Artificial neural networks as auxiliary tools for the improvement of bean plant architecture

Classification using a scale of visual notes is a strategy used to select erect bean plants in order to improve bean plant architectures. Use of morphological traits associated with the phenotypic expression of bean architecture in classification procedures may enhance selection. The objective of this study was to evaluate the potential of artificial neural networks (ANNs) as auxiliary tools in the improvement of bean plant architecture. Data from 19 lines were evaluated for 22 traits, in 2007 and 2009 winter crops. Hypocotyl diameter and plant height were selected for analysis through ANNs. For classification purposes, these lines were separated into two groups, determined by the plant architecture notes. The predictive ability of ANNs was evaluated according to two scenarios to predict the plant architecture - training with 2007 data and validating in 2009 data (scenario 1), and vice versa (scenario 2). For this, ANNs were trained and validated using data from replicates of the evaluated lines for hypocotyl diameter individually, or together with the mean height of plants in the plot. In each scenario, the use of data from replicates or line means was evaluated for prediction through previously trained and validated ANNs. In both scenarios, ANNs based on hypocotyl diameter and mean height of plants were superior, since the error rates obtained were lower than those obtained using hypocotyl diameter only. Lower apparent error rates were verified in both scenarios for prediction when data on the means of the evaluated traits were submitted to better trained and validated ANNs.

Diallel analysis to choose parents for black bean (Phaseolus vulgaris L.) breeding

In this study, conducted in two different seasons, we aimed to choose parents to obtain promising segregating populations for the extraction of black bean (Phaseolus vulgaris L.) lines that are superior in terms of disease resistance, plant architecture, and grain yield. Twelve parents were arranged in two groups to compose a partial diallel in a 5 x 7 scheme. Group 1 was composed of parents with black grains and erect plant architecture, while group 2 was composed of parents that had carioca grains and were resistant to the main fungal diseases that occur in the common bean. The following traits were evaluated: severity of angular leaf spot (ALS), plant architecture (PAG), and grain yield (YIELD). The data were analyzed according to a partial diallel model using parents and F₁ hybrids. In the genetic control of ALS and PAG, additive effects were predominant, while for YIELD, additive effects were predominant in one season and dominance effects were in another season, because it is a more complex trait than ALS and PAG. For YIELD, we observed an interaction between general combining ability and specific combining ability between seasons. The genes that control ALS, PAG, and YIELD were in eight of the 12 parents evaluated in the diallel. The cultivar 'BRS Estilo' is suitable to use as a parent in common bean breeding in terms of ALS, PAG and YIELD. Recurrent selection is the most recommended option for simultaneously breeding for PAG, YIELD, and resistance to angular leaf spot in bean culture.

Genetic progress resulting from forty-three years of breeding of the carioca common bean in Brazil

We aimed to evaluate 40 common bean cultivars recommended by various Brazilian research institutions between 1970 and 2013 and estimate the genetic progress obtained for grain yield and other agronomic traits. Additionally, we proposed a bi-segmented nonlinear regression model to infer the year in which breeding began to show significant gains in Brazil. The experiment was carried out in Viçosa/MG and Coimbra/MG, in the dry and winter seasons of 2013. For this, a randomized complete block design with three replications was employed. The following traits were evaluated: number of pods per plant (NPP); number of seeds per pod (NSP); 1000-seed weight (W1000); grain yield (Yield); plant architecture (Arch); and grain aspect (GA). Genotypic means were estimated over years using linear mixed models, and genetic gains were estimated using bi-segmented nonlinear regression models. In summary, the methodology proposed in the present study indicated that bean breeding programs in Brazil began to influence Yield beginning in 1990, resulting in a gain of 6.74% per year (68.15 kg/ha per year). The years from which estimated genetic progress for NPP (5.62% per year), NSP (4.59% per year), W1000 (2.08% per year), and GA (1.36% per year) began to increase were 1994, 1990, 1989, and 1986, respectively.

Morphoagronomic characterization and genetic diversity of a common bean RIL mapping population derived from the cross Rudá x AND 277

Recombinant inbred lines (RILs) are a valuable resource for building genetic linkage maps. The presence of genetic variability in the RILs is essential for detecting associations between molecular markers and loci controlling agronomic traits of interest. The main goal of this study was to quantify the genetic diversity of a common bean RIL population derived from a cross between Rudá (Mesoamerican gene pool) and AND 277 (Andean gene pool). This population was developed by the single seed descent method from 500 F2 plants until the F10 generation. Seven quantitative traits were evaluated in the field in 393 RILs, the parental lines, and five control cultivars. The plants were grown using a randomized block design with additional controls and three replicates. Significant differences were observed among the RILs for all evaluated traits (P < 0.01). A comparison of the RILs and parental lines showed significant differences (P < 0.01) for the number of days to flowering (DFL) and to harvest (DH), productivity (PROD) and mass of 100 beans (M100); however, there were no significant differences for plant architecture, degree of seed flatness, or seed shape. These results indicate the occurrence of additive x additive epistatic interactions for DFL, DH, PROD, and M100. The 393 RILs were shown to fall into 10 clusters using Tocher's method. This RIL population clearly contained genetic variability for the evaluated traits, and this variability will be crucial for future studies involving genetic mapping and quantitative trait locus identification and analysis.

Genetic potential of segregating populations of red beans conducted by the bulk method with selection

This study evaluated the performance and estimated the genetic potential of segregating populations of red bean. Twenty populations of the second cycle of recurrent selection for red bean breeding at Universidade Federal de Viçosa were advanced to the F5 generation in bulk with selection for grain appearance. Populations plus five controls were evaluated for grain yield in three dry seasons (2004, 2005, and 2007) in a 5 x 5 lattice design with three replications, in four 4-m long rows. In the mean of the three crops, populations formed three distinct groups in which some populations had a clearly superior grain yield. Populations 288RVCI, 291RVCI, 295RVCI, 297RVCI, 300RVCI, and 303RVCI were the most promising. Over generations, segregating populations by the bulk method with selection for grain appearance may have reduced variability in grain yield. The 300RVCI population deserves further attention as it combines variability, high mean, and a high probability of generating above-standard lines.

Similar Aggressiveness of Phenotypically and Genotypically Distinct Isolates of Sclerotinia sclerotiorum

Understanding how Sclerotinia sclerotiorum aggressiveness varies among isolates may be useful for breeding programs aimed at developing common bean cultivars resistant to white mold. The aggressiveness of 20 S. sclerotiorum isolates collected in common bean fields from four Brazilian states was tested against two common bean genotypes (Pérola and A195) using two inoculation methods. The isolates were characterized using 10 microsatellite (SSR) loci, mycelial compatibility groups (MCGs), partial sequences of the oxaloacetate acetylhydrolase (OAH) gene, and morphological traits. Twenty SSR and seven OAH haplotypes, 10 MCGs, and high variability in colony morphology were found. One isolate was more aggressive when inoculated on plants of the genotype A195, but all other isolates had similar aggressiveness. Aggressiveness was not related with MCGs, SSR, OAH haplotypes, mycelial pigmentation, growth rate, or sclerotia production.

Fungicide Sensitivity of Sclerotinia sclerotiorum: A Thorough Assessment Using Discriminatory Dose, EC50, High-Resolution Melting analysis, and Description of New Point Mutation Associated with Thiophanate-Methyl Resistance

Thiophanate-methyl (TM), fluazinam, and procymidone are fungicides extensively used for white mold control of common bean in Brazil. We assessed the sensitivity of Brazilian isolates of Sclerotinia sclerotiorum to these three fungicides using discriminatory doses and concentration that results in 50% mycelial growth inhibition (EC₅₀) values. In total, 282 isolates from the most important production areas were screened and none was resistant to fluazinam or procymidone. The EC₅₀ values varied from 0.003 to 0.007 and from 0.11 to 0.72 μg/ml for fluazinam and procymidone, respectively. One isolate was resistant to TM. The EC₅₀ of the TM-resistant isolate was greater than 100 μg/ml, whereas the EC₅₀ of the sensitive isolates varied from 0.38 to 2.23 μg/ml. The TM-resistant isolate had a L240F mutation in the β-tubulin gene. This is the first report of mutation at codon 240 causing resistance to a benzimidazole fungicide in S. sclerotiorum. The high-resolution melting analysis allowed the distinction of TM-sensitive and -resistant isolates by specific melting peaks and curves. The TM-resistant isolate had mycelial growth, sclerotia production, and aggressiveness comparable with that of the sensitive isolates, indicating that this genotype will likely compete well against sensitive isolates in the field. This study demonstrates that resistance to TM, fluazinam, and procymidone is nonexistent or rare. Resistance management practices should be implemented, however, to delay the spread of TM-resistant genotypes.

Potential of hypocotyl diameter in family selection aiming at plant architecture improvement of common bean

Cultivars of common bean with more erect plant architecture and greater tolerance to degree of lodging are required by producers. Thus, to evaluate the potential of hypocotyl diameter (HD) in family selection for plant architecture improvement of common bean, the HDs of 32 F2 plants were measured in 3 distinct populations, and the characteristics related to plant architecture were analyzed in their progenies. Ninety-six F2:3 families and 4 controls were evaluated in a randomized block design, with 3 replications, analyzing plant architecture grade, HD, and grain yield during the winter 2010 and drought 2011 seasons. We found that the correlation between the HD of F2 plants and traits related to plant architecture of F2:3 progenies were of low magnitude compared to the estimates for correlations considering the parents, indicating a high environmental influence on HD in bean plants. There was a predominance of additive genetic effects on the determination of hypocotyl diameter, which showed higher precision and accuracy compared to plant architecture grade. Thus, this characteristic can be used to select progenies in plant architecture improvement of common beans; however, selection must be based on the means of at least 39 plants in the plot, according to the results of repeatability analysis.

Adaptation and Resistance to Diseases in Brazil of Putative Sources of Common Bean Resistance to White Mold

Common bean breeding programs for white mold (WM) resistance are in their initial stages in Brazil. Sources of partial resistance to WM are available abroad but their performance in Brazil is unknown. In two greenhouse (straw test) and three field experiments conducted in three districts in the state of Minas Gerais, Brazil, we evaluated a total of 23 lines with putative WM resistance with the objective to select lines with resistance to WM and other diseases associated with high yield potential. Two field-resistant local lines, two susceptible local cultivars, and two susceptible international lines were also included in the study. In the greenhouse, Cornell 605, A 195, and G122 were among the lines with the highest partial resistance to WM. In the field, these three lines were highly resistant to WM and had intermediate resistance or were resistant to anthracnose, angular leaf spot, rust, and Fusarium wilt. Cornell 605 and A 195 had high-yield potential but G122 yielded 47% less than the local lines under WM pressure. Our results suggest that Cornell 605 and A 195 are the most useful sources of resistance to WM for use in common bean breeding programs in Brazil.

Effect of generations and environments in the analysis of a partial diallel to improve bean earliness

The objective of this study was to select genitors based on F1 and F2 generations, evaluated in different environments, to obtain segregating populations for the identification of strains showing improved earliness, yield, and carioca-type grains. Nine bean strains were crossed in a partial diallel scheme (4 x 5), in which group 1 included 4 strains with early cycles and group 2 included 5 elite strains. The F1 and F2 generations and the genitors were assessed in Coimbra and Viçosa in randomized blocks with 3 replications. The following characteristics were evaluated: days between sowing and emergence, and grain yield. We observed an interaction between the effects of general combining ability and specific combining ability with the environments (crop, location, and generation) for both grain earliness and yield. Genetic analysis of earliness revealed a predominance of additive effects and grain yield dominance effects. The strain Goiano Precoce may be used as a genitor in breeding programs to improve earliness, while strains RP1 and VC33 can be used to increase grain yield. We observed genetic complementation between strains Goiano Precoce and RP1, BRSMG Madrepérola and BRS Estilo for earliness and between RP1 and Rosinha Precoce for grain yield.

Genetic improvement of plant architecture in the common bean

Knowledge of genetic control of plant architecture in the common bean can help breeders define the most adequate breeding strategy to optimize gains. We examined genetic control of plant architecture in the common bean by means of partial diallel crosses. Fourteen bean lines were crossed under a partial diallel scheme, in which group 1 was composed of 8 erect plant lines and group 2 of 6 carioca-type grain lines. The F1 plants from the crosses and the 14 parents were evaluated during spring (March sowing) for the characteristics plant architecture score, hypocotyl diameter, mean plant height, and grain yield. The additive effects were found to predominate in the genetic control of plant architecture score and hypocotyl diameter. Thus, selection of more erect plants can be done in early generations. Heritability estimate in a wide sense was greater for hypocotyl diameter (0.81) than for plant architecture score (0.60), showing that the latter is a more complex characteristic than the former. Hypocotyl diameter has the potential to be used in the selection of more erect plants, either by considering selection between and within families, or by combined or phenotypic recurrent selection. The reason for this is that the diameter measurements are taken from individual plants inside the plots.

Distinction between plant samples according to allele dosage by semiquantitative polymerase chain reaction

The lack of informativity of samples from heterozygotic individuals is one of the hindrances in the mapping of quantitative trait loci of outbred populations, since it is not normally possible to identify the origin of each allele. One way to include these individuals in analyses would be to genotype their endosperm, considering that a heterozygote (Aa) has AAa or Aaa endosperm, when the female genitor donates the A or a allele, respectively. We used semiquantitative polymerase chain reaction to determine allele dosages in DNA mixtures, by simulating the observed conditions for endospermic tissue. Semiquantitative polymerase chain reaction on agarose gels, along with regression analysis, allowed differentiation of the samples according to the amount of DNA. This type of information will help decrease the number of non-informative individuals in quantitative trait locus mapping of outbred populations, thereby increasing mapping accuracy.