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.

Genomic selection models were investigated to predict several complex traits in breeding populations of Zea mays L. and Eucalyptus globulus 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.

ABSTRACT. Eucalyptus cladocalyx F. Muell is a tree endemic to southern Australia and is distributed across four isolated regions: Kangaroo Island, southern Flinders Ranges, and two geographical zones in Eyre Peninsula. E. cladocalyx is capable of growing under extreme environmental conditions, including dry and saline soils. The objective of this study was to analyze genetic diversity in 45 half-sib families planted in northern Chile that are distributed across five different zones (provenances). Genetic variability was assessed using ISSR (Inter Simple Sequence Repeat) molecular markers. The results showed low levels of genetic diversity within populations (He = 0.113 to 0.268) in contrast with other Eucalyptus species. In addition, there was a significant genetic differentiation among provenances (Φst = 0.14); populations from the Kangaroo Island provenance showed more differentiation than any other population. These results are in agreement with previous studies of the species. Our study revealed that Chilean resources are a representative sample of Australian populations; therefore, the germplasm planted in northern Chile would be sufficient for the development of improvement programs. ISSR-Marker technology could be an alternative to identify genotypes of interest in material selection.

In the dry regions of Chile, prolific flowering from forest plantation is particularly advantageous for honey production, in order to supplement the erratic flowering in native plants. Eucalyptus cladocalyx is a species suitable for areas with low water availability and their flowers provide a reliable source for the production of honey. The aim of this study was to examine the heritability of flowering intensity in 49 open-pollinated families of E. cladocalyx in southern Atacama Desert, Chile, with the view to the selection for prolific flowering, but with minimal impact on precocious flowering. The Bayesian variance component estimation model was assumed using the Gibbs sampling algorithm. Threshold models were fitted to flowering data (bi-character model). Flowering intensity was found to be highly heritable (posterior mean: h 2 = 0.48; and credible interval: 0.41-0.56). The posterior mean of the genetic correlation between flowering precocity and intensity was positive (r = 0.45) and according to the credible interval (0.341-0.542), it was significantly different from zero, indicating that selection on breeding values of early flowering at age three, would have significant and positive impact on flowering intensity 5 years later (or in 8-year-old trees). These results are important for the start of a small-scale breeding program for the species in southern Atacama Desert. The genetic variability found in these breeding populations may be used for breeding purposes in regions where arid environmental conditions are limiting to the establishment of eucalypts trees.

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Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

Maize is one of the species with greater genetic diversity among cereals and possibly the most diverse crop species known. Accessing this variability is essential for maize breeding, allowing breeders to achieve progress of yield increasing, overcome environmental challenges or deal with pests and diseases. Among the maize diseases, southern rust is one of the most important, causing significant losses in yield and presenting severe epidemics worldwide. In the present study, the AFLP technique was applied to analyze population structure and genetic diversity among 145 tropical maize inbred lines, and to test for preliminary evidence of association between AFLP markers and the reaction to southern rust. Disease severity was evaluated in two crop seasons and the accessions were genotyped through AFLP using four primer combinations.