Chromosome Evolution of Octoploid Strawberry

Hardigan, Michael A.; Feldmann, Mitchell J; Lorant, Anne; Famula, Randi; Acharya, Charlotte B.; Cole, Glenn; Edger, Patrick P.; Knapp, Steven J.

doi:10.1101/861526

Cited by 5 publications

(19 citation statements)

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“…We collected data from 67 wild octoploid individuals from Fragaria virginiana and Fragaria chiloensis genotyped with the 50K SNP array developed by Hardigan et al (2020a) and filtered to remove markers with >5% missing data and markers that were not polymorphic, which brought the final number to 32,200. Detailed sampling and sequencing information can be found in Hardigan et al (2020a). These samples include four subspecies of F. virginiana: subsp.…”

Section: Plant Materials and Genotypingmentioning

confidence: 99%

“…occidentalis alignment from an ancestrally related chromosome based on a previous analysis of chromosome synteny by Hardigan et al (2020a). The nucleotide state at the position in the R. occidentalis genome assembly corresponding to 50K array marker SNP sites was assigned as a homozygous outgroup genotype for the corresponding markers, except in cases where the R. occidentalis allele did not match one of the two nucleotide states assayed by the marker probe.…”

Section: Genetic Structure and Phylogenetic Relationshipsmentioning

confidence: 99%

“…The genotyping array used in this study was designed to capture diversity across subgenomes and identify subgenome-specific SNPs. Nicely designed SNP arrays results in even coverage across all subgenomes with minimal missing data for a relatively small cost (Hardigan et al, 2020a). There are some concerns for their application in population genomic studies.…”

Section: Another Genomic Tool In Our Boxmentioning

confidence: 99%

“…The ploidy of strawberrry, Fragaria sp., ranges from diploid to decaploid, and recent work has shown an impressive retention of karyotype and genome structure over tens of millions of years (Hardigan et al, 2020a). The prevalence of neopolyploids makes the genus a powerful system to study the immediate effects of polyploidy like subgenome dominance (Edger et al, 2019) and adaptability to new environments (Wei et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Here we leverage a recently published F. × ananassa genome (Edger et al, 2019) and 50K Axiom SNP array (Hardigan et al, 2020a) to study a phylogenetically diverse sample of F. virginiana and F. chiloensis populations collected throughout the natural geographic ranges of the underlying subspecies in North and South America. Using a variety of genetic and genomic methods, we show evidence that F. virginiana and F. chiloensis are monophyletic sister lineages, but subspecies designations show substantial paraphyly.…”

Section: Introductionmentioning

confidence: 99%

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Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere

Bird

Hardigan

Ragsdale

et al. 2021

Preprint

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Premise of the study: Octoploid strawberry (Fragaria sp.) has a complex evolutionary history that has until recently been intractable due to limitations of available genomic resources. While recent work has further uncovered the evolutionary history of the octoploid strawberry, there are still open questions. Much is still unknown about the evolutionary relationship of the wild octoploid species, Fragaria virginiana and Fragaria chiloensis, and gene flow within and among species after the original formation of the octoploid genome. Methods: We leveraged a diversity collection of wild octoploid ecotypes of strawberry representing the recognized subspecies and ranging from Alaska to Southern Chile, and a high density SNP array to investigate wild octoploid strawberry evolution. Evolutionary relationships are interrogated with phylogenetic analysis and genetic clustering algorithms. Additionally, admixture among and within species is assessed with model-based and tree-based approaches. Key Results: Phylogenetic analysis revealed that the two octoploid strawberry species are monophyletic sister lineages. The genetic clustering results show substructure between North Americana and South American F. chiloensis populations. Additionally, model-based and tree-based methods support gene flow within and among the two octoploid species, including newly identified admixture in the Hawaiian F. chiloensis subsp. sandwicensis population that appears to be from an ancestral F. chiloensis population. Conclusion: F. virginiana and F. chiloensis are supported as monophyletic and sister lineages. All but one of the subspecies recognized within both octoploid species show extensive paraphyly. Furthermore, the phylogenetic relationship among F. chiloensis populations supports a single population range expansion southward from North America. The inter- and intraspecific relationships of octoploid strawberry are complex and suggest substantial and deep gene flow between sympatric populations among and within species.

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Section: Plant Materials and Genotypingmentioning

confidence: 99%

Section: Genetic Structure and Phylogenetic Relationshipsmentioning

confidence: 99%

Section: Another Genomic Tool In Our Boxmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere

Bird

Hardigan

Ragsdale

et al. 2021

Preprint

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Assessment of Fermented Kiwifruit on Morpho‐Physiological and Productive Performances of Fragaria spp Plants, Grown Under Hydroponic Conditions

Nazeer,

Agosti,

Del Vecchio

et al. 2024

J of Sust Agri & Env

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Climate change poses a significant threat to global agriculture by altering weather patterns, increasing the frequency of extreme events, and reducing the availability of arable land. Hydroponic systems offer a sustainable solution allowing efficient resource use, including water and nutrients, and enabling cultivation in areas with poor soil quality or limited space. The incorporation of biostimulants derived from plant byproducts further enhances sustainability by improving plant growth and resilience, reducing the use of synthetic fertilizers and the environmental footprint of agriculture, promoting, at the same time, healtier crop production. This study investigates the effect of biostimulants, derived from fermented kiwifruit byproducts, on the morpho‐physiological and productive performances of Fragaria vesca (L.), cv. Malga, and of Fragaria x ananassa (Duch.), cv. Annabelle, grown in a column hydroponic system. Plants of both species, when treated with the biostimulant, demonstrated significant improvements for all the parameters evaluated, with healthier plants and improved quality features in fruits. These findings suggest that fermented kiwi byproduct could be an effective, sustainable integration to synthetic fertilizers, promoting better growth and fruit quality in strawberry cultivation under hydroponic systems.

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Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry

Jiménez¹,

Feldmann²,

Famula³

et al. 2022

The Plant Genome

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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.

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Chromosome Evolution of Octoploid Strawberry

Cited by 5 publications

References 81 publications

Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere

Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere

Assessment of Fermented Kiwifruit on Morpho‐Physiological and Productive Performances of Fragaria spp Plants, Grown Under Hydroponic Conditions

Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry

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