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The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.

Flavor is essential to consumer preference of foods and is an increasing focus of plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise to accelerate flavor improvement, but polyploidy and heterozygosity in many species have slowed progress. Here we use octoploid cultivated strawberry to demonstrate how genomic heterozygosity, transcriptomic intricacy and fruit metabolomic diversity can be treated as strengths and leveraged to uncover fruit flavor genes and their regulatory elements. Multi-omics datasets were generated including an expression quantitative trait loci map with 196 diverse breeding lines, haplotype-phased genomes of a highly-flavored breeding selection, a genome-wide structural variant map using five haplotypes, and volatile genome-wide association study (GWAS) with > 300 individuals. Overlaying regulatory elements, structural variants and GWAS-linked allele-specific expression of numerous genes to variation in volatile compounds important to flavor. In one example, the functional role of anthranilate synthase alpha subunit 1 in methyl anthranilate biosynthesis was supported via fruit transient gene expression assays. These results demonstrate a framework for flavor gene discovery in fruit crops and a pathway to molecular breeding of cultivars with complex and desirable flavor.

Charcoal rot caused by Macrophomina phaseolinais an increasing economic problem in annualized strawberry production systems around the world. Currently there are no effective postfumigation chemical controls for managing charcoal rot, and no information is available on the genetic architecture of resistance to M. phaseolina in strawberry (Fragaria ×ananassa). In this study, three multiparental discovery populations and two validation populations were inoculated at planting and evaluated for mortality in three consecutive growing seasons. Genome-wide SNP genotyping and pedigree-based analysis with FlexQTL™ software were performed. Two large-effect quantitative trait loci (QTL) increasing charcoal rot resistance were discovered and validated in cultivated germplasm. FaRMp1 was located on linkage group 2A in the interval 20.4to 24.9 cM, while FaRMp2 was located on linkage group 4B in the interval 41.1to 61.2 cM. Together these QTLs explained 27% and 17% of the phenotypic variance in two discovery populations consisting of elite breeding germplasm. For both QTLs, the resistant allele showed some evidence of partial dominance, but no significant interaction was detected between the two loci. As the dosage of resistant alleles increased from 0 to 4 across the two QTLs, mortality decreased regardless of the combination of alleles.A third locus, FaRMp3 on 4D, was discovered in FVC 11-58, a reconstituted F.×ananassa originating from diverse F. virginiana and F. chiloensis accessions. This locus accounted for 44% of phenotypic variation in four segregating crosses. These findings will form the basis for DNA-informed breeding for resistance to charcoal rot in cultivated strawberry.

Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, applications to polyploid organisms are still scarce, partly due to limited genome resources and the complexity of this system. Deep learning (DL) techniques comprise a heterogeneous collection of machine learning algorithms that have excelled at many prediction tasks. A potential advantage of DL for GP over standard linear model methods is that DL can potentially take into account all genetic interactions, including dominance and epistasis, which are expected to be of special relevance in most polyploids. In this study, we evaluated the predictive accuracy of linear and DL techniques in two important small fruits or berries: strawberry and blueberry. The two datasets contained a total of 1,358 allopolyploid strawberry (2n=8x=112) and 1,802 autopolyploid blueberry (2n=4x=48) individuals, genotyped for 9,908 and 73,045 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for five agronomic traits each. DL depends on numerous parameters that influence performance and optimizing hyperparameter values can be a critical step. Here we show that interactions between hyperparameter combinations should be expected and that the number of convolutional filters and regularization in the first layers can have an important effect on model performance. In terms of genomic prediction, we did not find an advantage of DL over linear model methods, except when the epistasis component was important. Linear Bayesian models were better than convolutional neural networks for the full additive architecture, whereas the opposite was observed under strong epistasis. However, by using a parameterization capable of taking into account these non-linear effects, Bayesian linear models can match or exceed the predictive accuracy of DL. A semiautomatic implementation of the

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry's complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

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

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.

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

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

[Background]: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array., [Results]: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM., [Conclusions]: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.