Improving cultivated strawberry diversity and disease resistance

Structure of the US National F. ananassa collection determined using (A.) PCA and K-means clustering, (B.) sparse non-negative matrix factorization followed by ancestry determined by LEA, and (C.) the distribution of groups were assigned by k-means clustering of geographic regions. Colors representing groups are standardized throughout the figure. Credit: Horticultural Research

Cultivated strawberries are now the basis of a multi-billion-dollar global industry. To meet the challenges caused by increasing demand, climate change, and water and land scarcity, it is necessary to collect new germplasm to improve cultivars. However, management of clonally propagated germplasm collections such as strawberry is expensive, while limited genotypic and phenotypic characteristics prevent the effective use of germplasm.

Genome assembly and genotyping platforms have enabled a deeper understanding of genetic diversity and trait genetics. The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon maintains the US strawberry collection, but little has been done to assess molecular diversity within the US National F. ananassa collection.

In May 2022, Horticultural Research published a research article titled “Exploring the diversity and genetic structure of the US National Cultivated Strawberry Collection.”

In this study, data curation included genotyping strawberry accessions using Axiom IStraw35 and Axiom FanaSNP arrays, which identified 27,968 and 40,424 SNP markers, respectively. Marker data shared by both arrays were analyzed for call quality, missing data, and minor allele frequency, resulting in 4,033 markers for structural assessment, diversity analysis, pedigree confirmation, core collection development , and identifying haplotypes associated with desirable traits.

Population structure was analyzed using Principal Component Analysis (PCA). K-means clustering and the sNMF algorithm both identify eight optimal subpopulations. F. ananassa has similar diversity in geographic regions. Hierarchical clustering using UPGMA identified seven to nine major clades that were also related to geographical strata.

STRUCTURE analysis identified three broad subgroups with diversity statistics showing similar richness and similarity among geographic populations. Two core collections were established, type 1 core collection (CC-I) and type 2 core collection (CC-X), each containing 100 individuals. These collections are very different compared to random sampling, representing major geographic regions and all groups from the population structure analysis.

COLONY output confirmed pedigree links for 241 of 308 accessions, with 78.0% appearing true-to-type. Trait-associated haplotype prevalence analyzes showed that only 3,943 of 4,033 markers uniquely mapped to the F. ananassa “Camarosa” assembly. Marker density was insufficient in some regions to identify trait-associated haplotypes. Notably, some accessions such as “Fletcher” and “L’Amour” have multiple resistance haplotypes. Finally, accessions with FaRCa1, FaRCg1, FaRMp1, and FaRPc2 resistance-related haplotypes were identified.

In summary, germplasm collections provide many resources for breeders to develop and improve cultivars. The core collections made in this study will be useful tools for identifying new genes and validating DNA information for breeding. These findings are valuable for breeding and research, providing a more efficient way to use the collection of F. ananassa.

More information:
Jason D Zurn et al, Exploring the diversity and genetic structure of the US National Cultivated Strawberry Collection, Horticultural Research (2022). DOI: 10.1093/hr/uhac125

Provided by Plant Phenomics

Citation: Development of cultivated strawberry diversity and disease resistance (2023, December 21) retrieved 21 December 2023 from

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