Sources, Spectrum, Genetics, and Inheritance of Phaseolus vulgaris Resistance Against Xanthomonas citri pv. fuscans.

Common bean (Phaseolus vulgaris) is one of the most consumed agricultural products in the world. Its production is affected by common bacterial blight (CBB) caused by Xanthomonas citri pv. fuscans and X. phaseoli pv. phaseoli. In this work, we investigated the spectrum, genetics, and inheritance of common bean resistance to X. citri pv. fuscans. Inoculation of nine selected cultivars with an X. citri pv. fuscans strain showed that BRS Radiante and IAPAR 16 were resistant. These two cultivars were also resistant to six X. phaseoli pv. phaseoli strains of different geographic origins, demonstrating their broad-spectrum resistances. BRS Radiante sustained smaller X. citri pv. fuscans populations than two susceptible cultivars. Stomatal densities of IAPAR 16 and BRS Radiante were significantly higher than or not different from susceptible cultivars. BRS Radiante showed the lowest general combining ability values and the combination BRS Radiante × Carioca MG the lowest specific combining ability (SCA) values, revealing the capacity of BRS Radiante to increase resistance to X. citri pv. fuscans. Positive and negative parental SCA values indicated dominant and recessive genes involved in X. citri pv. fuscans resistance. Resistance of the BRS Radiante × Carioca MG cross segregated in a 9:7 ratio in the F2 population, indicating that it is governed by two complementary dominant genes. Maximum likelihood analysis showed that the resistance of BRS Radiante to X. citri pv. fuscans is conferred by a gene of major effect with contribution of additional polygenes. This study contributes with important knowledge on the resistance against CBB in Brazilian common bean cultivars as well as with molecular tools for confirmation of common bean hybrids.

Unraveling candidate genes underlying biomass digestibility in elephant grass (Cenchrus purpureus).

BACKGROUND: Elephant grass [Cenchrus purpureus (Schumach.) Morrone] is used for bioenergy and animal feed. In order to identify candidate genes that could be exploited for marker-assisted selection in elephant grass, this study aimed to investigate changes in predictive accuracy using genomic relationship information and simple sequence repeats for eight traits (height, green biomass, dry biomass, acid and neutral detergent fiber, lignin content, biomass digestibility, and dry matter concentration) linked to bioenergetics and animal feeding. RESULTS: We used single-step, genome-based best linear unbiased prediction and genome association methods to investigate changes in predictive accuracy and find candidate genes using genomic relationship information. Genetic variability (p < 0.05) was detected for most of the traits evaluated. In general, the overall means for the traits varied widely over the cuttings, which was corroborated by a significant genotype by cutting interaction. Knowing the genomic relationships increased the predictive accuracy of the biomass quality traits. We found that one marker (M28_161) was significantly associated with high values of biomass digestibility. The marker had moderate linkage disequilibrium with another marker (M35_202) that, in general, was detected in genotypes with low values of biomass digestibility. In silico analysis revealed that both markers have orthologous regions in other C4 grasses such as Setaria viridis, Panicum hallii, and Panicum virgatum, and these regions are located close to candidate genes involved in the biosynthesis of cell wall molecules (xyloglucan and lignin), which support their association with biomass digestibility. CONCLUSIONS: The markers and candidate genes identified here are useful for breeding programs aimed at changing biomass digestibility in elephant grass. These markers can be used in marker-assisted selection to grow elephant grass cultivars for different uses, e.g., bioenergy production, bio-based products, co-products, bioactive compounds, and animal feed.

Evaluating the impact of modeling the family effect for clonal selection in potato-breeding programs.

Because of its wide distribution, high yield potential, and short cycle, the potato has become essential for global food security. However, the complexity of tetrasomic inheritance, the high level of heterozygosity of the parents, the low multiplication rate of tubers, and the genotype-by-environment interactions impose severe challenges on tetraploid potato-breeding programs. The initial stages of selection take place in experiments with low selection accuracy for many of the quantitative traits of interest, for example, tuber yield. The goal of this study was to investigate the contribution of incorporating a family effect in the estimation of the total genotypic effect and selection of clones in the initial stage of a potato-breeding program. The evaluation included single trials (STs) and multi-environment trials (METs). A total of 1,280 clones from 67 full-sib families from the potato-breeding program at Universidade Federal de Lavras were evaluated for the traits total tuber yield and specific gravity. These clones were distributed in six evaluated trials that varied according to the heat stress level: without heat stress, moderate heat stress, and high heat stress. To verify the importance of the family effect, models with and without the family effect were compared for the analysis of ST and MET data for both traits. The models that included the family effect were better adjusted in the ST and MET data analyses for both traits, except when the family effect was not significant. Furthermore, the inclusion of the family effect increased the selective efficiency of clones in both ST and MET analyses via an increase in the accuracy of the total genotypic value. These same models also allowed the prediction of clone effects more realistically, as the variance components associated with family and clone effects within a family were not confounded. Thus, clonal selection based on the total genotypic value, combining the effects of family and clones within a family, proved to be a good alternative for potato-breeding programs that can accommodate the logistic and data tracking required in the breeding program.

Overcoming collinearity in path analysis of soybean [Glycine max (L.) Merr.] grain oil content.

Path analysis allows understanding the direct and indirect effects among traits. Multicollinearity in correlation matrices may cause a bias in path analysis estimates. This study aimed to: a) understand the correlation among soybean traits and estimate their direct and indirect effects on gain oil content; b) verify the efficiency of ridge path analysis and trait culling to overcome colinearity. Three different matrices with different levels of collinearity were obtained by trait culling. Ridge path analysis was performed on matrices with strong collinearity; otherwise, a traditional path analysis was performed. The same analyses were run on a simulated dataset. Trait culling was applied to matrix R originating the matrices R1 and R2. Path analysis for matrices R1 and R2 presented a high determination coefficient (0.856 and 0.832, respectively) and low effect of the residual variable (0.379 and 0.410 respectively). Ridge path analysis presented low determination coefficient (0.657) and no direct effects greater than the effects of the residual variable (0.585). Trait culling was more effective to overcome collinearity. Mass of grains, number of nodes, and number of pods are promising for indirect selection for oil content.

Adaptability and stability analyses of plants using random regression models.

The evaluation of cultivars using multi-environment trials (MET) is an important step in plant breeding programs. One of the objectives of these evaluations is to understand the genotype by environment interaction (GEI). A method of determining the effect of GEI on the performance of cultivars is based on studies of adaptability and stability. Initial studies were based on linear regression; however, these methodologies have limitations, mainly in trials with genetic or statistical unbalanced, heterogeneity of residual variances, and genetic covariance. An alternative would be the use of random regression models (RRM), in which the behavior of the genotypes is characterized as a reaction norm using longitudinal data or repeated measurements and information regarding a covariance function. The objective of this work was the application of RRM in the study of the behavior of common bean cultivars using a MET, based on Legendre polynomials and genotype-ideotype distances. We used a set of 13 trials, which were classified as unfavorable or favorable environments. The results revealed that RRM enables the prediction of the genotypic values of cultivars in environments where they were not evaluated with high accuracy values, thereby circumventing the unbalanced of the experiments. From these values, it was possible to measure the genotypic adaptability according to ideotypes, according to their reaction norms. In addition, the stability of the cultivars can be interpreted as variation in the behavior of the ideotype. The use of ideotypes based on real data allowed a better comparison of the performance of cultivars across environments. The use of RRM in plant breeding is a good alternative to understand the behavior of cultivars in a MET, especially when we want to quantify the adaptability and stability of genotypes.

Genetic insights into elephantgrass persistence for bioenergy purpose.

Persistence may be defined as high sustained yield over multi-harvest. Genetic insights about persistence are essential to ensure the success of breeding programs and any biomass-based project. This paper focuses on assessing the biomass yield persistence for bioenergy purpose of 100 elephantgrass clones measured in six growth seasons in Brazil. To assess the clones' persistence, an index based on random regression models and genotype-ideotype distance was proposed. Results suggested the existence of wide genetic variability between elephantgrass clones, and that the yield trajectories along the harvests generate genetic insights into elephantgrass clones' persistence and G x E interaction. A gene pool that acts over the biomass yield (regardless of the harvest) was detected, as well as other gene pools, which show differences on genes expression (these genes are the major responsible for clones' persistence). The lower and higher clones' persistence was discussed based on genome dosage effect and natural biological nitrogen fixation ability applied to bioenergy industry. The huge potential of energy crops necessarily is associated with genetic insights into persistence, so just this way, breeding programs could breed a new cultivar that fulfills the bioenergy industries.

Quantile regression for genome-wide association study of flowering time-related traits in common bean.

Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower-DFF; Days for flowering-DTF; Days to end of flowering-DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean.

Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production.

Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines. The objectives of this study were: to perform phenotypic and molecular characterization of 100 sweet sorghum accessions from the germplasm bank of the Embrapa Maize and Sorghum breeding program; to examine the relationship between the phenotypic and the molecular diversity matrices; and to infer about the population structure in the sweet sorghum accessions. Morphological and agro-industrial traits related to sugar and biomass production were used for phenotypic characterization, and single nucleotide polymorphisms (SNPs) were used for molecular diversity analysis. Both phenotypic and molecular characterizations revealed the existence of considerable genetic diversity among the 100 sweet sorghum accessions. The correlation between the phenotypic and the molecular diversity matrices was low (0.35), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and the molecular diversity analyses. Furthermore, the clusters obtained by the molecular diversity analysis were more consistent with the genealogy and the historic background of the sweet sorghum accessions than the clusters obtained through the phenotypic diversity analysis. The low correlation observed between the molecular and the phenotypic diversity matrices highlights the complementarity between the molecular and the phenotypic characterization to assist a breeding program.

Estimates of genetic parameters, genetic variability, and selection in the S1 generation of peach / Estimativas de parâmetros genéticos, variabilidade genética e seleção em geração S 1 de pessegueiros

ABSTRACT: The growing of peach in mild winter regions is made viable through the use of genotypes that have low need for cold conditions, and this is one of the main aims of breeding for these regions. Thus, the aims of this study were to estimate genetic parameters, evaluate genetic variability, and select families adapted to mild winter regions in the S1 generation of peach through mixed model methodology (REML/BLUP). For that purpose, 22 populations, 84 families, and 2090 individuals were evaluated for the following traits: bud burst rate (BR), node density (ND), plant height (PH), and trunk diameter (TD). Genetic variability was found for all the traits. Individual heritability in the broad sense was of low and medium magnitudes. The PH trait had positive genotypic correlation of high magnitude with TD. The ND trait had moderate negative genotypic correlation with PH and TD. Clustering by the Tocher method resulted in the formation of six mutually exclusive groups. Considering selection intensity of 25%, simultaneous selection for BR, ND, and TD led to predicted gains of 11.3% for BR, 9.7% for ND, -14.2% for PH, and -14.3% for TD, showing the great potential of the germplasm evaluated.

RESUMO: O cultivo do pessegueiro em regiões de inverno ameno é viabilizado pela utilização de genótipos que apresentam baixa necessidade de frio, sendo este um dos principais objetivos do melhoramento para essas regiões. Assim, os objetivos deste estudo foram estimar parâmetros genéticos, avaliar a variabilidade genética e selecionar famílias adaptadas a regiões de inverno ameno em geração S1 de pessegueiros via metodologia de modelos mistos (REML/BLUP). Para isso, 22 populações, 84 famílias e 2090 indivíduos foram avaliados quanto as características: taxa de brotação (TB), densidade de nós (DN), altura da planta (AP) e diâmetro do tronco (DT). Verificou-se variabilidade genética para todas as características. As herdabilidades individuais no sentido amplo foram de baixa e média magnitudes. A característica AP apresentou correlação genética positiva de magnitude elevada com DT. A característica DN apresentou correlação genética negativa moderada com AP e DT. O agrupamento pelo método de Tocher resultou na formação de seis grupos mutuamente excludentes. Considerando intensidade de seleção de 25%, a seleção simultânea para TB, DN e DT propiciou ganhos preditos de 11.3% para TB, 9.7% para DN, -14.2% para AP e -14.3% para DT, evidenciando o grande potencial do germoplasma avaliado.

Adaptabilidade e estabilidade e a produtividade de grãos em cultivares de feijão preto recomendadas no Brasil nas últimas cinco décadas / Adaptability and stability and grain yield of black common bean cultivars used in Brazil in the last five decades

RESUMO:O objetivo deste trabalho foi estudar os parâmetros de adaptabilidade e estabilidade fenotípica e avaliar o incremento na produtividade de grãos em genótipos de feijão preto, desenvolvidos pelos programas brasileiros de melhoramento genético entre os anos de 1960 a 2013. Os experimentos foram realizados considerando 38 cultivares e duas linhagens em quatro ambientes (Coimbra e Viçosa nas safras da seca e de inverno de 2013), usando um delineamento em blocos casualizados com três repetições. Os resultados evidenciaram incremento efetivo na produtividade de grãos, proporcionado pela recomendação de novas cultivares pelos programas de melhoramento de feijão do Brasil nas últimas cinco décadas. Além disso, a análise da interação GxA indicou que as cultivares recomendadas após o ano de 2005 foram as que apresentaram conjuntamente altas produtividades de grãos, ampla adaptabilidade e alta previsibilidade de comportamento.

ABSTRACT:The objective of this research was to study the parameters of adaptability and phenotypic stability and estimate the increase in grain yield in black common bean genotypes developed by brazilian breeding programs between the years 1960-2013. The experiments were carried out considering 38 cultivars and two lines in four different environments (Coimbra and Viçosa cities, and dry and winter seasons of 2013 year) by using a randomized block design with three replications. Results showed an effective increasing of the grain yield provided by the recommendation of new cultivars from different Brazilian breeding programs in the past five decades. In addition, the GxE analysis interaction indicated that cultivars recommended after the year 2005 were those with high average grain yield, wide adaptability and high predictability.

Minimum number and best combinations of harvests to evaluate accessions of tomato plants from germplasm banks

This study presents the minimum number and the best combination of tomato harvests needed to compare tomato accessions from germplasm banks. Number and weight of fruit in tomato plants are important as auxiliary traits in the evaluation of germplasm banks and should be studied simultaneously with other desirable characteristics such as pest and disease resistance, improved flavor and early production. Brazilian tomato breeding programs should consider not only the number of fruit but also fruit size because Brazilian consumers value fruit that are homogeneous, large and heavy. Our experiment was a randomized block design with three replicates of 32 tomato accessions from the Vegetable Germplasm Bank (Banco de Germoplasma de Hortaliças) at the Federal University of Viçosa, Minas Gerais, Brazil plus two control cultivars (Debora Plus and Santa Clara). Nine harvests were evaluated for four production-related traits. The results indicate that six successive harvests are sufficient to compare tomato genotypes and germplasm bank accessions. Evaluation of genotypes according to the number of fruit requires analysis from the second to the seventh harvest. Evaluation of fruit weight by genotype requires analysis from the fourth to the ninth harvest. Evaluation of both number and weight of fruit require analysis from the second to the ninth harvest.