Publications by authors named "Carlos Alberto Scapim"

10 Publications

  • Page 1 of 1

A Deep Learning Approach to Population Structure Inference in Inbred Lines of Maize.

Front Genet 2020 24;11:543459. Epub 2020 Nov 24.

Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil.

Analysis of population genetic variation and structure is a common practice for genome-wide studies, including association mapping, ecology, and evolution studies in several crop species. In this study, machine learning (ML) clustering methods, K-means (KM), and hierarchical clustering (HC), in combination with non-linear and linear dimensionality reduction techniques, deep autoencoder (DeepAE) and principal component analysis (PCA), were used to infer population structure and individual assignment of maize inbred lines, i.e., dent field corn ( = 97) and popcorn ( = 86). The results revealed that the HC method in combination with DeepAE-based data preprocessing (DeepAE-HC) was the most effective method to assign individuals to clusters (with 96% of correct individual assignments), whereas DeepAE-KM, PCA-HC, and PCA-KM were assigned correctly 92, 89, and 81% of the lines, respectively. These findings were consistent with both Silhouette Coefficient (SC) and Davies-Bouldin validation indexes. Notably, DeepAE-HC also had better accuracy than the Bayesian clustering method implemented in InStruct. The results of this study showed that deep learning (DL)-based dimensional reduction combined with ML clustering methods is a useful tool to determine genetically differentiated groups and to assign individuals into subpopulations in genome-wide studies without having to consider previous genetic assumptions.
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http://dx.doi.org/10.3389/fgene.2020.543459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7732446PMC
November 2020

Genome-Wide Prediction of Complex Traits in Two Outcrossing Plant Species Through Deep Learning and Bayesian Regularized Neural Network.

Front Plant Sci 2020 27;11:593897. Epub 2020 Nov 27.

Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil.

Genomic selection models were investigated to predict several complex traits in breeding populations of L. and Labill. For this, the following methods of Machine Learning (ML) were implemented: (i) Deep Learning (DL) and (ii) Bayesian Regularized Neural Network (BRNN) both in combination with different hyperparameters. These ML methods were also compared with Genomic Best Linear Unbiased Prediction (GBLUP) and different Bayesian regression models [Bayes A, Bayes B, Bayes Cπ, Bayesian Ridge Regression, Bayesian LASSO, and Reproducing Kernel Hilbert Space (RKHS)]. DL models, using Rectified Linear Units (as the activation function), had higher predictive ability values, which varied from 0.27 (pilodyn penetration of 6 years old eucalypt trees) to 0.78 (flowering-related traits of maize). Moreover, the larger mini-batch size (100%) had a significantly higher predictive ability for wood-related traits than the smaller mini-batch size (10%). On the other hand, in the BRNN method, the architectures of one and two layers that used only the pureline function showed better results of prediction, with values ranging from 0.21 (pilodyn penetration) to 0.71 (flowering traits). A significant increase in the prediction ability was observed for DL in comparison with other methods of genomic prediction (Bayesian alphabet models, GBLUP, RKHS, and BRNN). Another important finding was the usefulness of DL models (through an iterative algorithm) as an SNP detection strategy for genome-wide association studies. The results of this study confirm the importance of DL for genome-wide analyses and crop/tree improvement strategies, which holds promise for accelerating breeding progress.
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http://dx.doi.org/10.3389/fpls.2020.593897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728740PMC
November 2020

Genetic Progress of Seed Yield and Nitrogen Use Efficiency of Brazilian Common Bean Cultivars Using Bayesian Approaches.

Front Plant Sci 2020 5;11:1168. Epub 2020 Aug 5.

Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil.

Common bean ( L.) is one of the most important crops worldwide and is considered an essential source of proteins, fibers, and minerals in the daily diet of several countries. Nitrogen (N) is considered the most important nutrient for common bean crop. On the other hand, the reduction of chemical fertilizers is a global challenge, and the development of cultivars with more N use efficiency (NUsE) is considered one of the main strategies to reduce the amount of N fertilizers. Genetic progress of NUsE has been reported in several crops; however, there was still no quantity in common bean. In this study, our goal was to analyze the genetic progress of seed yield (SY) and NUsE-related traits of 40 common bean cultivars release from 1970 to 2017 in eight environments under low (zero) or high N (40 kg ha) in top-dressing. Genetic progress, principal component analysis, correlations among traits, and cultivar stability were analyzed using Bayesian approaches. The lowest values of the deviance information criterion (DIC) for the full model tested indicated the presence of the genotype × N × environment interaction for all evaluated traits. Nitrogen utilization efficiency (NUtE) and nitrogen uptake efficiency (NUpE) were the traits that most contributed to discriminate cultivars. The genetic progress of SY under high N (0.53% year, 95% HPD = 0.39; 0.65% year) was similar to that obtained in low N conditions (0.48% year, 95% HPD = 0.31; 0.64% year). These results indicate that modern cultivars do not demand more N fertilizers to be more productive. In addition, we observed a high genetic variability for NUsE-related traits, but there was no genetic progress for these variables. SY showed negative correlation with seed protein content (Prot) in both N conditions, and there was no reduction in Prot in modern cultivars. Both modern and old cultivars showed adaptability and stability under contrasting N conditions. Our study contributed to improve our knowledge about the genetic progress of common bean breeding program in Brazil in the last 47 years, and our data will help researchers to face the challenge of increase NUsE and Prot in the next few years.
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http://dx.doi.org/10.3389/fpls.2020.01168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419646PMC
August 2020

Azospirillum brasilense promotes increases in growth and nitrogen use efficiency of maize genotypes.

PLoS One 2019 18;14(4):e0215332. Epub 2019 Apr 18.

Department of Agronomy, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.

The development of cultivars with an improved nitrogen use efficiency (NUE) together with the application of plant growth-promoting bacteria is considered one of the main strategies for reduction of fertilizers use. In this sense, this study: i) evaluated the effect of Azospirillum brasilense on the initial development of maize genotypes; ii) investigated the influence of A. brasilense inoculation on NUE under nitrogen deficit; and iii) sought for more NUE genotypes with higher responsiveness to A. brasilense inoculation. Twenty-seven maize genotypes were evaluated in three independent experiments. The first evaluated the initial development of maize genotypes with and without A. brasilense (strain Ab-V5) inoculation of seeds on germination paper in a growth chamber. The second and third experiments were carried out in a greenhouse using Leonard pots and pots with substrate, respectively, and the genotypes were evaluated at high nitrogen, low nitrogen and low nitrogen plus A. brasilense Ab-V5 inoculation. The inoculation of seeds with A. brasilense Ab-V5 intensified plant growth, improved biochemical traits and raised NUE under nitrogen deficit. The inoculation of seeds with A. brasilense can be considered an economically viable and environmentally sustainable strategy for maize cultivation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215332PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472877PMC
January 2020

Genome wide association study for gray leaf spot resistance in tropical maize core.

PLoS One 2018 28;13(6):e0199539. Epub 2018 Jun 28.

Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Paraná, Brasil.

Gray leaf spot is a maize foliar disease with worldwide distribution and can drastically reduce the production in susceptible genotypes. Published works indicate that resistance to gray leaf spot is a complex trait controlled by multiple genes, with additive effect and influenced by environment. The aim of this study was to identify genomic regions, including putative genes, associated with resistance to gray leaf spot under natural conditions of disease occurrence. A genome wide association study was conducted with 355,972 single nucleotide polymorphism markers on a phenotypic data composed by 157 tropical maize inbred lines, evaluated at Maringá -Brazil. Seven single nucleotide polymorphisms were significantly associated with gray leaf spot, some of which were localized to previously reported quantitative trait loci regions. Three gene models linked to the associated single nucleotide polymorphism were expressed at flowering time and tissue related with gray leaf spot infection, explaining a considerable proportion of the phenotypic variance, ranging from 0.34 to 0.38. The gene model GRMZM2G073465 (bin 10.07) encodes a cysteine protease3 protein, gene model GRMZM2G007188 (bin 1.02) expresses a rybosylation factor-like protein and the gene model GRMZM2G476902 (bin 4.08) encodes an armadillo repeat protein. These three proteins are related with plant defense pathway. Once these genes are validated in next studies, they will be useful for marker-assisted selection and can help improve the understanding of maize resistance to gray leaf spot.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199539PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6023161PMC
December 2018

Genome-wide association mapping for flowering and maturity in tropical soybean: implications for breeding strategies.

Breed Sci 2017 Dec 16;67(5):435-449. Epub 2017 Nov 16.

Dow Agrosciences, Rod. Anhanguera S/N Km 330, Cravinhos SP, 14140-000, Brazil.

Knowledge of the genetic architecture of flowering and maturity is needed to develop effective breeding strategies in tropical soybean. The aim of this study was to identify haplotypes across multiple environments that contribute to flowering time and maturity, with the purpose of selecting desired alleles, but maintaining a minimal impact on yield-related traits. For this purpose, a genome-wide association study (GWAS) was undertaken to identify genomic regions that control days to flowering (DTF) and maturity (DTM) using a soybean association mapping panel genotyped for single nucleotide polymorphism (SNP) markers. Complementarily, yield-related traits were also assessed to discuss the implications for breeding strategies. To detect either stable or specific associations, the soybean cultivars (N = 141) were field-evaluated across eight tropical environments of Brazil. Seventy-two and forty associations were significant at the genome-wide level relating respectively to DTM and DTF, in two or more environments. Haplotype-based GWAS identified three haplotypes (Gm12_Hap12; Gm19_Hap42 and Gm20_Hap32) significantly co-associated with DTF, DTM and yield-related traits in single and multiple environments. These results indicate that these genomic regions may contain genes that have pleiotropic effects on time to flowering, maturity and yield-related traits, which are tightly linked with multiple other genes with high rates of linkage disequilibrium.
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http://dx.doi.org/10.1270/jsbbs.17024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790042PMC
December 2017

A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis.

PLoS One 2017 2;12(2):e0171105. Epub 2017 Feb 2.

Dow Agrosciences, Rod. Anhanguera, Cravinhos, SP, Brazil.

Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information. The soybean cultivars (N = 169) were field-evaluated across four locations of southern Brazil. The genome-wide haplotype association analysis (941 haplotypes) identified eleven, seventeen and fifty-nine SNP-based haplotypes significantly associated with SY, SW and PH, respectively. Although most marker-trait associations were environment and trait specific, stable haplotype associations were identified for SY and SW across environments (i.e., haplotypes Gm12_Hap12). The haplotype block 42 on Chr19 (Gm19_Hap42) was confirmed to be associated with PH in two environments. These findings enable us to refine the breeding strategy for tropical soybean, which confirm that haplotype-based GWAS can provide new insights on the genetic determinants that are not captured by the single-marker approach.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171105PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289539PMC
August 2017

A collection of popcorn as a reservoir of genes for the generation of lineages.

Mol Biotechnol 2013 Mar;53(3):300-7

Department of Cell Biology and Genetics, State University of Maringá, Maringá, PR, Brazil.

In the present study, we analyze the genetic structure and diversity among accessions of popcorn obtained from the CIMMYT International Maize and Wheat Improvement Center that represent the diversity available for current use by breeding programs. The main objectives were to identify SSR loci that were the best indicators of genetic diversity, to measure the genetic diversity within popcorn genotypes, and to analyze the genetic structure of the promising populations destined for use in breeding programs. The mean gene diversity of all SSR loci was 0.6352. An extremely high population differentiation level was detected (F(st) = 0.3152) with F(st) for each locus ranging from 0.1125 (Umc1229) to 0.4870 (Umc1755). Analyzing the genetic structure of eight popcorn accessions was especially important for identifying both SSR loci with high levels of heterozygosity and genotypes showing high heterozygosity (BOYA462 and ARZM13 050). This analysis should be the medium and long-term selection goal for the generation of inbred lines and the future production of new cultivars. Plant accessions ARZM05 083, ARZM13 050, and URUG298 may also be useful varieties that exhibit important agronomic characteristics that can be used through crosses to broaden the genetic basis of popcorn.
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http://dx.doi.org/10.1007/s12033-012-9527-6DOI Listing
March 2013

Stress-induced synthesis of proline confers tolerance to water deficit in transgenic wheat.

J Plant Physiol 2007 Oct 2;164(10):1367-76. Epub 2007 Jul 2.

Universidade Federal do Paraná-Campus Palotina, Rua Pioneiro, 2153, CEP 85950-000 Palotina-Pr, Brazil.

Water deficit is one of the main abiotic factors that affect spring wheat planted in subtropical regions. Accumulation of proline appears to be a promising approach to maintain the productivity of plants under stress condition. However, morphological alterations and growth reduction are observed in transgenic plants carrying genes coding for osmoprotectants controlled by constitutive promoters. We report here the effects of water deficit on wheat plants transformed with the Vigna aconitifolia Delta(1)-pyrroline-5-carboxylate synthetase (P5CS) cDNA that encodes the key regulatory enzyme in proline biosynthesis, under the control of a stress-induced promoter complex-AIPC. Transgenic wheat plants submitted to 15 days of water shortage presented a distinct response. We have found that drought resulted in the accumulation of proline. The tolerance to water deficit observed in transgenic plants was mainly due to protection mechanisms against oxidative stress and not caused by osmotic adjustment.
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http://dx.doi.org/10.1016/j.jplph.2007.05.001DOI Listing
October 2007

Genetic divergence of the common bean (Phaseolus vulgaris L.) group Carioca using morpho-agronomic traits by multivariate analysis.

Hereditas 2007 Mar;144(1):1-9

Departamento de Agronomia, Universidade Estadual de Maringá, Maringá-Paraná, Brazil.

The objective of this study was to evaluate the genetic divergence among the common bean group Carioca by the Tocher method (based on Mahalanobis distance) and graphic dispersion of canonic variables, aiming to identify populations with wide genetic variability. Eighteen genotypes were evaluated in four seasons using a randomized block design with four replications. The mean weight of 100 seeds, in three experiments, and the mean number of pods per plant, in one experiment, were the most important characteristics for the genetic divergence, representing more than 46% of the total variation in the first canonic variable. The first two canonic variables were sufficient to explain about 88.23% of the total variation observed in the average of the four environments. The results showed that CNFC 8008 and CNFC 8009 genotypes presented the best yield averages in all the experiments. While Pérola, Princesa and CNFC 8005 cultivars were the most dissimilar for morpho-agronomic traits. Therefore, the combinations of PérolaxCNFC 8008, CNFC 8005xCNFC 8009, PérolaxCNFC 8009, PrincesaxCNFC 8008 and PrincesaxCNFC 8009 were indicated for interpopulational breeding.
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http://dx.doi.org/10.1111/j.2006.0018-0661.01943.xDOI Listing
March 2007