ASHS 2024 Conference

In this interactive workshop, participants will be provided training on how to use Rosaceae (GDR, www.rosaceae.org), Vaccinium (GDV, www.vaccinoum.org) and Citrus (www.citrusgenomedb.org) specialty crop databases resources, as well as the Breeding Data Management tools, BIMS (www.breedwithbims.org), and the Field Book App for phenotype data collection. Using a case-study approach we will focus on how to use these integrated resources most efficiently for research and crop improvement efforts, how to apply FAIR data principles to sharing and submitting research data to these databases at the time of publication and facilitate a robust dialogue between researcher, breeders and the development team on needed improvements and long-term sustainability options for these resources.

This interactive workshop will bring together researchers and breeders to accelerate research and crop improvement in specialty crops. It will provide training and feedback on how to most effectively use the NIFA SCRI and National Research Support project 10 (NRSP10) funded Rosaceae, Citrus, and Vaccinium specialty crop databases and breeding data management resources (BIMS and Field Book), learn how to follow FAIR data principles, foster better two-way communication for increased feedback from researchers on further development of these resources, and continue to build a robust community around these research and crop improvement tools. The trainers include users and developers of these resources, ranging from early career to well-known and respected research enabling resource generators.

The Genome Database for Rosaceae (GDR), Genome Database for Vaccinium, and Citrus Genome Database (CGD) offer critical resources and tools to enable genomic, genetic, and breeding research for fruit, nut, and ornamental crops of great economic importance to the U.S. In addition, BIMS (BreedwithBIMS.org) and the Field Book APP provide widely used tools for managing plant breeding program data. While these resources are heavily used worldwide, many researchers are unaware of the full potential of using them and how they can contribute their own data for wider recognition and reuse. This interactive workshop aims to bridge this knowledge gap by providing hands-on training for specialty crop researchers on how to best use these resources and contribute their data. The workshop will also solicit ideas from participants on how to improve these databases and discuss the various options to make them sustainable in the long term. The workshop will bolster the utilization of integrated big data, promote future data sharing, and ensure that data is FAIR (Findable, Accessible, Interoperable, and Reusable).

The workshop aims to bring together researchers to accelerate research by more effective use of specialty crop databases and breeding data management resources, encouraging data submission at the time of publication, and gaining feedback from researchers. Through hands-on training, participants will become more familiar with the database resources and breeding data management tools, learn how to submit their data, and provide essential input for improving these databases and their long-term sustainability.

Coordinator(s)

• Dorrie Main, Washington State University, Pullman, WA, United States

Moderator(s)

• Cameron Peace, Washington State University, Horticulture, Pullman, WA, United States

Speaker/Participant(s)

• Dorrie Main, Washington State University, Pullman, WA, United States

Introduction to the Workshop and Specialty Crop Research Databases (15 mins)

• Jodi Humann, Washington State University, Horticulture, Pullman, WA, United States

How to efficiently use integrated genomics data and tools for research (20 mins)

• Sook Jung, Washington State University, Horticulture, Pullman, WA, United States
  How to efficiently use integrated genetics data and tools for research (20 mins)
  
  
• Nahla Bassil, USDA ARS, National Clonal Germplasm Repository, Corvallis, OR, United States
  How to efficiently use integrated germplasm and genotype data for research (15 mins)
  Summary:
  
  
• Trevor Rife, Clemson University, Plant and Environmental Sciences Department, Florence, SC, United States
  How to use the Field Book App for phenotypic data collection (15 mins)
• Sushan Ru, Auburn University, Auburn, United States
  How to use the Breeding Information Management System, BIMS, for Crop Improvement (20 mins)
• Cameron Peace, Washington State University, Horticulture, Pullman, WA, United States

ASHS Intellectual Property Interest Group Session
Proposal Proposed by: Fruit Breeding Interest Group and Intellectual Property Interest Group

Plant intellectual property is an important topic for plant breeders, universities and private companies who handle the release and exchange of plant materials. On the one hand, properly protecting new cultivars is critical to protect the genetic integrity of the genotype and credit the developer. On the other hand, understanding the types of intellectual property laws relevant to plants is important for breeders/researchers to exchange materials for collaborative evaluation and development. Therefore, this interest group session will focus on plant intellectual protection and material transfer. We will invite speakers from public and private plant breeding programs as well as experts on intellectual property laws to share their knowledge and advice on following areas: Domestic plant protection, International plant protection, Domestic plant material transfer, and International plant material transfer. The topic of intellectual property was voted by members of both interest groups (Fruit Breeding Interest Group and Intellectual Property Interest Group) as a high priority area. This session will greatly benefit plant breeders, researchers, and intellectual property officers.

Coordinator(s)

• Sushan Ru, Auburn University, Auburn, United States

Moderator(s)

• Julia Harshman, Duda Farm Fresh Foods, United States

Speaker/Participant(s)

• Matthew Clark, University of Minnesota, Department of Horticulture, United States
  Plant Protection and Material Transfer in the University of Minnesota Grape and Apple Breeding Program

Haplotype-Phased Genome Assemblies of ‘Sulhyang’ Strawberry (Fragaria ×ananassa) using PacBio Revio Sequencer - Youngjae Oh
Exploring the molecular basis of rootstock-mediated growth vigour in macadamia: Unravelling aquaporin gene dynamics - Pragya Dhakal Poudel
Multivariate Analysis of Fruit Composition Diversity Among the North Carolina Strawberry Germplasm Collection - Gina Fernandez
Improving Blueberry By Dissecting Fruit Texture - juan david jimenez pardo
Assessment of Fruit Composition and its Influence on Flavor and Consumer Preferences in Blackberry - Katelyn Lust-Moore
Sugar Content and Gene Expression Dynamics in Apple Spurs in Response to Fruit Load and Gibberellins - Qiuyi Fu
A Census and The Conservation of Malus coronaria in Michigan - Lily Christian

Cultivated strawberry (Fragaria ×ananassa Duch, 2n = 8× = 56) belongs to the family Rosaceae and is an allo-octoploid species. We report here a high-quality haplotype-phased genome assembly of a representative Korean short-day cultivar, ‘Sulhyang’ using a trio-binning approach. Using PacBio Revio long reads of ‘Sulhyang’ and whole genome paired-end reads (Illumina) of two parents ‘Akihime’, and ‘Yukbo’, we completed telomere-to-telomere phased genome assemblies of both haplotypes. The ‘Sulhyang’ genome was 797 Mb , with a long terminal repeat (LTR) assembly index (LAI) of 17.28. The genome was phased into two haplotypes, phase-1 (784.9 Mb with contig N50 of 12.34) and phase-2 (781 Mb with contig N50 of 16.04 Mb). The BUSCO analysis detected over 99% of conserved genes in the combined phased-1 and phased-2 assembly. Both haploid assemblies were annotated using RNA-Seq data representing various F. ×ananassa tissues from the NCBI sequence read archive, resulting in a total of 104,099 genes in the primary assembly. This haplotype-phased reference genome for ‘Sulhyang’ will broaden our knowledge of strawberry genome evolution and gene functions.

Rootstocks play a crucial role in shaping plant growth and vigour, driven by a complex interplay of physiological, molecular, and genetic factors. Aquaporins (AQPs), as key water transport proteins, are emerging as pivotal component in understanding rootstock-mediated vigour. However, evidence for rootstock effects in macadamia remains limited with no exploration into the mechanisms of rootstock-mediated vigour control, hindering progress in rootstock development for this crop. In this study, we aimed to explore the role of AQPs by conducting a genome-wide investigation on whole genome sequence of Macadamia integrifolia (‘HAES741’). This study identified 37 putative macadamia AQP (miAQP) genes belonging to 5 different sub-families including 11 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, 10 Nod26-like intrinsic proteins, 2 small and basic proteins and 6 X-intrinsic proteins. miAQP genes are unevenly distributed across 11 chromosomes with chromosome 7 possessing the most genes. To investigate the differential expression of plasma membrane intrinsic proteins (PIPs), in high- and low-vigour rootstocks, root, leaf, and stem tissues were collected from trees with a single scion ‘HAES741’ grafted on to 7 different rootstock genotypes . RNA from tissue samples were extracted by a modified CTAB RNA extraction protocol using the Zymo-spin™ IICR Column. RNA quality and quantity was checked via nano spectrophotometer and gel electrophoresis. Primer pairs for 11 PIP genes and 2 housekeeping genes (ACT and EF1b) were designed using Primer BLAST in NCBI. RNA samples were subjected to a real time quantitative RT-PCR. The tissue specific expression data will be analysed to observe differential expressions, if any, between high and low vigour rootstocks and scions. Differential expression patterns reveal the PIP genes associated with vigour control. The correlation between gene expression levels and rootstock vigour provides better understanding on the intrinsic molecular mechanism vigour regulation in macadamia. Moreover, comparative analysis of PIP gene expression between rootstock and scion can provide insights into the rootstock-scion interactions. Overall, results from this study offer a better understanding of the molecular basis of rootstock-mediated vigour control with implications for rootstocks development and orchard optimization in macadamia.

Strawberries are a highly sought-after fruit for their flavor, color, and nutritional benefits. In this study, strawberry fruit from 268 commercial cultivars and advanced selections from the North Carolina breeding program were evaluated to determine and characterize genotype diversity, relationships, and overall trends in fruit composition. Fifteen marketable, fully red, firm fruit were harvested per genotype between April and June of 2022 from a greenhouse core collection and held at -20°C until analysis. Juice from thawed fruit was used to collect total soluble solids (SSC), total titratable acidity (TTA), and pH data. Strawberry juice was also extracted with acidified methanol (0.1ml/1.6 ml total) and supernatants used to determine monomeric anthocyanin content (TA) using the pH differential method. Agglomerative hierarchical clustering (AHC) and multivariate analysis of variance (MANOVA) sorted genotypes into four clusters, highlighting significant differences in fruit composition profiles. The majority of commercial cultivars, and 38 advanced selections, were grouped together in Cluster 1. This cluster was distinguished by lowest SSC (7.0%), TTA (0.72%), and TA (31.22 mg/100g) values. In contrast, Cluster 2 containing 41.4% of germplasm had fruit highest in TA (54.57 mg/100g). Fruit from genotypes in Cluster 3 had high pH and %SSC, and the smallest group (Cluster 4), with 13.1% of the germplasm, had low pH and was significantly greater in %TTA. Regional strawberry breeding programs were found to group together. The Florida germplasm were grouped in Cluster 1, North Carolina commercial genotypes in Cluster 2, and two advanced New Jersey genotypic lines were found in Cluster 3. California day-neutrals were found in Cluster 1, while short-day genotypes were split between the first two clusters. Additionally, the first two principal components in PCA analysis captured 64.88% of the total variance, with both pH and TTA largely contributing to PC1 (91.1%), SSC in PC2 (71.1%), and TA associated with PC3 (77.4%). Variation in pH and %TTA had a more pronounced effect on genotype profiles and were the primary driving force for germplasm separation and differentiation. This work represents the first instance where an entire germplasm collection was assessed together in a single evaluation. The determination of genotype diversity, characterization of relationships among the genotypes and the fruit composition parameters, and visualization of trends within the collection will help guide future breeding decisions for developing new strawberry cultivars with improved quality.

Breeding efforts to improve blackberry (Rubus subgenus Rubus) flavor have previously been a subjective and imprecise process. The flavor perception of blackberries is largely controlled by interactions between sugars, acids, and volatile components. The aim of this study was to determine what combinations of these biochemical compounds result in positive flavor perception by the average consumer to assist in determining breeding targets. In the first year of data collection, consumer panelists assessed pureed frozen blackberries from the University of Arkansas Fruit Breeding Program for overall liking, aroma, flavor, sweetness and sourness across 24 sensory panels. Pearson correlation coefficients were generated to determine the relationship between overall liking and significant effects. Positive correlations to overall liking were significant for flavor intensity (0.99), aroma intensity (0.50), and sweetness intensity (0.89) indicating increases in flavor, aroma, and sweetness resulted in greater liking. Sourness was found to have a negative correlation with overall liking (-0.81). The positive correlation between liking and Brix (0.54) aligns with the perceived sweetness relationship, similarly the negative relationship between liking and titratable acidity (-0.59) aligns with perceived sourness. Panelists’ perceptions of fruity or indulgent flavors such as grape, banana, strawberry, apple, jam and candy produced significant positive correlations with overall liking. While fruit presenting flavors described as citrus, grassy, earthy, musty, pine, or chemical produced significant negative correlations with overall liking. The volatiles associated with these perceived flavors were also assessed using gas chromatography mass spectrometry.

Blueberry texture is a critical trait impacting mechanical harvesting, transportation resilience, shelf life, and consumer preference. Its complexity arises from multiple attributes, requiring a depth understanding for developing breeding tools to generate varieties with superior texture profiles. In this study, a diverse group of southern highbush blueberry (SHB) genotypes, reflecting various textures, were subjected to mechanical phenotyping, consumer perception analysis, and cell wall composition analysis. By conducting instrumental analysis using a texture analyzer, three key parameters crucial for genotype differentiation based on texture were identified. Consumer perception analysis revealed moderate agreement in texture classification between breeders and panelists. Additionally, cell wall composition analysis highlighted galacturonic acid as a potential monosaccharide capable of categorizing texture. The integration of mechanical phenotyping, consumer perception analysis, and cell wall composition analysis offers a comprehensive approach to dissecting blueberry texture. This enables breeders to select and develop blueberry varieties meeting consumer expectations, enhancing market competitiveness, and supporting the growth and sustainability of the global blueberry industry.

Many commercial apple (Malus x domestica Borkh.) cultivars follow a biennial bearing cycle, alternating between an “on” year with a heavy crop load and an "off" year with few if any fruit. It is commonly thought that biennial bearing is conditioned by repression of floral initiation by developing fruit. Although various studies have provided some insights into the regulation of flowering and biennial bearing by fruit load, the associated molecular-genetic pathway involved remains unclear. The objective of this study is to evaluate the influence of fruit load on the expression of specific, presumed flowering genes in the spur leaves and shoot apex, focusing on the potential role of sugars in this process. The hypothesis is that the potential accumulation of photosynthates in the leaf or shoot apex related to the absence of a strong sink (developing fruit) promotes floral initiation by directing the expression of floral-promotive genes. To test this, physiologically similar ‘Royal Red Honeycrisp’ trees were manipulated to influence fruit load. The accumulation of soluble sugars (fructose, sorbitol, glucose, and fructose) in the spur leaf and shoot apex was evaluated using a gas chromatograph. RNAs were extracted and gene expression patterns in the leaf and apex were evaluated using quantitative RT-PCR and direct sequencing; results will be presented. This study should provide new insights into the fundamental mechanisms of biennial bearing in apple. This may lead to approaches to limit the impact of biennial bearing in existing orchards, and genetic information useful for apple cultivar improvement.

Crop wild relatives are important genetic resources for cultivar improvement. Domesticated apple (M. x domestica) cultivars grown in North America are heterogeneous hybrids of Asian and European Malus species, with no known genetic contribution from native apples. M. coronaria (Sweet Crabapple) is the only native apple species found within the major apple-producing Great Lakes region. In spite of its potential importance for apple cultivar improvement, the genetics of this species has not been well studied, and only a few accessions are maintained in the USDA National Plant Germplasm System (NPGS). The objective of this research was to identify and collect new accessions of M. coronaria for the NPGS, focusing on the northernmost extent of its range in Michigan. To locate living trees, we combined analyses of historical records in 12 herbaria and the North America Fruit and Nut Tree Data, along with crowdsourcing using the popular online platform, iNaturalist. We identified a total of 158 M. coronaria records from herbaria and the fruit tree dataset. Records were removed from consideration if they were cataloged earlier than 1950, did not include collection coordinates, were redundant, or were not collected in the state of Michigan. iNaturalist listed 309 sightings of M. coronaria in Michigan; of these, we determined that a majority were likely misidentified based on the phenotypic characteristics in the images provided by the observer. Finally, Google Earth was used to rule out locations where the M. coronaria individuals had likely been lost due to anthropogenic activity. Ultimately, this three-factored approach identified only 64 sites within the state of Michigan where a living tree would likely be found. Our results provide strong evidence that M. coronaria is in decline within its native range in Michigan, underscoring the importance of conservation efforts for this species.

Validation of Diagnostic Markers for Stenospermocarpic Seedlessness and Flower Sex in Diverse Muscadinia and Vitis Grape - Isabella Vaughn
High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Leaf-Scab Resistance in Pecan - Gaurab Bhattarai
Genome Wide Association Studies Unmasks Loci Associated With Fruit Size and Sugar Content in Mango - Vincent Njung'e Michael
A Genome-Wide Association Study To Identify Loci Underlying Fruit Color In Red Raspberry - Claudia Baldassi
Relatedness of Luther Burbank’s Plum (Prunus sp.) Introductions based on Genotyping by Sequencing (GBS) - Rachel Spaeth
A Deep Learning‐based Smartphone App for Blueberry Yield Prediction - Sushan Ru
Utilizing Optical Sorting Technology for High-Throughput Phenotyping in Sweet Cherry Breeding - Per McCord

Muscadine grapes (Muscadinia rotundifolia) are perennial vines grown commercially in the Southeast United States for the fresh market and as wine and juice grapes. Two highly sought-after traits in fresh market muscadine cultivars are stenospermocarpic seedlessness and perfect-flowered vines. However, the genetic disparity between Vitis and Muscadinia subgenera, coupled with differing chromosome numbers (Vitis=38 chromosomes, Muscadinia=40 chromosomes), presents challenges in introgression of stenospermocarpy from V. vinifera to M. rotundifolia. Although conventional breeding has introduced stenospermocarpy into M. rotundifolia, no molecular markers for this trait have been validated in muscadines. Recently, two Kompetitive Allele Specific PCR (KASP) markers targeting candidate genes for male sterility (VviINP1) and stenospermocarpy (VviAGL11) in V. vinifera have shown promise. Sequence comparisons with published V. rotundifolia genomes suggest that these markers might be effective across diverse Vitis, Muscadinia, and wide hybrid germplasm. In this study, we validated the predictive ability of KASP markers for flower sex and stenospermocarpy across thirteen Vitis x Muscadinia hybrid seedling populations and 191 diverse genotypes. In 2023, 891 seedlings were evaluated for seedlessness, with an additional 214 seedlings assessed for flower sex. Furthermore, 191 diverse accessions underwent evaluation for both flower sex and seedlessness. Of the 891 seedlings, 66 were seedless, 490 were seeded, and 335 could not be phenotyped due to fruit absence. Among the 214 seedlings assessed for flower sex, 88 were perfect, 106 were female, and 20 could not be phenotyped due to flower absence. The stenospermocarpy marker accurately predicted 771 of 783 seedlings and diverse material, while the flower sex marker matched 366 of 383 seedlings and diverse accessions. Discrepancies between marker predictions and observed phenotypes may be due to human error or pollen sterility. Notably, most fruitless seedlings were predicted to be stenospermocarpic, indicating potential issues with partial sterility or cold hardiness in seedless hybrids. We intend to reevaluate the populations for flower sex and seedlessness in summer 2024 to address discrepancies. Overall, the KASP markers developed in V. vinifera exhibited excellent predictive ability across diverse germplasm, offering valuable insights for muscadine breeding programs.

Genetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan mapping population of 119 F 1 trees was derived from a cross of the widely planted cultivars Pawnee and Elliott. Whereas ‘Pawnee’ is susceptible, ‘Elliott’ has long- standing resistance to pecan scab caused by the fungal pathogen Venturia effusa. Molecular markers were developed using genotyping-by-sequencing, and linkage maps were constructed for each parent following the two-way pseudo-test-cross strategy used for cross-pollinated species. The ‘Pawnee’ and ‘Elliott’ maps contain 1,347 and 1,050 single nucleotide polymorphism markers spanning a genetic distance of 4,493.0 and 3,758.4 cM, respectively. While these map lengths are likely inflated due to genotyping errors, a high level of synteny between genetic and physical distances of the markers in both parental maps was achieved. Scab resistance was evaluated through controlled inoculations in the greenhouse using two scab isolates, and a significant quantitative trait locus (QTL) for scab resistance was identified on chromosome 5 in ‘Elliott’. Candidate gene searches within the 2-logarithm of the odds interval of the scab-resistant QTL identified a number of disease resistance related genes, including genes encoding wall-associated receptor kinases, cytochrome P450s, leucine-rich repeats receptor-like serine/threonine-protein kinases, a pectinesterase inhibitor, a cellulose synthase, a flavonol synthase, a 4-coumarate-CoA ligase, a caffeic acid 3-O-methyltransferase, and a MYB domain transcription factor.

Mango (Mangifera indica L.) is a popular fruit produced widely along tropical climates for fresh consumption. In this study, mature fruits from a collection of 189 mango cultivars were evaluated for fruit weight and sugar content at horticultural maturity. Subsequently, a total of 10958 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing (GBS) were used to identify quantitative trait nucleotides (QTNs) associated with fruit weight and sugar content through genome wide association studies (GWAS). Fruit weight over three seasons averaged 454 g. ‘Lancetilla’ and ‘Webber’ cultivars produced the heaviest fruits averaging 1127.5 g and 1108.5 g respectively and the lowest average fruit weights (166.16 g, 184.5 g, and 189.5 g) were observed in ‘Itamaraca’, ‘13-1' and ‘Fralan’ cultivars respectively. The mango cultivars had a mean degrees Brix (°Bx) value of 14.8 with ‘Venus,’ ‘Peach Cobbler’ and ‘Julie’ displaying the highest degrees Brix (°Bx) values of 25.6, 22.4 and 20.6 respectively. Three QTNs in chromosomes 5, 8 and 10 were significantly associated with fruit weight using Fixed and random model Circulating Probability Unification (FarmCPU) association model, while two QTNs in chromosome 2 and chromosome 20 were significantly associated with sugar content using Bayesian-information, Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Genetic characterization of loci associated with these two traits in mango provides a solid foundation for SNP marker assisted selection (MAS) to accelerate molecular screening of segregating populations and germplasm in a mango breeding program.

Red raspberry (Rubus idaeus L.) is a high-value crop, acclaimed for its fruit quality characteristics and putative health benefits. Among fruit quality characteristics, color is a critical trait in determining market acceptability and consumer preference. Red raspberry fruit encompasses a wide array of colors, notably yellow, orange, and red. Red fruited cultivars are the most common in commercial settings and market selection is dependent on the color intensity: while the processing industry needs dark berries for most applications, the fresh market requires bright red and non-darkening fruit. Anthocyanins, a group of water-soluble phenolic compounds, are regarded as the major contributors to raspberry red fruit color. Knowledge on the genetics of raspberry fruit pigmentation would be valuable for breeding programs, but to date the genetic control of the different red intensities of raspberries remains elusive. This research aims to map the genetic regions underlying the red shades of raspberry fruit through a genome-wide association study (GWAS). Fruits from 765 red raspberry cultivars and selections – including red-, orange-, and yellow-fruited genotypes – were harvested over four seasons (2018-2021) and analyzed for total anthocyanin content and color. Total anthocyanins were measured through the pH differential methods and color was assessed using a high-throughput digital phenotyping protocol. Leaves from all genotypes were harvested in summer 2022 and used for genomic DNA extraction. Whole-genome sequencing of DNA samples was achieved through Illumina NovaSeq6000, with an average coverage of 30×. Sequences were aligned to the ‘Malling Jewel’ reference genome using BWA-MEM and single nucleotide polymorphisms (SNPs) were identified following the GATK pipeline. Total anthocyanin content ranged between zero (yellow genotypes) and 113.21 mg/100 g fresh weight (FW) of peonidin-3-O-glucoside equivalents (P3OG eq.) and averaged 42.09 mg/100 g FW P3OG eq. Color coordinates L* (lightness) varied between 11.99 and 48.21 and averaged 21.21, a* (red-green) spanned -1.18 and 38.38 and averaged 26.85, b* (yellow-blue) ranged between 4.57 and 30.04 and averaged 18.05. The association between the detected genetic variants and the phenotypic data (fruit color and total anthocyanins) will enable the identification of SNP markers that explain the variation in observed red shades of berries. Such markers will be used in raspberry breeding programs to facilitate the development of cultivars with desired fruit color.

The renowned horticultural artist and plant breeder Luther Burbank worked with many different species of plants. During his 50-year career, he introduced over 800 cultivars, including more than 150 accessions of plums (Prunus spp.) in the late 1800’s and early 1900’s. Burbank preferred utilizing wide, interspecific crosses to create a vast range of phenotypic variation and then artificially select from the extremes. While a very great artist, Burbank was a substandard scientist because he was derelict in pedigree note-taking. Though many of his introductions are extinct, hobbyists, enthusiasts, and international collections retain nearly a third of the economically viable cultivars he bred. For a century, many of his hybridizations remained inscrutable mysteries until modern genomic and computational tools developed their resolution and statistical power. Today, genotyping by sequencing (GBS) is a useful tool for pedigree reconstruction in the absence of reliable records. GBS can inform principal component analyses (PCA), identity by descent (IBD) kinship, and phylogenetic admixture, revealing complex relationships among taxa. In this study, whole genome sequencing was performed on 53 Prunus taxa used by Luther Burbank in his breeding experiments in the most comprehensive genetic survey of his work to date. Exact parent-offspring relationships between this population may be impossible to discern due to years of back crossing, sibling mating, and open pollination. However, the proportion of genomic similarity amongst these taxa provides information on the relatedness of the genotypes in Burbank’s Prunus experiments, defining four primary lineages within his breeding population. These lineages are comprised primarily of P. salicina and P. simonii, but also have influences from P. americana, P. cerasifera, P. domestica, and P. rivularis. The prevalence of P. simonii in Burbank’s Prunus introductions appears to have been vastly underreported, indicating that some of the seedstock founders of his breeding population could have been P. salicina x P. simonii hybrids at the inception of his career. This research has implications for pedigree reconstruction and prioritizing conservation in collections curation for future studies.

The global blueberry market has been expanding vastly driven by consumer demand for healthier food. As a top blueberry producer, United States generated a revenue of $932 million in 2020. A profitable blueberry industry relies on continued cultivar improvement. One challenge faced by blueberry breeders, researchers, and growers, is yield data collection. Measuring blueberry yield by manual sampling is labor-intensive and time-consuming. We developed a smartphone application leveraging deep learning techniques to automate yield prediction and maturity assessment for different blueberry cultivars under field conditions. State of the art YOLOv8 models were fine-tuned and evaluated using a dataset of side-view images of various southern highbush and rabbiteye blueberry cultivars. The best performing DL model of YOLOv8-x achieved a mean average precision of 0.708 and 0.372 under 0.5 and 0.5-0.95 Intersection over Union thresholds on validation datasets, respectively. Blueberry yield was predicted using non-linear regression-based machine learning models using the image-derived mature berry count multiplied by user-defined average berry weight and cultivar as explanatory variables with satisfactory accuracy. This proposed smartphone app can enable image-based yield prediction for blueberry growers and breeders, which is valuable for management decision making and accelerated selection for high-yielding cultivars.

Phenotyping remains a bottleneck in many breeding programs, including sweet cherry. Current fruit evaluation protocols require extensive manual sorting and visual evaluation, which reduces throughput and is subject to evaluator bias and fatigue. The Washington State University Cherry Breeding Program is seeking more efficient methods of evaluating fruit quality. In 2023, the program acquired an optical fruit sorter. Our objective was to customize the sorter parameters according to breeding program needs and compare the results of the sorter with traditional methods. Our Tomra InVision 2 sorter has the same optics, software and computer hardware as a commercial sorter, but operates on a single lane. Fruit are loaded onto an infeed system which passes fruit in single file into the detection area. A combination of fruit rotation, multiple cameras and mirrors is designed to image the entire surface of individual fruit. Both visual and infrared images are captured, generally > 24 images per fruit at a rate of approximately 15 fruit per second. The sorter software identifies fruit and classifies them according to a set of tunable quality parameters or grades. Air-actuated valves then eject the fruit into one of four grade-determined exits. The sorter generates reports that include the fruit size profile as well as the percentage of fruit sorted into the various exits and/or grades. The sorter shipped with a pre-loaded map (sorting algorithm), which we modified by updating with data from representative images of various quality parameters. We then used the sorter to grade fruit from Phase 2 variety trials. We analyzed 50-fruit subsamples in the traditional manner for size and defects. All remaining fruit from each sample were analyzed via the sorter. Out of 20 samples evaluated, the average number of fruit per sample evaluated by the sorter was 154, vs. 50 for manual evaluation. Overall, the sorter detected a lower percentage of cracking, doubles (polycarpy), and pitting vs. manual evaluation, and a higher percentage of skin blemishes. Continued testing will be required to determine whether these differences are due to the effects of small sample size or bias due to the methods themselves (human evaluator vs. sorter). While the sorter required a similar number of personnel as for manual evaluation, it required less time to evaluate each sample even though more fruit were analyzed. We will expanding the use and testing of the sorter in 2024, including evaluation of postharvest quality.

A Century of Pear Breeding at the USDA - Christopher Gottschalk
Differential Thermal Analysis of Cold Hardiness in Interspecific Hybrid Grapevine for Breeding Applications - Douglas Vines
Ovary and Fruit Shape Variation Associated with Novel ClSUN25-26-27a Alleles in Watermelon - Samuel Josiah
Linking Cultivar Evaluations – Phenology, Metabolomics, Consumer Preferences, and Postharvest Handling of ‘Glenn’ Mango - Jonathan H Crane
Evaluation of Small Fruit Germplasm at the North Willamette Research and Extension Center - Patrick Jones
Developing a Genomic Framework for Selection of Fruit Attributes in Cold Climate Interspecific Grapes (Vitis Spp.) - Venkateswara Rao Kadium
U.S. Peach Production and Breeding Overview - Chunxian Chen
Introduction of modern tools to the University of Arkansas System Division of Agriculture Fruit Breeding Program - Carmen A. Johns

The U.S. Department of Agriculture (USDA) Agriculture Research Service (ARS) has operated a European pear (Pyrus communis) scion breeding program for over a century. The breeding program started in the early 1900s by Merton B. Waite in the Washington D.C. area with the primary objective to develop host resistance to fire blight, a devastating disease caused by Erwinia amylovora. The USDA pear breeding program has continued this effort throughout its history, spanning over six generations of breeders and two cooperative research programs in Michigan and Ohio. The program has released ten named pear varieties, with the first one, 'Waite,' being released in 1938 and the most recent, 'Bell,' in 2022. In this presentation, we discuss the program's history by detailing each generation of breeder(s) aims, their parental selection, and releases. In addition, we present corrected pedigrees for important breeding lines and the releases. Lastly, we present the current objectives of the program, the pedigree complexity of newly generated populations, and the overall success of the program’s primary breeding goal – fire blight resistance.

Interspecific hybrid grapevine cultivars have been developed to expand grape cultivation into cold-climate areas. Cold weather events can lead to bud death and trunk injury which reduce yields and can result in plant death. Phenotyping cold hardiness is challenging, and developing a standardized phenotypic protocol would enable efficient evaluation of University of Minnesota grape breeding germplasm. The objective of this study is to utilize differential thermal analysis as an assay to quantify the low temperature exotherm response of grapevine buds. We phenotyped 28 varieties and advanced breeding selections from October 10th, 2023 through March 20th, 2024. Commercial cultivars (e.g. Marquette, Itasca, Frontenac) and breeding selections (wine grape, table grape, and rootstocks) were sampled weekly or bi-weekly based on availability of plant material. Differences in acclimation and deacclimation patterns between time points were observed in the low temperature exotherm readings, indicating that there may be differences in the genetic mechanisms for cold hardy responses. After the coldest day of the season, January 14, 2024, which had a low of -23°C, the temperature at which 50% of the buds would die, or LT50, for ‘Marquette’, ‘Itasca’, and ‘Frontenac’ were -29.7 °C, -30.9 °C, and -30.5 °C, which is consistent with field observations. The LT50s were rated at lower temperatures than the ambient air temperature, thus all genotypes were able to survive the weather conditions for this cold event. Future analysis aims to utilize K-means cluster analysis to determine groups that differ in responses to winter fluctuations in temperature and to determine the genetic controls for these responses.

The genetic mechanisms controlling fruit morphology in watermelon is not fully understood. Only one candidate gene, ClSUN25-26-27a (Cla011257), has been identified as a significant contributor to the ovary and fruit shape. ClSUN25-26-27a is a member of the SUN gene family, which has been extensively studied in relation to fruit morphology in tomatoes. In tomato, the effect on fruit shape facilitated by this gene is detectable during the early stages of fruit development, with the cell patterns established pre-anthesis. In watermelon, three alleles of ClSUN25-26-27a are known to be associated with ovary and fruit shape variation: the wild-type, a SNP, and a 159bp deletion in the 3rd exon. This study aims to determine the effect of the novel allelic variation for ClSUN25-26-27a on ovary and fruit shape. Four novel alleles have been identified and sequenced in the coding region of ClSUN25-26-27a across three Citrullus species. Marker assisted backcrossing was used to introgress the different alleles into a common genetic background. The NILs were phenotyped in the field to determine the effect of the novel alleles on ovary and fruit shape. Ovary length and width were measured four days pre-enthesis, at anthesis, and four days post-anthesis and used to calculate the ovary shape index (OSI). Mature fruit was also phenotyped using Tomato Analyzer. One of the novel alleles was significantly associated with ovary and fruit shape. These findings contribute to the understanding of the important SUN gene family and the genetic mechanisms contributing to watermelon fruit shape. Future research will determine the gene expression patterns of the different alleles and the effect of the alleles on the cell number or cell size in watermelon.

Mangos are the fifth most consumed fruit in the world (World Atlas). The top five mango producers include India, China, Indonesia, Pakistan, and Mexico (World population). Puerto Rico is the largest U.S. mango producer (2,666 acres), followed by Florida (2,455 acres), Hawaii (497 acres), California (328 acres), and Texas (10 acres). There are thousands of mango cultivars worldwide and the development and selection of new cultivars is ongoing. However, relatively few cultivars have a combination of information on their phenology, metabolomic profiles, consumer preferences, and postharvest handling. Describing and linking these cultivar evaluations and attributes may improve marker-assisted breeding efforts to develop and select for superior mango flavor, aroma, and nutritional value, improve understanding of hedonic consumer preferences, and result in improved postharvest handling and processing of mango. For example, ‘Glenn’ mango is a moderately vigorous tree with an upright open canopy that is generally dormant from November through December-January that flowers during February-March in response to warming ambient temperatures and is harvested during June-July. Historical descriptions are that it is a fruit of excellent eating quality with a rich, aromatic (pineapple notes) flavor, low fiber, and sweet pulp. This is borne out by the nonvolatile physiochemical characteristics of the cultivar including an average TSS of 15.93, TA of 0.65, and TSS/TA ratio of 24.41, with high concentrations of fructose, glucose, isocitric acid, and ketoglutaric acid. Defining nonvolatile flavor constituents from partial least-squares discriminant analysis for ‘Glenn’ mango were fructose, glucose, sucrose, isocitric acid, ketoglutaric acid, malonic acid, and gallic acid whereas defining volatile aroma constituents included ten esters (e.g., ethyl acetate, ethyl butanoate, and ethyl octanoate) that have floral, citrus, sweet, fruity, pineapple, and coconut notes. Results from a consumer sensory (taste, flavor, texture, fibrousness, juiciness, etc.) acceptance study indicated consumers like ‘Glenn’ mango because of its sweetness, tropical flavor, low fiber content, and juiciness, bearing out historical descriptions of this fruit. More detailed metabolic biosynthesis mapping linked flavor precursors and intermediates to the constituents responsible for flavor and aroma of ‘Glenn’. Postharvest evaluations reported ‘Glenn’ was moderately susceptible to hot water treatment injury, significant anthracnose incidence, only slight chilling injury (if stored below the 13°C recommended temperature) and could be stored for at least 3 weeks.

Since the 1920’s, Oregon State University (OSU) and the United States Department of Agriculture (USDA) Horticultural Crops Production and Genetic Improvement Research Unit have cooperated in the public breeding and development of small fruit cultivars to support Pacific Northwest (PNW) production. Together, the PNW states of Oregon and Washington have significant berry production with 152,407 metric tons of blueberry (Vaccinium spp.), 24,494 metric tons of red and black raspberry (Rubus idaeus; R. occidentalis), 9,525 metric tons of blackberry (Rubus spp.), and 6,804 metric tons of strawberry (Fragaria x ananassa) in 2022. Processed berries are the primary regional market, with fresh market production a lesser but still important driver for small farms. To continue to improve regional production of high-quality fruit, cultivar development has been a top tier research priority for PNW berry commodity commissions over the past decade. The cooperative breeding program has a continual germplasm improvement cycle that includes plant material in all stages of development, from seedlings, observational and replicated field trials, grower trials, and cultivar releases. After seedling evaluation, promising advanced selections of strawberry, blueberry, blackberry, red raspberry, and black raspberry crops are assessed at the OSU North Willamette Research and Extension Center in Aurora, Oregon. The USDA and OSU cooperative breeding program, in collaboration with Washington State University, has a uniquely strong focus on developing machine harvestable small fruit cultivars. Over 20 cultivars have been released with a value to PNW industries of over $450 million in the last ten years. ‘Tillamook’ strawberry, and ‘Black Diamond’ and ‘Columbia Star’ blackberry lead the acreage in Oregon and were developed by the program. More than 50 berry cultivars have been released since 1942 exclusively by the USDA with another 16 jointly-released with other agricultural universities and international corporations. This presentation will outline the cooperative breeding framework, discuss breeding priorities, and highlight new and upcoming cultivar releases.

Hybrid grapevines (Vitis spp.) grown in cold climate regions have fruit chemistries which do not adhere to the standard ranges of European wine grapes (Vitis vinifera L.) that many consumers may be accustomed to. The variation in fruit chemistry observed in hybrid grapevines is driven by a combination of genetics of parent material, which often builds on wild Vitis species, and the environmental conditions of production, which are often characterized by low heat accumulation and limited duration of growing season. Characterizing the genetic basis of fruit attributes enables breeders to understand and improve the relative quality of interspecific grapevines for future cultivar development. To address this knowledge gap for breeders, an incomplete diallel population of interspecific hybrid grapevines was assessed over a period of three years. Fruit chemistry (total soluble solids, pH, total acidity, glucose, fructose, malic acid, tartaric acid, citric acid, and yeast assimilable nitrogen content) and berry mass were examined at three distinct time points within each growing season to yield a total of nine phenotyping events. Best linear unbiased predictors (BLUPs) calculated from multi-year phenotype data were then interrogated via GWAS analysis to identify significant marker-trait associations. Chromosomes 16, 6, and 17 were noted to have the highest number of associations observed. To further understand the specificity of observed loci, gene annotation was conducted to reveal several important genes potentially related to the phenotypes. Due to the quantitative nature of fruit attributes, genomic selection strategies were explored to assess their accuracy for improving population performance in a systematic manner. Cumulatively, this analysis provides important information regarding the role of genetics in major fruit traits of interspecific cold hardy grapevines, regions of interest for fine mapping, and strategies for genomic selection. These analyses contribute towards the goals of improving breeding efficiency and selection accuracy to reduce generation timeline in grapevines.

Peach is an introduced crop with a relatively short production and breeding history in the U.S. The peach industries have been facing declines and challenges in both production and breeding activities over the past decades. Understanding of the statuses and issues facilitates gaining insights and finding solutions. This presentation is to provide an overview of U.S. peach production and breeding, including trends, issues, and prospects. Both U.S. peach acreage and production are declining, but market values increasing. Public peach breeding programs were established at the early time and helped establish considerable production in many states. But most of them have been terminated, phased out, or de-emphasized, largely due to declining production and economic impact. Taken into consideration all factors, visionary peach horticulture research and breeding solutions for some cost-related and yield-limiting production issues are essential for profitable and sustainable peach production in the future.

The University of Arkansas System Division of Agriculture (UADA) has a legacy breeding program that has spanned three fruit breeders and 60 years. The UADA Fruit Breeding Program is large, complex, and works on multiple crops. A recent program initiative has been the introduction of modern tools for breeding approaches and data collection and management. This talk will outline the process for developing a molecular breeding pipeline for blackberry (Rubus subgenus Rubus Watson) and muscadine grape (Muscadinia rotundifolia) and outline how these approaches benefit program progress. Additionally, advances in data collection techniques such as digital evaluations using an application and development of barcoding systems for streamlining processes and minimizing error will be described.