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2019 ASHS Annual Conference

Genomic Resources for Cross-Referencing Physical and Genetic Mapping Information, Reconciling Independent Linkage Group Nomenclatures, and Enabling Genome-Informed Breeding in Octoploid Strawberry

Tuesday, July 23, 2019: 10:45 AM
Montecristo 4 (Tropicana Las Vegas)
Michael A. Hardigan, University of California, Davis, Davis, CA
Mitchell J. Feldmann, University of California, Davis, Davis, CA
Dominique D.A. Pincot, University of California, Davis, Davis, CA
Nicolas Cobo, University of California, Davis, Davis, CA
Anne Lorant, University of California, Davis, Davis, CA
Mirko Ledda, University of California, Davis, Davis, CA
Charlotte Acharya, University of California, Davis, Davis, CA
Randi A. Famula, University of California, Davis, Davis, CA
Glenn S. Cole, University of California, Davis, Davis, CA
Steven J. Knapp, University of California, Davis, Davis, CA
Patrick Edger, Michigan State University, East Lansing, MI
The genome of garden strawberry (Fragaria × ananassa) is a mosaic of multiple wild species genomes, albeit dominated by the contributions of the original octoploid progenitors F. virginana and F. chiloensis. Our laboratories, along with several collaborators, reported the first chromosome-scale assembly of the octoploid strawberry genome in early 2019. Over the last year, we developed additional genomic resources built on the backbone of the octoploid reference genome. Here, we describe those resources, in addition to presenting highlights of results from genome-scale analyses of nucleotide diversity and high-density genetic mapping of the genomes of the octoploid progenitors. The genomes of 142 octoploid individuals were whole-genome shotgun sequenced. These included phylogenetically and demographically diverse F. virginiana and F. chiloensis ecotypes and horticulturally diverse heirloom and modern F. × ananassa cultivars. We identified 95M DNA variants—astonishingly, 45M DNA variants were identified in F. × ananassa. Through stringent filtering and selection of sub-genome specific DNA sequences, two high-density single nucleotide polymorphism (SNP) genotyping arrays were developed, one with 850,000 and another with 49,000 SNPs anchored to the octoploid reference genome. SNPs on the 850K array target an estimated 94% of the 108,000 annotated genes in the octoploid. Through population genomic analyses of 850K SNP array profiles, we clearly resolved the population structure of a global collection of F. × ananassa cultivars spanning nearly 200 years of breeding. The genomes of F. virginiana, F. chiloensis, and F. × ananassa were densely genetically mapped using DNA variants identified by whole-genome shotgun sequencing, 49K SNP array genotyping, or a combination thereof. This yielded a high density of genetically mapped DNA markers across the genome—2M DNA variants in 12,000 bins were genetically and physically mapped in F. chiloensis alone. The resources and results described here facilitate the reconciliation and unification of independent linkage group nomenclatures and supply the community with a facile and highly accessible platform for cross-referencing genetic and physical mapping information. This is particularly important because multiple independent linkage group nomenclatures have emerged over the last two decades in strawberry without DNA-sequence information critical for cross-referencing. Finally, these resources should empower and broadly impact genome-informed agricultural and biological research in octoploid strawberry.
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