No abstract

The present study evaluated the importance of auxiliary traits of a principal trait based on phenotypic information and previously known genetic structure using computational intelligence and machine learning to develop predictive tools for plant breeding. Data of an F2 population represented by 500 individuals, obtained from a cross between contrasting homozygous parents, were simulated. Phenotypic traits were simulated based on previously established means and heritability estimates (30%, 50%, and 80%); traits were distributed in a genome with 10 linkage groups, considering two alleles per marker. Four different scenarios were considered. For the principal trait, heritability was 50%, and 40 control loci were distributed in five linkage groups. Another phenotypic control trait with the same complexity as the principal trait but without any genetic relationship with it and without pleiotropy or a factorial link between the control loci for both traits was simulated. These traits shared a large number of control loci with the principal trait, but could be distinguished by the differential action of the environment on them, as reflected in heritability estimates (30%, 50%, and 80%). The coefficient of determination were considered to evaluate the proposed methodologies. Multiple regression, computational intelligence, and machine learning were used to predict the importance of the tested traits. Computational intelligence and machine learning were superior in extracting nonlinear information from model inputs and quantifying the relative contributions of phenotypic traits. The R2 values ranged from 44.0% - 83.0% and 79.0% - 94.0%, for computational intelligence and machine learning, respectively. In conclusion, the relative contributions of auxiliary traits in different scenarios in plant breeding programs can be efficiently predicted using computational intelligence and machine learning.

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.

Genomic‐wide selection (GWS) consists of the use of a large number of molecular markers for the prediction of genetic values and has been shown to be highly relevant for genetic improvement. The objective of this work was to evaluate and compare the predictive performance of statistical (ridge regression‐best linear unbiased predictor [RR‐BLUP] and BayesB) and machine learning methods through GWS in simulated populations with traits presenting different levels of heritability and quantitative trait loci (QTL) numbers in the presence of dominant and epistatic effects. The simulated genome of population F2 was formed by 1,000 individuals and genotyped with 2,010 single nucleotide polymorphism (SNP) markers. Twenty‐six traits were simulated considering QTL numbers ranging from two to 88 and heritabilities of .3 and .6. The selective and predictive performances were evaluated using the multilayer perceptron (MLP), radial basis function (RBF), decision trees (DT), bagging (BA), random forest (RF), and boosting (BO) machine learning models and the classical RR‐BLUP and BayesB methods. A high effect of heritability was observed for the results of selective accuracy when compared to the increased QTL number. In addition, the selective accuracy based on the number of QTL demonstrates that the application of alternative machine learning models, such as RBF, BA, BO, and RF, can be suitable for the analysis according to QTL number. Machine learning methods are powerful tools for predicting genetic values with epistatic gene control in traits with different degrees of heritability and different numbers of controlling genes.

The performance of genotypes in a wide range of environments can be affected by extensive genotype × environment (G × E) interactions, making the subdivision of the testing environments into relatively more homogeneous groups of locations (mega‐environments) a necessary strategy. The genotype main effects + genotype × environment interaction biplot method (GGE) allows identification of mega‐environments and selection of stable genotypes adapted to specific environments and mega‐environments. The objectives of this study were to identify mega‐environments regarding sorghum [Sorghum bicolor (L.) Moench] grain yield and demonstrate that the GGE biplot method can identify essential locations for conducting tests in different mega‐environments. A total of 22 competition trials of grain sorghum genotypes were conducted over three crop seasons across several production locations in Brazil. A total of 25, 22, and 30 genotypes were evaluated during the first, second, and third crop seasons, respectively. After identifying the presence of G × E interactions, the data were subjected to adaptability and stability analyses using the GGE biplot method. A phenotypic correlation network was used to express functional relationships between environments. The GGE biplot was found to be an efficient approach for identifying three mega‐environments in grain sorghum in Brazil, selecting representative and discriminative environments, and recommending more adaptive and stable grain sorghum genotypes.