Luis F. Osorio

Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels.

The genetic control of carbon allocation and partitioning in woody perennial plants is poorly understood despite its importance for carbon sequestration, biofuels and other wood-based industries. It is also unclear how environmental cues, such as nitrogen availability, impact the genes that regulate growth, biomass allocation and wood composition in trees. We phenotyped 396 clonally replicated genotypes of an interspecific pseudo-backcross pedigree of Populus for wood composition and biomass traits in above- and below-ground organs. The loci that regulate growth, carbon allocation and partitioning under two nitrogen conditions were identified, defining the contribution of environmental cues to their genetic control. Sixty-three quantitative trait loci were identified for the 20 traits analyzed. The majority of quantitative trait loci are specific to one of the two nitrogen treatments, demonstrating significant nitrogen-dependent genetic control. A highly significant genetic correlation was observed between plant growth and lignin/cellulose composition, and quantitative trait loci co-localization identified the genomic position of potential pleiotropic regulators. Pleiotropic loci linking higher growth rates to wood with less lignin are excellent targets to engineer tree germplasm improved for pulp, paper and cellulosic ethanol production. The causative genes are being identified with a genetical genomics approach.

An experimental validation of genomic selection in octoploid strawberry.

The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013–2014 and 2014–2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial. High-density genotyping was performed with the Affymetrix Axiom IStraw90 single-nucleotide polymorphism array, and 17 479 polymorphic markers were chosen for analysis. Several methods were compared, including Genomic BLUP, Bayes B, Bayes C, Bayesian LASSO Regression, Bayesian Ridge Regression and Reproducing Kernel Hilbert Spaces. Cross-validation within training populations resulted in higher values than for true validations across trials. For true validations, Bayes B gave the highest predictive abilities on average and also the highest selection efficiencies, particularly for yield traits that were the lowest heritability traits. Selection efficiencies using Bayes B for parent selection ranged from 74% for average fruit weight to 34% for early marketable yield. A breeding strategy is proposed in which advanced selection trials are utilized as training populations and in which genomic selection can reduce the breeding cycle from 3 to 2 years for a subset of untested parents based on their predicted genomic breeding values.

Pedigree-based analysis in a multiparental population of octoploid strawberry reveals QTL alleles conferring resistance to phytophthora cactorum

Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.

‘Florida Beauty’ Strawberry

The leading strawberry (Fragaria ×ananassa) cultivar grown in Florida is currently ‘Florida Radiance’ (Chandler et al., 2009; U.S. Patent PP20,363) which was commercialized in 2009 and by the 2015–16 season, accounted for ≈70% of the acreage in west-central Florida. This cultivar is preferred for its early and total yields, its uniformly shaped and attractive fruit, and its open plant architecture and long pedicels which allow efficient harvesting. Sweet Sensation® ‘Florida127’ (Whitaker et al., 2015; hereafter referred to as ‘Florida127’; U.S. Patent PP25,574) is currently the second leading cultivar with ≈20% of acreage in 2016–17. This cultivar is preferred for its combination of high yields, large fruit size, excellent eating quality, and long shelf life. However, neither of these current commercial standards are well adapted for early transplanting dates in west-central Florida. High temperatures during transplanting tend to reduce early yields of ‘Florida Radiance’ and cause elongated fruit, which may be unmarketable, and ‘Florida127’ often becomes too vegetative when exposed to high temperatures. The planting window in west-central Florida has shifted earlier in recent years in an attempt to produce higher yields in late November and December when market prices are highest (Wu et al., 2015). There is currently a need for additional cultivars with uniformly shaped fruit and harvesting efficiency similar to ‘Florida Radiance’ and flavor characteristics similar to ‘Florida127’. There is also a need for cultivars that are adapted to early planting, between 25 Sept. and 1 Oct., when environmental conditions in west-central Florida are hot and unfavorable for flower initiation and ideal fruit shape. ‘Florida Beauty’ strawberry is the product of a collaborative breeding effort between the University of Florida and the Queensland Department of Agriculture and Fisheries. It has demonstrated adaptation to early planting, maintaining excellent fruit quality, and a yield distribution that complements current commercial standards. Experimental trials have been conducted under the direction of the University of Florida on the research plots of the Gulf Coast Research and Education Center (GCREC) (Balm, FL), at the Florida Strawberry Growers Association (FSGA) headquarters in Dover, FL, and on several farms in west-central Florida and Southern Spain.

Genome-Assisted Breeding in the Octoploid Strawberry

The application of genomic information to the breeding of allo-octoploid (2n = 8x = 56) cultivated strawberry (Fragaria × ananassa) has increased rapidly in the last five years. These advances have been fueled by technological improvements in high-throughput genotyping and genome sequencing, as well as concerted efforts to develop DNA tests for routine use in breeding. Genome-wide and subgenome-specific markers have advanced availability of DNA tests for major loci, as well as the development and validation of genomic selection methodology for complex traits in strawberry. Eight DNA tests for fruit quality and disease resistance loci are fully or partially in the public sphere. Genome-wide predictions have delivered genetic gain efficiencies for parent selection larger than 50% of conventional methods but without the need for phenotypic information. Meanwhile, the construction of haploblocks and haplotypes allows increased understanding of genome structure as it relates to breeding applications. With octoploid sequence assemblies merely months away and the development of gene editing technologies, precision manipulation of genes may shape the future of strawberry genetic improvement.