SimpleMating: R-package for prediction and optimization of breeding crosses using genomic selection.

Selecting parents and crosses is a critical step for a successful breeding program. The ability to design crosses with high means that will maintain genetic variation in the population is the goal for long-term applications. Herein, we describe a new computational package for mate allocation in a breeding program.

Understanding the genetic basis of blueberry postharvest traits to define better breeding strategies.

Blueberry (Vaccinium spp.) is among the most-consumed soft fruit and has been recognized as an important source of health-promoting compounds. Highly perishable and susceptible to rapid spoilage due to fruit softening and decay during postharvest storage, modern breeding programs are looking to maximize the quality and extend the market life of fresh blueberries.

Molecular breeding of flower load related traits in dioecious autotetraploid .

Unlabelled: Flowering plants exhibit a wide range of sexual reproduction systems, with the majority being hermaphroditic. However, some plants, such as (kiwiberry), have evolved into dioecious species with distinct female and male vines. In this study, we investigated the flower load and growth habits of female kiwiberry genotypes to identify the genetic basis of high yield with low maintenance requirements.

Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.

Background: Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis.

AGHmatrix: genetic relationship matrices in R.

Motivation: The resemble between relatives computed from pedigree and genomic data is an important resource for geneticists and ecologists, who are interested in understanding how genes influence phenotypic variation, fitness adaptation, and population dynamics.

Results: The AGHmatrix software is an R package focused on the construction of pedigree (A matrix) and/or molecular markers (G matrix), with the possibility of building a combined matrix of pedigree corrected by molecular markers (H matrix). Designed to estimate the relationships for any ploidy level, the software also includes auxiliary functions related to filtering molecular markers, and checks pedigree errors in large data sets.

Terpene volatiles mediates the chemical basis of blueberry aroma and consumer acceptability.

Flavor is among the most important traits valued by consumers of fresh fruits. Human perception of flavor occurs primarily through two main sensory inputs, taste and aroma. Through retronasal olfaction, volatile organic compounds (VOCs) emitted by the fruit are able to produce the sensation of aroma which when combined with gustatory inputs from the tongue together underly our perception of the thousands of flavors we experience throughout our lives.

Haplotype reconstruction in connected tetraploid F1 populations.

In diploid species, many multiparental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase the power of QTL detection in comparison with the marker-based association analysis. However, such software tools for polyploid species are few and limited to a single biparental F1 population.

QTL mapping in outbred tetraploid (and diploid) diallel populations.

Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects.

Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding.

Blueberry ( and hybrids) is a specialty crop with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to expanding production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on recurrent phenotypic selection.

Construction of a High-Density Genetic Map of (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations.

, known as feijoa or pineapple guava, is a diploid, (2 = 2 = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited.

High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry.

Blueberry ( and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry.

Optimizing whole-genomic prediction for autotetraploid blueberry breeding.

Blueberry (Vaccinium spp.) is an important autopolyploid crop with significant benefits for human health. Apart from its genetic complexity, the feasibility of genomic prediction has been proven for blueberry, enabling a reduction in the breeding cycle time and increasing genetic gain.

Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.

A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage.

Genomic prediction applied to multiple traits and environments in second season maize hybrids.

Genomic selection has become a reality in plant breeding programs with the reduction in genotyping costs. Especially in maize breeding programs, it emerges as a promising tool for predicting hybrid performance. The dynamics of a commercial breeding program involve the evaluation of several traits simultaneously in a large set of target environments.

Signatures of selection for resistance to Haemonchus contortus in sheep and goats.

Background: Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode, Haemonchus contortus.

How can a high-quality genome assembly help plant breeders?

The decreasing costs of next-generation sequencing and the improvements in de novo sequence assemblers have made it possible to obtain reference genomes for most eukaryotes, including minor crops such as the blueberry (Vaccinium corymbosum). Nevertheless, these genomes are at various levels of completeness and few have been anchored to chromosome scale and/or are haplotype-phased. We highlight the impact of a high-quality genome assembly for plant breeding and genetic research by showing how it affects our understanding of the genetic architecture of important traits and aids marker selection and candidate gene detection.

Genomic Selection with Allele Dosage in Jacq.

Genomic selection is an efficient approach to get shorter breeding cycles in recurrent selection programs and greater genetic gains with selection of superior individuals. Despite advances in genotyping techniques, genetic studies for polyploid species have been limited to a rough approximation of studies in diploid species. The major challenge is to distinguish the different types of heterozygotes present in polyploid populations.

Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction.

Estimation of allele dosage, using genomic data, in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Some progress has been made when using SNP arrays, but the major challenge is when using next generation sequencing data. Here we compare the use of read depth as continuous parameterization with ploidy parameterizations in the context of genomic selection (GS).

High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Cultivated Under Suboptimal Temperature and Humidity Conditions.

Rubber tree () cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross.

Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars.

Metabolic composition is known to exert influence on several important agronomic traits, and metabolomics, which represents the chemical composition in a cell, has long been recognized as a powerful tool for bridging phenotype-genotype interactions. In this work, sixteen truly representative sugarcane Brazilian varieties were selected to explore the metabolic networks in buds and culms, the tissues involved in the vegetative propagation of this species. Due to the fact that bud sprouting is a key trait determining crop establishment in the field, the sprouting potential among the genotypes was evaluated.

AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example.

Progress in the rate of improvement in autopolyploid species has been limited compared with diploids, mainly because software and methods to apply advanced prediction and selection methodologies in autopolyploids are lacking. The objectives of this research were to (i) develop an R package for autopolyploids to construct the relationship matrix derived from pedigree information that accounts for autopolyploidy and double reduction and (ii) use the package to estimate the level and effect of double reduction in an autotetraploid blueberry breeding population with extensive pedigree information. The package is unique, as it can create A-matrices for different levels of ploidy and double reduction, which can then be used by breeders to fit mixed models in the context of predicting breeding values (BVs).