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Key MessageSeveral Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant toFusarium oxysporumf. sp.fragariae, a devastating soil-borne pathogen of strawberry.Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria×ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

The development of strawberry (Fragaria × ananassa Duchesne ex Rozier) cultivars resistant to Phytophthora crown rot (PhCR), a devastating disease caused by the soil‐borne pathogen Phytophthora cactorum (Lebert & Cohn) J. Schröt., has been challenging partly because the resistance phenotypes are quantitative and only moderately heritable. To develop deeper insights into the genetics of resistance and build the foundation for applying genomic selection, a genetically diverse training population was screened for resistance to California isolates of the pathogen. Here we show that genetic gains in breeding for resistance to PhCR have been negligible (3% of the cultivars tested were highly resistant and none surpassed early 20th century cultivars). Narrow‐sense genomic heritability for PhCR resistance ranged from 0.41 to 0.75 among training population individuals. Using multivariate genome‐wide association studies (GWAS), we identified a large‐effect locus (predicted to be RPc2) that explained 43.6–51.6% of the genetic variance, was necessary but not sufficient for resistance, and was associated with calcium channel and other candidate genes with known plant defense functions. The addition of underutilized gene bank resources to our training population doubled additive genetic variance, increased the accuracy of genomic selection, and enabled the discovery of individuals carrying favorable alleles that are either rare or not present in modern cultivars. The incorporation of an RPc2‐associated single‐nucleotide polymorphism (SNP) as a fixed effect increased genomic prediction accuracy from 0.40 to 0.55. Finally, we show that parent selection using genomic‐estimated breeding values, genetic variances, and cross usefulness holds promise for enhancing resistance to PhCR in strawberry. Core Ideas The strongest sources of resistance were heirloom cultivars developed before the advent of soil fumigation. The addition of exotic genetic resources to an elite training population doubled genetic variation. Although resistance is genetically complex, a single locus accounted for 44–52% of the genetic variance. Genetic gains can be accelerated by genomic prediction of breeding values and cross usefulness. A global effort is needed to improve resistance to PhCR, which appears to be inadequate among modern cultivars.

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.

Allo-octoploid cultivated strawberry ( × ) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in . subsp. , and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in . × . These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.

Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × $\\times$ananassa), has caused economic losses for nearly a century. This disease is caused by the soil‐borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW‐resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids (n=564 $n = 564$ ) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids (n=386 $n = 386$ ), genomic prediction accuracies of 0.47–0.48 were achieved and were predicted to explain 70%–75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations. Core Ideas For the second half of the 20th century, strawberries were cultivated with high levels of chemical inputs. Genetic gains for resistance to verticillium wilt (VW) have been low, or negative, since the 1960s. VW is heritable, and breeding values can be accurately predicted to improve populations and individuals. The genetic architecture of resistance is similar among modern hybrids, heirloom varieties, and crop wild relatives

English walnut (Juglans regia L.) is an economically important crop with > 99% of US walnuts produced in California. Changes in climate and recent drought cycles have raised concerns regarding the future of nut production and responsible water use in California agriculture. Our study used an association genetics approach to characterize ecophysiological traits such as water use efficiency as estimated by carbon isotope discrimination (Δ13C), and photosynthetic capacity through foliar nitrogen composition, in important individuals of the Walnut Improvement Program, located at the University of California, Davis. Stable isotope and leaf measurements of 241 mature trees, representing 60 scion genotypes in established orchards were sampled in 2015 and 2016, followed by genotyping with the Walnut Axiom 700 k SNP Array. A mean Δ13C of 21.7‰ (σ: 0.9‰) was calculated for all individuals, as well as a mean nitrogen/leaf area (N/area) of 3.0 gN/m2 (σ: 0.5 gN/m2). A Bayesian analysis utilizing genomic relationships revealed rankings of the most water use efficient accessions as Solano (95-011-16), 67-013 (unreleased cross), and Tulare (67-011). 126,554 SNPs were used in a two-step association genetics approach identifying four loci associated with Δ13C after correction for multiple testing. Investigation of identified loci revealed an annotation on the J. regia genome of protein FAR1-related sequence 5-like, related to abiotic stress response. For uncharacterized markers, homologs were identified in Arabidopsis for two loci, similarly related to drought stress.

Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high‐density genetic marker platforms designed for strawberry. We developed mid‐density panels of molecular inversion probes (MIPs) to be deployed with the “DArTag” marker platform to provide a low‐cost, high‐throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype segregation, amplicon coverage, and their ability to produce subgenome‐specific amplicon alignments to the FaRR1 assembly and subsequent alignment‐based variant calls with strong concordance to DArT's alignment‐free, count‐based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K and 5K production panels for genotyping of large strawberry populations. We show that the 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low‐amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism in diverse F. × ananassa germplasm and UC Davis cultivars, with mean pairwise diversity (π) estimates of 0.40 and 0.32 and mean heterozygous genotype frequencies of 0.35 and 0.33, respectively. Core Ideas Routine deployment of genomic selection (GS) requires access to cost‐effective genotyping tools and technologies. We present a medium‐density genotyping platform with 3k and 5k subgenome‐specific sites for octoploid strawberry. The core sites cover the FARR1 octoploid reference genome and accurately captures genomic relatedness for GS.

Verticillium wilt, a soil‐borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a persistent challenge, in part because the genetics of resistance is complex. The heritability of resistance and genetic gains in breeding for resistance to this pathogen have not been well documented. To elucidate the genetics, assess long‐term genetic gains, and estimate the accuracy of genomic selection for resistance to Verticillium wilt, we analyzed a genetically diverse population of elite and exotic germplasm accessions (n = 984), including 245 cultivars developed since 1854. We observed a full range of phenotypes, from highly susceptible to highly resistant: < 3% were classified as highly resistant, whereas > 50% were classified as moderately to highly susceptible. Broad‐sense heritability estimates ranged from 0.70–0.76, whereas narrow‐sense genomic heritability estimates ranged from 0.33–0.45. We found that genetic gains in breeding for resistance to Verticillium wilt have been negative over the last 165 years (mean resistance has decreased over time). We identified several highly resistant accessions that might harbor favorable alleles that are either rare or non‐existent in modern populations. We did not observe the segregation of large‐effect loci. The accuracy of genomic predictions ranged from 0.38–0.53 among years and whole‐genome regression methods. We show that genomic selection has promise for increasing genetic gains and accelerating the development of resistant cultivars in strawberry by shortening selection cycles and enabling selection in early developmental stages without phenotyping.

Fusarium wilt, a vascular disease of strawberry (Fragaria × $\\times$ananassa) caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. fragariae, has emerged over the past 20 years as a leading cause of severe plant wilt and death in California and many other parts of the world. We previously described several sources of resistance to race 1 of the pathogen; showed that resistance was conferred by dominant resistance genes (R‐genes) on chromosomes 2B (FW1, FW2, and FW5), 1A (FW3), and 6B (FW4); and identified a cultivar (Earliglow) that was hypothesized to be a source of novel R‐genes. Earliglow S1 ${\\mathrm{S}_{1}}$progeny segregated 15 resistant:1 susceptible (χ2=0.03;p=0.87 $\\chi ^2 = 0.03; p = 0.87$ ), the Mendelian distribution expected when the phenotypes are caused by unlinked dominant duplicate epistasis. Here, we show that Earliglow carries a dominant R‐gene (FW6) in the FW1 cluster on chromosome 2B and an incompletely dominant R‐gene (FW7) on chromosome 2A, where Fusarium wilt R‐genes have not been previously reported. The effect of FW7 was masked by the epistatic effect of FW6; this was determined by self‐pollinating an S1 ${\\mathrm{S}_{1}}$individual predicted to be homozygous for the recessive (susceptible) FW6 allele and heterozygous for FW7 alleles, creating and whole‐genome sequencing Fusarium wilt resistant and susceptible S2 ${\\mathrm{S}_{2}}$bulks, and physically mapping the FW7 locus by bulked segregant analysis. Lastly, we identified candidate genes for FW7, in addition to highly predictive FW6‐ and FW7‐associated SNPs for marker‐assisted selection of FW6 and FW7 alleles. This study laid the foundation for identifying the causal gene underlying FW7 and increasing the durability of resistance to Fusarium wilt by pyramiding FW7 with independent R‐genes. Core Ideas The resistance of the heirloom cultivar Earliglow to Fusarium wilt race 1 is conferred by a dominant gene on chromosome 2B (FW6) and a nearly additive gene on chromosome 2A (FW7). The effect of FW7 was weaker than and masked by the epistatic effect of FW6. Whole‐genome sequencing bulked segregant analysis (WGS‐BSA) was validated as an approach for discovering and physically mapping DNA markers associated with large‐effect loci in octoploid strawberry. Highly predictive FW6‐ and FW7‐associated DNA markers were identified by genome‐wide association studies and WGS‐BSA. FW6 and FW7 can be pyramided to increase the durability of resistance to Fusarium wilt race 1. Plain Language Summary Fusarium wilt, a strawberry disease that causes wilting and death in susceptible genotypes, has become an increasingly serious problem in home gardens and farms around the world. There are, however, natural genetic sources of resistance to the causal pathogen (Fusarium oxysporum f. sp. fragariae), including wild relatives and heirloom and modern cultivars. We previously identified genes on three chromosomes (1A, 2B, and 6A) that confer resistance to the most common race of the pathogen found in California (race 1). Using insights gained from previous studies, we discovered that the heirloom cultivar Earliglow carries a novel race 1 resistance gene on chromosome 2A (FW7). The effect of this newly identified resistance gene was hidden by the epistatic effect of a dominant gene (FW6) found in a previously identified cluster of resistance genes on chromosome 2B. We uncovered and physically mapped FW7 using high‐throughput sequencing of resistant and susceptible bulks in combination with physical mapping of sequences to an octoploid reference genome, a tried‐and‐true approach known as bulked segregant analysis. Our study shows that strawberry has evolved multiple Fusarium wilt resistance genes that can be combined through marker‐assisted selection to prevent losses to the disease and increase the durability of resistance.

Strawberry (Fragaria × $\\times$ananassa) reproduces sexually through seeds and asexually through stolons. The ability to cost‐effectively clonally propagate hybrid individuals on a large scale has shaped strawberry breeding and production practices. Despite the technical and economic importance of clonal propagation, little is known about the genetic regulation of runnering in strawberry, apart from the pleiotropic effects of PERPETUAL FLOWERING (PF), a dominant gene introgressed from a wild relative that abolishes temperature‐dependent photoperiod sensitivity and incompletely and variably suppresses runnering. Here, we show that runnering phenotypes are heritable and highly variable in strawberry, ranging from runnerless to prolific in short‐day (pfpf) and day‐neutral (PF_) plants. The PF locus was physically mapped to Mb 26.4–27.3 on chromosome 4B and found to explain 22% of the genetic variance for runnering (78% of the heritability was missing). PF was the only runnering‐associated locus identified by genome‐wide association studies among diverse clonal genetic resources and progeny from narrow and wide crosses (1537 individuals). The pleotropic effect of PF on runnering was temporal, variable, and incompletely dominant. Genomic selection was found to be a viable strategy for modifying runnering phenotypes in strawberry. Genomic prediction accuracies ranged from 0.53 to 0.79 for runnering, were greater within than between populations, and increased when corrected for PF. Our study builds the foundation for improving the productivity of strawberry by developing runnerless cultivars for seed‐propagation or reduced runnering cultivars for clonal‐propagation through phenotypic or genomic selection. Core Ideas Variation for runnering is substantial and heritable within seasonal and perpetual flowering strawberry populations. The pleiotropic suppression of runnering by the PERPETUAL FLOWERING (PF) allele is continuously variable, temporal, and incompletely dominant. The accuracy of breeding value prediction is sufficient for modifying the runner growth characteristics of the strawberry plant by genomic selection. The productivity of strawberry can be improved by introducing seed‐propagated cultivars with runnerless and clone‐propagated cultivars with reduced runnering phenotypes. Plain Language Summary The ability to clone individual plants has shaped strawberry breeding and production practices, and runner (stolon) growth is well known to home gardeners and farmers alike and important for the propagation of strawberry cultivars. The energy that the strawberry plant diverts into runner growth can decrease fruit yield. To circumvent maximize fruit yield, farmers mechanically trim runners. The genetic factors that control runner growth are complex but mostly unknown apart from PERPETUAL FLOWERING, a gene controlling photoperiod sensitive flowering and affecting runnering. We observed a full spectrum of runner growth phenotypes in seasonal and perpetual flowering populations, found that runnering phenotypes are heritable, and showed that the runner growth of strawberry plants can be modified by phenotypic or genomic selection. Lastly, we identified extreme transgressive segregates for runnering and showed that runnerless and reduced runnering cultivars can be developed to reduce production costs and improve productivity.