose of this study was to evaluate the genetic diversity of sorghum breeding lines using structure analysis, principal components (PC) and clustering analyses. A total of 160 sorghum lines were genotyped with 29,649 SNP markers generated by genotyping-by-sequencing (GBS). The PC and clustering analyses consistently divided the R (restorer) and B (maintainer) lines based on their pedigree, generating four groups. Thirty-two B and 21 R lines were used to generate 121 single-cross hybrids, whose performances were compared based on the diversity clustering of each parental line. The genetic divergence of B and R lines indicated a potential for increasing heterotic response in the development of hybrids. The genetic distance was correlated to heterosis, allowing for the use of markers to create heterotic groups in sorghum.

Genetic diversity and heterotic grouping of sorghum lines using SNP markers

Sorghum breeding programs are based predominantly on developing homozygous lines to produce single cross hybrids, frequently with relatively narrow genetic bases. The adoption of complementary strategies, such as genetic diversity study, enables a broader vision of the genetic structure of the breeding germplasm. The purpose of this study was to evaluate the genetic diversity of sorghum breeding lines using structure analysis, principal components (PC) and clustering analyses. A total of 160 sorghum lines were genotyped with 29,649 SNP markers generated by genotyping-by-sequencing (GBS). The PC and clustering analyses consistently divided the R (restorer) and B (maintainer) lines based on their pedigree, generating four groups. Thirty-two B and 21 R lines were used to generate 121 single-cross hybrids, whose performances were compared based on the diversity clustering of each parental line. The genetic divergence of B and R lines indicated a potential for increasing heterotic response in the development of hybrids. The genetic distance was correlated to heterosis, allowing for the use of markers to create heterotic groups in sorghum.(AU)

Half a century of studying adaptability and stability in maize and soybean in Brazil

The study of adaptability and stability underlies the cultivar recommendation process for all crops. There is a considerable number of statistical methods available for this purpose, but little is known about their actual adoption by the Brazilian scientific community. The objective of this study was to carry out a systematic review of the scientific literature on the adaptability and stability methods used in maize and soybean in Brazil from scientific articles published between 1970 and 2017 in Brazilian journals. Article searches were carried out in journals indexed through the SciELO database. The articles were classified according to the year of publication and the adaptability and stability methods used. We also evaluated the pattern of association between methods. We found 113 articles on adaptability and stability in maize and soybean, in which 21 methods were listed. The most commonly used method was the Eberhart and Russell methodology. The Cruz, Torres, and Vencovsky along with the AMMI methods were also widely used. The number of articles using most methods decreased in the current decade, except for the GGE Biplot, MHPRVG, and Centroid methods. In studies with more than one method, the methods were more likely to be used together with the Eberhart and Russell methodology. Adaptability and stability in maize and soybean have been widely studied over the last several decades in Brazil, although the number of publications on this subject has decreased over this time period.(AU)

Population structure analysis and identification of genomic regions under selection associated with low-nitrogen tolerance in tropical maize lines.

Increasing low nitrogen (N) tolerance in maize is an important goal for food security and agricultural sustainability. In order to analyze the population structure of tropical maize lines and identify genomic regions associated with low-N tolerance, a set of 64 inbred lines were evaluated under low-N and optimal-N conditions. The low-N Agronomic Efficiency index (LNAE) of each line was calculated. The maize lines were genotyped using 417,112 SNPs markers. The grouping based on the LNAE values classified the lines into two phenotypic groups, the first comprised by genotypes with high LNAE (named H_LNAE group), while the second one comprised genotypes with low LNAE (named L_LNAE group). The H_LNAE and L_LNAE groups had LNAE mean values of 3,304 and 1,644, respectively. The population structure analysis revealed a weak relationship between genetic and phenotypic diversity. Pairs of lines were identified, having at the same time high LNAE and high genetic distance from each other. A set of 29 SNPs markers exhibited a significant difference in allelic frequencies (Fst > 0.2) between H_LNAE and L_LNAE groups. The Pearson's correlation between LNAE and the favorable alleles in this set of SNPs was 0.69. These SNPs could be useful for marker-assisted selection for low-N tolerance in maize breeding programs. The results of this study could help maize breeders identify accessions to be used in the development of low-N tolerant cultivars.

Multi-trait multi-environment models in the genetic selection of segregating soybean progeny.

At present, single-trait best linear unbiased prediction (BLUP) is the standard method for genetic selection in soybean. However, when genetic selection is performed based on two or more genetically correlated traits and these are analyzed individually, selection bias may arise. Under these conditions, considering the correlation structure between the evaluated traits may provide more-accurate genetic estimates for the evaluated parameters, even under environmental influences. The present study was thus developed to examine the efficiency and applicability of multi-trait multi-environment (MTME) models by the residual maximum likelihood (REML/BLUP) and Bayesian approaches in the genetic selection of segregating soybean progeny. The study involved data pertaining to 203 soybean F2:4 progeny assessed in two environments for the following traits: number of days to maturity (DM), 100-seed weight (SW), and average seed yield per plot (SY). Variance components and genetic and non-genetic parameters were estimated via the REML/BLUP and Bayesian methods. The variance components estimated and the breeding values and genetic gains predicted with selection through the Bayesian procedure were similar to those obtained by REML/BLUP. The frequentist and Bayesian MTME models provided higher estimates of broad-sense heritability per plot (or heritability of total effects of progeny; [Formula: see text]) and mean accuracy of progeny than their respective single-trait versions. Bayesian analysis provided the credibility intervals for the estimates of [Formula: see text]. Therefore, MTME led to greater predicted gains from selection. On this basis, this procedure can be efficiently applied in the genetic selection of segregating soybean progeny.

Genetic diversity among accessions of sacha inchi (Plukenetia volubilis) by phenotypic characteristics analysis / Diversidade genética entre acessos de sacha inchi (Plukenetia volubilis) por análise de características fenotípicas

Sacha inchi (Plukenetia volubilis) is native to the Amazon region and has a high seed content of mono and polyunsaturated fatty acids, making it interesting for the pharmaceutical and cosmetic industry. The purpose of this study was to analyze sacha inchi genetic diversity and describe accessions based on phenotypic characteristics. Fruits and seeds of 25 accessions from the sacha inchi genebank of Embrapa Amazônia Ocidental in Manaus, Amazonas state, were sampled and biometrically measured. The data were subjected to analysis of variance, Mahalanobis distance, canonical correlation, and genetic diversity among and within accessions by analysis of molecular variance (AMOVA). There were significant differences among the means of the analyzed traits, but no significant canonical correlation for the groups of traits. According to AMOVA, approximately 60% of the observed variation was within accessions. The results showed variability among accessions, and that the variation within accessions should be explored to obtain best results in breeding programs.(AU)

Sacha inchi (Plukenetia volubilis) é nativa da região amazônica e suas sementes tem um alto teor de ácidos graxos mono e poliinsaturados, tornando-a interessante para a indústria farmacêutica e cosmética. O objetivo deste estudo foi analisar a diversidade genética de sacha inchi e caracterizar os acessos com base em características fenotípicas. Foi realizada coleta e biometria de frutos e sementes de 25 acessos do banco de germoplasma de sacha inchi da Embrapa Amazônia Ocidental em Manaus-AM. Os dados foram submetidos a análise de variância, distância de Mahalanobis, correlação canônica e diversidade genética por análise de variância molecular (AMOVA). Houve diferenças significativas entre as médias das variáveis analisadas, contudo, não houve correlação canônica significativa para os grupos de variáveis. De acordo com AMOVA, aproximadamente 60% da variação observada esteve dentro de acessos. Os resultados mostram variabilidade entre acessos, sendo importante explorar a variação intra-acessos para obter melhores resultados em programas de melhoramento.(AU)

Genetic diversity among accessions of sacha inchi (Plukenetia volubilis) by phenotypic characteristics analysis / Diversidade genética entre acessos de sacha inchi (Plukenetia volubilis) por análise de características fenotípicas

Sacha inchi (Plukenetia volubilis) is native to the Amazon region and has a high seed content of mono and polyunsaturated fatty acids, making it interesting for the pharmaceutical and cosmetic industry. The purpose of this study was to analyze sacha inchi genetic diversity and describe accessions based on phenotypic characteristics. Fruits and seeds of 25 accessions from the sacha inchi genebank of Embrapa Amazônia Ocidental in Manaus, Amazonas state, were sampled and biometrically measured. The data were subjected to analysis of variance, Mahalanobis distance, canonical correlation, and genetic diversity among and within accessions by analysis of molecular variance (AMOVA). There were significant differences among the means of the analyzed traits, but no significant canonical correlation for the groups of traits. According to AMOVA, approximately 60% of the observed variation was within accessions. The results showed variability among accessions, and that the variation within accessions should be explored to obtain best results in breeding programs.

Sacha inchi (Plukenetia volubilis) é nativa da região amazônica e suas sementes tem um alto teor de ácidos graxos mono e poliinsaturados, tornando-a interessante para a indústria farmacêutica e cosmética. O objetivo deste estudo foi analisar a diversidade genética de sacha inchi e caracterizar os acessos com base em características fenotípicas. Foi realizada coleta e biometria de frutos e sementes de 25 acessos do banco de germoplasma de sacha inchi da Embrapa Amazônia Ocidental em Manaus-AM. Os dados foram submetidos a análise de variância, distância de Mahalanobis, correlação canônica e diversidade genética por análise de variância molecular (AMOVA). Houve diferenças significativas entre as médias das variáveis analisadas, contudo, não houve correlação canônica significativa para os grupos de variáveis. De acordo com AMOVA, aproximadamente 60% da variação observada esteve dentro de acessos. Os resultados mostram variabilidade entre acessos, sendo importante explorar a variação intra-acessos para obter melhores resultados em programas de melhoramento.

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization.

Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits. In this study, we analyzed conserved and divergent root transcriptional responses between flood-tolerant Embrapa 45 and flood-sensitive BR 4 soybean cultivars under hypoxic stress conditions with RNA-seq. To understand how soybean genes evolve and respond to hypoxia, stable and differentially expressed genes were characterized structurally and compositionally comparing its mechanistic relationship. Between cultivars, Embrapa 45 showed less up- and more down-regulated genes, and stronger induction of phosphoglucomutase (Glyma05g34790), unknown protein related to N-terminal protein myristoylation (Glyma06g03430), protein suppressor of phyA-105 (Glyma06g37080), and fibrillin (Glyma10g32620). RNA-seq and qRT-PCR analysis of non-symbiotic hemoglobin (Glyma11g12980) indicated divergence in gene structure between cultivars. Transcriptional changes for genes in amino acids and derivative metabolic process suggest involvement of amino acids metabolism in tRNA modifications, translation accuracy/efficiency, and endoplasmic reticulum stress in both cultivars under hypoxia. Gene groups differed in promoter TATA box, ABREs (ABA-responsive elements), and CRT/DREs (C-repeat/dehydration-responsive elements) frequency. Gene groups also differed in structure, composition, and codon usage, indicating biological significances. Additional data suggests that cis-acting ABRE elements can mediate gene expression independent of ABA in soybean roots under hypoxia.

Phenotypic correlation and path analysis in cultivars and strains of upland rice for drought tolerance / Correlação fenotípica e análise de trilha em cultivares e linhagens de arroz de sequeiro para tolerância à seca

The purpose of this study was to estimate the phenotypic correlations between 14 traits obtained in a thematic core collection of upland rice for drought tolerance and partition them into direct and indirect effects by path analysis. Two experiments were carried out (with and without water stress). One hundred samples were evaluated in a triple 10x10 lattice design. The plot was formed by four rows, 3.0 metres long, spaced at 0.35 m. The plot useful area was constituted by two central rows of 2.0 m in length, totalling 1.4 m2, where data from 14 traits were collected, five from the root system and nine from the aerial part of the plant. Of the evaluated traits, spikelet sterility was the main grain yield determinant, presenting relevant negative correlations of -0.77 and -0.59 in environments with and without drought stress, respectively. The partitioning of spikelet sterility correlations presented negative direct effects on grain yield in environments with (-0.60) and without (-0.62) water stress, corroborating the negative correlations between these traits. The obtained data confirmed that spikelet sterility is an important variable for the selection of rice strain submitted to water deficit. Partial correlation coefficients indicated that only 70.33% in the environment with stress and 50.30% in the environment without stress of grain yield variation were phenotypically explained by variables considered in path analysis, thereby showing the complexity of the selection for drought-tolerant rice.

O objetivo desse trabalho foi estimar as correlações fenotípicas entre 14 características obtidas em uma coleção nuclear temática de arroz de terras altas para tolerância à seca e desdobrá-las em seus efeitos diretos e indiretos por meio da análise de trilha. Foram conduzidos dois experimentos (com e sem estresse hídrico). Avaliou-se 100 materiais no delineamento experimental em látice triplo 10x10. A parcela foi formada por quatro linhas de 3,0 metros de comprimento espaçadas de 0,35 metros. A área útil da parcela foi constituída pelas duas linhas centrais de 2,0 metros de comprimento, perfazendo 1,4 m2 de onde foram coletados dados de 14 características sendo, cinco do sistema radicular e nove da parte aérea da planta. Das características avaliadas, esterilidade das espiguetas foi a principal determinante da produtividade de grãos apresentando correlação negativa de elevada magnitude de -0,78 e -0,59 nos ambientes com e sem estresse de seca, respectivamente. No desdobramento das correlações esterilidade das espiguetas apresentou efeitos diretos negativos na produtividade de grãos nos ambientes com (-0,60) e sem (-0,62) estresse hídrico, corroborando as correlações negativas entre estas características. Os dados obtidos enfatizaram que a esterilidade das espiguetas é uma variável importante para a seleção de linhagens de arroz submetidas à deficiência de água. Os coeficientes de determinações parciais indicaram que apenas 70,33% no ambiente com estresse e 50,30% no ambiente sem estresse da variação da produtividade de grãos foram explicados, fenotipicamente, pelas variáveis consideradas na análise de trilha evidenciando a complexidade da seleção para tolerância à seca em arroz.

Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents.

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms.

QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance.

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.

Genetic potential of common bean parents for plant architecture improvement

In common bean (Phaseolus vulgaris L.) breeding, plant selection that associate erect plant architecture, high yield, and grains with good commercial acceptance has been the choice of breeders. Thus, this study aimed to evaluate potential parents, to obtain promising segregating populations that associate high yield, erect plant architecture and carioca grain type, as well as to obtain information on heterosis, general and specific combining ability of these parents regarding grain yield and traits related to plant architecture. Fourteen common bean lines were crossed under a partial diallel scheme. Group 1 was composed by eight erect plant lines and group 2 by six carioca grain type lines. The F1's plants from the crosses and the 14 parents were evaluated during spring (Mar. sowing) for plant architecture grade, diameter of the hipocotyl, plant mean height, and grain yield. Predominance of additive effects was observed for plant architecture grade and diameter of the hypocotyls. For grain yield and plant mean height, there was a greater contribution of the dominance effects. Thus, selection of erect plants, with a larger diameter of the hypocotyl can be carried out in early generations; while for grain yield and plant mean height, it must be delayed, preferably, to later generations.

Genetic potential of common bean parents for plant architecture improvement

In common bean (Phaseolus vulgaris L.) breeding, plant selection that associate erect plant architecture, high yield, and grains with good commercial acceptance has been the choice of breeders. Thus, this study aimed to evaluate potential parents, to obtain promising segregating populations that associate high yield, erect plant architecture and carioca grain type, as well as to obtain information on heterosis, general and specific combining ability of these parents regarding grain yield and traits related to plant architecture. Fourteen common bean lines were crossed under a partial diallel scheme. Group 1 was composed by eight erect plant lines and group 2 by six carioca grain type lines. The F1's plants from the crosses and the 14 parents were evaluated during spring (Mar. sowing) for plant architecture grade, diameter of the hipocotyl, plant mean height, and grain yield. Predominance of additive effects was observed for plant architecture grade and diameter of the hypocotyls. For grain yield and plant mean height, there was a greater contribution of the dominance effects. Thus, selection of erect plants, with a larger diameter of the hypocotyl can be carried out in early generations; while for grain yield and plant mean height, it must be delayed, preferably, to later generations.

An improved method for genomic DNA extraction from strawberry leaves / Otimização de um método para extração de DNA genômico a partir de folhas de morangueiro

Several extraction methods of genomic DNA for identification and characterization of genetic diversity in different plant species are routinely applied during molecular analysis. However, the presence of undesirable compounds such as polyphenols and polysaccharides is one of the biggest problems faced during the isolation and purification of high quality DNA in plants. Therefore, achievement of fast and accurate methods for DNA extraction is crucial in order to produce pure samples. Leaves of strawberry genotypes (Fragaria ananassa) have high contents of polysaccharides and polyphenols which increase the sample viscosity and decrease the DNA quality, interfering with the PCR performance. Thereby, in this study we evaluated the quality and amount of genomic DNA extracted from young leaves of strawberry after tissue lyophilization and maceration in presence of polivinilpirrolidone (PVP). The CTAB method was used as reference procedure and it was modified to improve the DNA extraction. The modifications consisted of tissue lyophilization overnight until it was completely freeze-dried and addition of PVP during the tissue maceration in liquid nitrogen. The results showed the efficiency and reliability of the modified method compared to the unmodified method, indicating that combination of lyophilization and PVP improve the quality and amount of the DNA extracted from strawberry leaves.

Vários métodos de extração de DNA genômico para a identificação e caracterização da diversidade genética em diferentes espécies de plantas são rotineiramente aplicados durante a análise molecular. Entretanto, a presença de compostos indesejáveis, tais como polifenóis e polissacarídeos, é um dos maiores problemas que ocorrem durante o isolamento e purificação de DNA de alta qualidade em plantas. Dessa forma, o sucesso no desenvolvimento de métodos de extração de DNA rápidos e acurados é crucial para produzir amostras puras. Folhas de genótipos de morangueiro (Fragaria ananassa) têm elevado conteúdo de polissacarídeos e polifenóis que aumentam a viscosidade da amostra e reduzem a qualidade do DNA, interferindo no desempenho da PCR. Neste estudo, avaliamos a qualidade e a quantidade de DNA genômico extraído de folhas jovens de morangueiro após a liofilização do tecido e a maceração na presença de polivinilpirrolidona (PVP). O método CTAB foi utilizado como procedimento de referência e foi modificado para melhorar a extração do DNA. As modificações consistiram na liofilização do tecido a baixa temperatura até que ele tivesse sido desidratado completamente, associada à adição de PVP durante a maceração do tecido no nitrogênio líquido. Os resultados demonstraram a eficiência e a confiabilidade do método modificado comparado ao método não modificado, indicando que a combinação da liofilização com PVP melhora a qualidade e quantidade do DNA extraído de folhas de morangueiro.