Samuel B Fernandes

University of Arkansas | U of A

Key message: We compare genomic selection methods that use correlated traits to help predict biomass yield in sorghum, and find that trait-assisted genomic selection performs best. Genomic selection (GS) is usually performed on a single trait, but correlated traits can also help predict a focal trait through indirect or multi-trait GS. In this stu...

Key message We demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree of observed improvement is highly dependent on the genetic architecture of the trait. Abstract Breeders commonly use genetic markers to predict the performance of untested individuals as a way to imp...

Understanding how plants adapt to specific environmental changes and identifying genetic markers associated with phenotypic plasticity can help breeders develop plant varieties adapted to a rapidly changing climate. Here, we propose the use of marker effect networks as a novel method to identify markers associated with environmental adaptability. T...

Maintaining the past decades current genetic gains for tree species is a challenging task for foresters and tree breeders due to biotic and abiotic factors. Planting a mixture of genotypes or clonal composites can be an alternative to increase the phytosanitary security and yield of forest plantations. These clonal composites are more complex than...

K loss in runoff represents a potential financial concern since fertilizer‐K is routinely applied to sustain optimal crop K nutrition and yield potential. Our research objectives were to quantify and characterize the soluble‐K loss in runoff from fields used for continuous cotton (Gossypium hirsutum L.) production while determining if time of year...

Breeders commonly use genetic markers to predict the performance of untested individuals as a way to improve the efficiency of breeding programs. These genomic prediction models have almost exclusively used single nucleotide polymorphisms (SNPs) as their source of genetic information, even though other types of markers exist, such as structural var...

Understanding how plants adapt to specific environmental changes and identifying genetic markers associated with phenotypic plasticity can help breeders develop plant varieties adapted to a rapidly changing climate. Here, we propose the use of marker effect networks as a novel method to identify markers associated with environmental adaptability. T...

Genomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance-controlling loci in association studies will be critical for future breeding efforts. Two statistical approaches that have already b...

The ability to accurately quantify the simultaneous effect of multiple genomic loci on multiple traits is now possible due to current and emerging high‐throughput genotyping and phenotyping technologies. To date, most efforts to quantify these genotype‐to‐phenotype relationships have focused on either multi‐trait models that test a single marker at...

Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, little is known about the genetic basis for natur...

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modelling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotypin...

Stomata are adjustable pores on leaf surfaces that regulate the trade-off of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited discoveries about the genetic basis of stomatal patterning. A high...

Genomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance quantitative trait loci (vQTL) in association studies will be critical for future breeding efforts. Two statistical approaches that...

Stomata allow CO 2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO 2 and water fluxes and are essential to maintenance of water-use efficiency (WUE). However, little is known about the genetic basis for n...

Previous studies have found that maximum quantum yield of CO2 assimilation (ΦCO2,max,app) declines in lower canopies of maize and Miscanthus, a maladaptive response to self-shading. These observations were limited to single genotypes, leaving it unclear that the maladaptive shade response is a general property of this C4 grass tribe, the Andropogon...

Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analysed ~13 million variants identified from whole-genome resequencing of 499 sorghum lines together with 25 million variants previously identified in 1,2...

Quantification of the simultaneous contributions of loci to multiple traits, a phenomenon called pleiotropy, is facilitated by the increased availability of high-throughput genotypic and phenotypic data. To understand the prevalence and nature of pleiotropy, the ability of multivariate and univariate genome-wide association study (GWAS) models to d...

Sorghum is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is also studied as a feedstock for biofuel and forage. Mechanistic modelling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping for discove...

Background Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy). As the demand for multivariate analyses increases,...

Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum...

Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum...

Maize inflorescence is a complex phenotype that involves the physical and developmental interplay of multiple traits. Given the evidence that genes could pleiotropically contribute to several of these traits, we used publicly available maize data to assess the ability of multivariate genome-wide association study (GWAS) approaches to identify pleio...

Background: Exserohilum turcicum is an important pathogen of both sorghum and maize, causing sorghum leaf blight and northern corn leaf blight. Because the same pathogen can infect and cause major losses for two of the most important grain crops, it is an ideal pathosystem to study plant-pathogen evolution and investigate shared resistance mechani...

Motivation Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy). As the demand for multivariate analyses increases,...

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height...

Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13 million variants identified from whole genome resequencing of 468 sorghum lines together with 25 million variants previously identified in 1,21...

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum ( Sorghum bicolor (L.) Moench] lines, which had been genotyped with 100,435 SNP markers, for plant heigh...

We have previously hypothesized that relatively small and isolated rural communities may experience founder effects, defined as the genetic ramifications of small population sizes at the time of a community's establishment. To explore this, we used an Illumina Infinium Omni2.5Exome-8 chip to collect data from 157 individuals from four Illinois comm...

Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how d...

Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. Though selection keeps deleterious mutations rare, their complete removal from the genome is impeded due to lack of recombination, drift, and t...

The common bean is a food with high mineral content. Of the various types of beans cultivated in Brazil, carioca type beans are the most consumed. The aim of this study was to identify promising common bean populations with an emphasis toward the selection of carioca type bean lines with high calcium content. We also aimed to verify whether and how...

The aim of this study was to undertake the theoretical derivations of non-parametric methods, which use linear regressions based on rank order, for stability analyses. These methods were extension different parametric methods used for stability analyses and the result was compared with a standard non-parametric method. Intensive computational metho...