Understanding strawberry (Fragaria) genome composition.

The cultivated strawberry, Fragaria xananassa, is an octoploid (2n=8x=56) hybrid species (hence the “x” in its name), having arisen in a French botanical garden via hybridization between a white-fruited, cultivated Chilean strawberry (F. chiloensis) and a red-fruited wild species from Northeastern North America (F. virginiana subsp. virginiana. The ancestries of these octoploid species trace ultimately to two or more diploid species, known to include F. vesca and F. iinumae. We continue to be deeply involved in developing knowledge (Davis et al. 2009, 2010; DiMeglio et al., 2014; Liu et al., 2016) and implementing genomic resources for Fragaria, including linkage maps (Yu and Davis 1995; Sargent et al., 2016; Mahoney et al., 2016) and genomic assemblies of F. vesca (Shulaev et al., 2011; Sargent et al., 2011) and F. iinumae (in prep).

Fragaria germplasm collection and development. 

We have collected wild Fragaria germplasm from many areas of the world, and have participated in the contribution of over 100 Fragaria and other germplasm accessions to the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. One highlight was the 2004 collection trip with Dr. Kim Hummer, Director of the NCGR, to Hokkaido, Japan. This expedition was a collaborative effort between the United States Department of Agriculture, the Japanese Ministry of Agriculture, Forestry and Fisheries, the University of New Hampshire, and Akita Prefectural University, College of Agriculture, Japan. Additional assistance was provided by the Hokkaido Governmental Plant Genetic Resources Center, several Forest Research stations of the University of Hokkaido, and private botanists. Fragaria iinumae accessions collected in Hokkaido, Japan have been used in the development of the first F. iinumae genetic linkage map, and our F. iinumae genome assembly is nearing public release. Expedition Final Report.

Developing tools for marker-assisted strawberry breeding.

The F. vesca Hawaii 4 genome assembly (Shulaev et al. 2011; Sargent et al., 2011) provided a reference genome as a basis for next generation sequence alignments and SNP discovery, providing the basis for design of the first SNP arrays, for the cultivated strawberry (Bassil and Davis et al., 2015). This resource was developed within the framework of the USDA-SCRI-supported RosBREED project . The new F. iinumae linkage map (Mahoney et al., 2016) and genome assembly (coming soon) provide a complementary reference genome for a second round of SNP discovery, enabling improvement in the very successful first generation arrays.

Strawberry Breeding

Our goal is to develop locally adapted strawberry varieties for New Hampshire and the Northern New England region. Our approach is that of conventional breeding supplemented by a DNA fingerprinting approach known as marker-assisted breeding (MAB), taking advantage of the high-throughput genotyping platform provided by the Axiom® IStraw90®strawberry SNP array. Our initiative is integrated with the USDA-SCRI RosBREED II project aimed at using MAB to combine disease resistance with fruit quality traits in crops of the Rosaceae family.  Implementation of MAB will enable a more rapid breeding response to local needs and opportunities, among which is the shortfall of strawberry production in New Hampshire in relation to unmet demand for locally produced, high quality fruit. We also see opportunity to release attractive ornamental varieties for the home garden and landscape. Thus, we expect to create new varieties that will serve the interests of local growers, gardeners, and consumers, and to expand the dollar value of regional strawberry production.

Weed  and quinoa projects

These projects grew out of a collaborative initiative involving the three Northern New England (NNE) States: New Hampshire, Vermont, and Maine. We began by seeking to establish a baseline census of weed species present on organically managed vegetable farms, as a starting point for assessing the possible emergence of new weed problems in the NNE region as a consequence of climate change. From this foundation, a focus has emerged on weeds of the genus Chenopodium, including lambsquarters (C. album) and their possible use as germplasm resources for genomic study and genetic improvement of quinoa (Chenopodium quinoa).