# Publications

2022
Nolen HB, Smith C, Davis TM, A. P. Evaluation of disease severity and molecular relationships among Peronospora variabilis isolates on Chenopodium species in New Hampshire. Plant Disease. 2022;106 (2) :564-571.Abstract
Quinoa is a potential new crop for New England; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle for cultivation. The objectives of this study were to evaluate differential resistance within the Chenopodium genus, identify novel sources of resistance for use in future genetic studies or breeding programs, and investigate phylogenetic relationships of P. variabilis isolates from different Chenopodium hosts. The long-term goal of this research is to develop a resistant variety of quinoa to be grown in New England. Field trials conducted at the University of New Hampshire evaluated downy mildew disease severity on 10 Chenopodium accessions representing four species. Disease severity for each treatment was compared and significant differences in disease severity were observed between accessions. C. berlandieri var. macrocalycium ecotypes collected from Rye Beach, New Hampshire and Appledore Island, Maine exhibited the lowest disease severity over the growing season. P. variabilis was isolated from each accession, and COX2 sequences were compared. Phylogenetic analyses suggest no effect of host species on P. variabilis sequence similarity; however, isolates are shown to cluster by geographic location. This research provides the first step in identifying potential New England native sources of resistance to downy mildew within the genus Chenopodium and provides preliminary information needed to further investigate resistance at the genomic level in Chenopodium spp.
Frailey DC, Zhang Q, Wood DJ, Davis TM. Defining the mutation sites in chickpea nodulation mutants PM233 and PM405. BMC Plant Biology. 2022;22 (66) :1-12.Abstract
Background: Like most legumes, chickpeas form specialized organs called root nodules. These nodules allow for a symbiotic relationship with rhizobium bacteria. The rhizobia provide fixed atmospheric nitrogen to the plant in a usable form. It is of both basic and practical interest to understand the host plant genetics of legume root nodulation. Chickpea lines PM233 and PM405, which harbor the mutationally identified nodulation genes rn1 and rn4, respectively, both display nodulation-deficient phenotypes. Previous investigators identified the rn1 mutation with the chickpea homolog of Medicago truncatula nodulation gene NSP2, but were unable to define the mutant rn1 allele. We used Illumina and Nanopore sequencing reads to attempt to identify and characterize candidate mutation sites responsible for the PM233 and PM405 phenotypes. Results: We aligned Illumina reads to the available desi chickpea reference genome, and did a de novo contig assembly of Nanopore reads. In mutant PM233, the Nanopore contigs allowed us to identify the breakpoints of a ~ 35 kb deleted region containing the CaNSP2 gene, the Medicago truncatula homolog of which is involved in nodulation. In mutant PM405, we performed variant calling in read alignments and identified 10 candidate mutations. Genotyping of a segregating progeny population narrowed that pool down to a single candidate gene which displayed homology to M. truncatula nodulation gene NIN. Conclusions: We have characterized the nodulation mutation sites in chickpea mutants PM233 and PM405. In mutant PM233, the rn1 mutation was shown to be due to deletion of the entire CaNSP2 nodulation gene, while in mutant PM405 the rn4 mutation was due to a single base deletion resulting in a frameshift mutation between the predicted RWP-RK and PB1 domains of the NIN nodulation gene. Critical to characterization of the rn1 allele was the generation of Nanopore contigs for mutant PM233 and its wild type parent ICC 640, without which the deletional boundaries could not be defined. Our results suggest that efforts of prior investigators were hampered by genomic misassemblies in the CaNSP2 region of both the desi and kabuli reference genomes.
2021
Subedi M, Neff E, Davis TM. Developing Chenopodium ficifolium as a potential B genome diploid model system for genetic characterization and improvement of allotetraploid quinoa (Chenopodium quinoa). BMC Plant Biology. 2021;21 (1) :490.Abstract
Background: Quinoa (Chenopodium quinoa) is a high-value grain known for its excellent nutritional bal- ance. It is an allotetraploid species (AABB, 2n = 4x = 36) formed by the hybridization between AA and BB genome diploid (2n = 2x = 18) species. This study reports genetic studies in Chenopodium ficifolium as a potential B genome diploid model system to simplify the genetic studies of quinoa including gene identification and marker-assisted breeding.
2020
Iezzoni AF, McFerson J, Luby J, et al. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. Horticulture Research. 2020;7 (1) :1-23. Publisher's Version
Von Wettberg E, Davis TM, Smýkal P. Wild Plants as Source of New Crops. Frontiers in Plant Science. 2020;11 :1426.
Davis TM, Yang Y, Mahoney LL, Frailey DC. A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination. Horticulture Research. 2020;7 (77). Publisher's VersionAbstract
The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species, Fragaria virginiana, was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygous F. virginiana hybrid “LB48” as a paternal parent with diploid (2n = 2x = 14) Fragaria vesca “Hawaii 4”. The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an “A” subgenome associated with ancestral diploid Fragaria vesca, while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously published Fragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders.
2018
Neff E, Sullivan JR, Davis TM. Enhanced Documentation of Chenopodium foggii (Amaranthaceae) in Northern New England. Rhodora. 2018;120 (983) :257-259. Publisher's Version
Smith RG, Birthisel SK, Bosworth SC, et al. Environmental correlates with germinable weed seed banks on organic farms across northern New England . Weed Science. 2018;66 (1) :78-93. Publisher's VersionAbstract
The northern New England region includes the states of Vermont, New Hampshire, and Maine and encompasses a large degree of climate and edaphic variation across a relatively small spatial area, making it ideal for studying climate change impacts on agricultural weed communities. We sampled weed seed banks and measured soil physical and chemical characteristics on 77 organic farms across the region and analyzed the relationships between weed community parameters and select geographic, climatic, and edaphic variables using multivariate procedures. Temperature-related variables (latitude, longitude, mean maximum and minimum temperature) were the strongest and most consistent correlates with weed seed bank composition. Edaphic variables were, for the most part, relatively weaker and inconsistent correlates with weed seed banks. Our analyses also indicate that a number of agriculturally important weed species are associated with specific USDA plant hardiness zones, implying that future changes in climate factors that result in geographic shifts in these zone will likely be accompanied by changes in the composition of weed communities and therefore new management challenges for farmers.
2017
Yang Y, Davis TM. A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis . Genome Biology and Evolution. 2017;9 (12) :3433-3448. Publisher's VersionAbstract

The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria(strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vescaF. iinumaeF. bucharicaF. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis.

Opazo MC, Lizana R, Stappung Y, et al. XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues. BMC Genomics. 2017;18 (1) :852. Publisher's VersionAbstract
Fragaria vesca or ‘woodland strawberry’ has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes. Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell wall-associated enzyme, which is encoded by a multigene family. Its action modifies the structure of xyloglucans, a diverse group of polysaccharides that crosslink with cellulose microfibrills, affecting therefore the functional structure of the cell wall. The aim of this work is to identify the XTH-encoding genes present in F. vesca and to determine its transcription level in ripening fruit.
Hummer KE, Davis TM. Seeking the northern boundary of the Cascade strawberry . Acta Hortic. 2017;1156 :111-116. Publisher's VersionAbstract

Fragaria cascadensis K.E. Hummer, an endemic decaploid strawberry species, was described from the Oregon Cascade Mountains in the Pacific North-western United States. Its range occurs near Mt. Hood, the highest peak in the northern Oregon Cascades, in a band of higher elevation sites southwards to near Crater Lake in southern Oregon. The objective of this study was to examine in more detail, the distribution of this species at the northern end of its range. During summer and fall 2015, several excursions were taken in the vicinity of Mt. Hood to seek the wild distribution of Fragaria species. These excursions encircled the mountain by road and hiking. The most northerly observation of the occurrence of F. cascadensis was at Lolo Pass near the junction of the Pacific Crest Trail (PCT) and Route 18; the highest elevation occurrence was observed on Mt. Hood, 2 miles south of Timberline Lodge at 1589 m (5213RSQUO). Interestingly, the region to the east of the PCT and north of Hood, was populated with octoploid strawberries, Fragaria virginiana ssp. platypetala. This region included the Cooper Spur Recreational Area. The decaploid F. cascadensis was not observed in the north to northeast sector of the mountain. While the diploid F. vesca spp. bracteata (A. Heller) Staudt was present at the PCT at Cascade Locks near the Columbia River, no higher ploidy species were observed in that vicinity. Further research is ongoing regarding the distribution and phylogeny of the Cascade strawberry in Oregon.

Mathey MM, Mookerjee S, Mahoney LL, et al. Genotype by environment interactions and combining ability for strawberry families grown in diverse environments . Euphytica. 2017;213 (5) :112. Publisher's VersionAbstract

Ten seedlings from 36 crosses representing eastern and western North American short day and remontant genotypes were evaluated in 2011 and 2012 in California, Michigan, New Hampshire and Oregon, for phenology, flower related traits, plant characteristics, fruit characteristics and fruit chemistry traits. There was significant variability among genotypes, locations and evaluation year for most of the characteristics; however, few genotype × location and genotype × year interactions were detected. General combining ability variance components were significant for all traits and greater than SCA variance components for peduncle length, total flowering weeks, flowering cycles, truss size, growing degree days for harvest data, remontancy, achene position, ease of capping, fruit weight, percent soluble solids, titratable acidity and soluble solids/titratable acidity. ‘Sarian’ was identified as the best contributing parent for remontancy. Narrow-sense heritability estimates were moderate to high (0.33–0.78) for total flowering weeks, flowering cycle, truss size, remontancy, number of runners, fruit weight, pH, and titratable acidity. Having a better understanding of these attributes will provide breeders guidance on the most effective breeding strategies for incorporating superior traits from this germplasm into their programs.

Verma S, Bassil NV, Van De Weg E, et al. Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa . Acta Hortic. 2017;1156 :75-82. Publisher's VersionAbstract

The Axiom® IStraw90 SNP (single nucleotide polymorphism) array was developed to enable high-throughput genotyping in allo-octoploid cultivated strawberry (Fragaria ×ananassa). However, high cost ($80-105 sample-1) limits throughput for certain applications. On average the IStraw90 has yielded 50 to 60% usable data points, defined as PHR (Poly High Resolution) and NMH (No Minor Homozygote) marker classes. Thus, an array is needed with a higher percentage of usable data points at a lower cost. We initiated an effort to identify IStraw90 SNP markers that were genetically mapped in one or more strawberry populations from research programs around the world. Seven programs participated in this endeavor. A total of 41,183 SNP probes were submitted to Affymetrix for quality check, 38,506 of which were accommodated on the Axiom® IStraw35 384HT design. In order to assess the performance of the Axiom® IStraw35 384HT array, 384 DNA samples from the University of Florida strawberry breeding program were assayed at a cost of$ 50 per sample, all inclusive. The performance of the array met expectations. More than 87% of markers belonged to the PHR and NMH categories. This array is expected to provide high-quality genome scanning at a more affordable price for strawberry researchers worldwide.

2016
Jing JW, Davis TM, Zhang Q. Perspectives on Elevated Ploidy in Regenerants from Plant Tissue Culture and Transformation. Research & Reviews: Journal of Botanical Sciences. 2016;5 (4) :19-21. Publisher's VersionAbstract

Elevated ploidy is a common phenomenon among plants regenerated
from tissue culture. Contributors to this effect include cells of elevated ploidy
present within normally diploid or polyploidy explant tissues, endoreduplication
by individual cultured cells, and effects of
in vitro
environmental factors on cell
division. Because polyploidization can result in morphological changes and thus,
different adaptabilities, the determination of ploidy in transgenic regenerants
plants is recommended when evaluating phenotypes and conducting mutant
screens subsequent to genetic transformation.
Sargent DJ, Yang Y, Šurbanovski N, et al. HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria ×ananassa) . Plant Science. 2016;242 (4) :140-150. Publisher's VersionAbstract

The cultivated strawberry, Fragaria × ananassa possesses a genetically complex allo-octoploid genome. Advances in genomics research in Fragaria, including the release of a genome sequence for F. vesca, have permitted the development of a high throughput whole genome genotyping array for strawberry, which promises to facilitate genetics and genomics research. In this investigation, we used the Axiom® IStraw90® array for linkage map development, and produced a linkage map containing 8,407 SNP markers spanning 1,820 cM. Whilst the linkage map provides good coverage of the genome of both parental genotypes, the map of ‘Monterey’ contained significantly fewer mapped markers than did that of ‘Darselect’. The array contains a novel marker class known as haploSNPs, which exploit homoeologous sequence variants as probe destabilization sites to effectively reduce marker ploidy. We examined these sites as potential indicators of subgenomic identities by using comparisons to allele states in two ancestral diploids. On this basis, haploSNP loci could be inferred to be derived from F. vesca, F. iinumae, or from an unknown source. When the identity classifications of haploSNPs were considered in conjunction with their respective linkage map positions, it was possible to define two discrete subgenomes, while the remaining homoeologues of each chromosome could not be partitioned into two discrete subgenomic groupings. These findings suggested a novel hypothesis regarding octoploid strawberry subgenome structure and evolutionary origins

Mahoney LL, Sargent DJ, Abebe-Akele F, et al. A High-Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae, Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing . The Plant Genome. 2016;9 (2). Publisher's VersionAbstract

Fragaria iinumae Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for F. iinumae. The F. iinumae linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter "Array"), and genotyping by sequencing (GBS). The F2 generation mapping population was derived by selfing F. iinumae hybrid F1D, the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the Fragaria vesca ssp. vesca L. 'Hawaii 4' pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between F. iinumae and F. vesca, and/or to F. vesca genomic assembly errors. The Fii map provides a basis for anchoring a F. iinumae genome assembly as a prerequisite for constructing a second diploid reference genome for Fragaria.

Liu B, Poulsen EG, Davis TM. Insight into octoploid strawberry (Fragaria) subgenome composition revealed by GISH analysis of pentaploid hybrids . Genome. 2016;59 (2) :79-86. Publisher's VersionAbstract

As the product of interspecific hybridization between its two ancestral octoploid (2n = 8x = 56) species (Fragaria chiloensis and F. virginiana), the cultivated strawberry (F. ×ananassa) is among the most genomically complex of crop plants, harboring subgenomic components derived from as many as four different diploid ancestors. To physically visualize the octoploids’ subgenome composition(s), we launched molecular cytogenetic studies using genomic in situ hybridization (GISH), comparative GISH (cGISH), and rDNA-FISH techniques. First, GISH resolution in Fragaria was tested by using diploid and triploid hybrids with predetermined genome compositions. Then, observation of an octoploid genome was implemented by hybridizing chromosomes of pentaploid (2n = 5x = 35) hybrids from F. vesca × F. virginiana with genomic DNA probes derived from diploids (2n = 2x = 14) F. vesca and F. iinumae, which have been proposed by phylogenetic studies to be closely related to the octoploids yet highly divergent from each other. GISH and cGISH results indicated that octoploid-derived gametes (n = 4x = 28) carried seven chromosomes with hybridization affinities to F. vesca, while the remaining 21 chromosomes displayed varying affinities to F. iinumae, indicating differing degrees of subgenomic contribution to the octoploids by these two putatively ancestral diploids. Combined rDNA-FISH revealed severe 25S rDNA loss in both the F. vesca- and F. iinumae-like chromosome groups, while only the prior group retained its 5S loci.

2015
Vining KJ, Davis TM, Jamieson AR, Mahoney LL. Germplasm resources for verticillium wilt resistance breeding and genetics in strawberry (Fragaria) . Journal of Berry Research. 2015;5 (4) :183-195,. Publisher's VersionAbstract

BACKGROUND: The fungal disease verticillium wilt has been recognized as an obstacle to strawberry production since its initial description in 1931. The full potential of genetic resistance as a solution to this problem has yet to be determined or realized.

OBJECTIVE: Our investigations are concerned with defining new sources of resistance to verticillium wilt disease in cultivated and wild strawberry germplasm, and with advancing genetic studies on the basis of resistance/susceptibility.

METHODS: We screened 23 diploid, 1 decaploid, and 26 octoploid Fragaria (strawberry) germplasm accessions and cultigens for response to root-dip inoculation with Verticillium dahliae.

Bassil NV, Davis TM, et al. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genomics. 2015;16 (155). Publisher's VersionAbstract

### Background

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.

### Results

About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.

### Conclusions

The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.

2014
Mathey MEGANM, Mookerjee S, Mahoney LL, et al. Using general and specific combining ability to further advance strawberry (Fragaria sp.) breeding. Acta Hort. 2014;1049 :193-200.Abstract
Strawberry is one of the five fruit crops included in the USDA-funded multiinstitutional and trans-disciplinary project, "RosBREED: Enabling Marker- Assisted Breeding in Rosaceae". A Crop Reference Set (CRS) was developed of 900 genotypes and seedlings from 40 crosses representing the breadth of relevant diversity and encompassing founders used in breeding the domesticated strawberry. Individual native species and cultivar genotypes were included along with 10 progeny from 36 of the crosses of genotypes representing eastern and western North American and European short day and remontant cultivars. This CRS has been phenotyped in five U.S. states. Over 14 fruit quality traits have been studied, as well as remontancy, truss size, peduncle length, crop estimate, plant architecture, and disease resistance. The phenotyping conducted in the first growing season showed considerable variability amongst the genotypes and the locations for all of the characteristics. General and specific combining ability variance components were determined from the populations in order to provide breeders with guidance on the most effective breeding strategies for incorporating the superior traits from this germplasm into their programs.