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.
