Population Structure and Phylogeny of Some U.S. Peach Cultivars

Peach (Prunus persica) cultivars maintained at the U.S. Department of Agriculture program at Byron, GA, have never been characterized with any molecular markers. In this study, 20 microsatellite markers were used to genotype 112 cultivars and the data were analyzed to discern their population structure and phylogenetic relationships. STRUCTURE simulations revealed four K clusters and broad genetic admixture among the cultivars. Principal coordinate analysis (PCoA) showed the cultivar groups from western, northeastern, and southeastern U.S. states were adjacent to each other except cultivars from Michigan (close to most southeastern state groups) and Florida (most distant from the other groups). Principal component analysis (PCA) showed that these cultivars had no obvious PCA partitioning boundaries. The intertwined distribution in both PCoA and PCA partitions suggested many of them were genetically closely related to each other largely because most shared same ancestral parentages. Most pairwise distance means within and between the cultivar groups were relatively low, suggesting close phylogenetic relations among those cultivars, as were demonstrated in the phylogenetic tree. Limiting factors and perspectives relevant to peach breeding are discussed.

Transcriptome-wide Identification and Characterization of microRNAs and Their Targets in a Highly Adaptable Conifer Platycladus orientalis

MicroRNAs (miRNAs) are short noncoding RNAs (20–25 nucleotides) that regulate gene expression posttranscriptionally. However, identification and characterization of miRNAs remain limited for conifer species. In this study, we applied transcriptome-wide miRNAs sequencing to a conifer species Platycladus orientalis, which is highly adaptable to a wide range of environmental adversities, including drought, barren soil, and mild salinity. A total of 17,181,542 raw reads were obtained from the Illumina sequencing platform; 31 conserved and 91 novel miRNAs were identified, and their unique characteristics were further analyzed. Ten randomly selected miRNAs were validated by quantificational real-time polymerase chain reaction. Through miRNA target predictions based on psRNATarget, 2331 unique mRNAs were predicted to be targets of P. orientalis miRNAs that involved in 187 metabolic pathways in KEGG database. These targets included not only important transcription factors (e.g., class III homeodomain leucine zipper targeted by por-miR166d) but also indispensable nontranscriptional factor proteins (i.e., por-miR482a-3p regulated nucleotide-binding site leucine-rich repeat protein). Interestingly, six miRNAs (por-miR16, -miR44, -miR60-5p, -miR69–3p, -miR166b-5p, and -miR395c) were found in adaptation-related pathways (e.g., drought), indicating their possible involved in this species’ stress-tolerance characteristics. The present study provided essential information for understanding the regulatory role of miRNAs in P. orientalis and sheds light on their possible use in tree improvement for stress tolerance.

Artificial Shading Can Adversely Affect Heat-tolerant Lettuce Growth and Taste, with Concomitant Changes in Gene Expression

Shading has been used to produce high-quality lettuce (Lactuca sativa) in locations where production conditions are not optimal for this cool-season crop. To learn what additional benefits shading provides if heat-tolerant cultivars are used and to understand the effects of shading on growth, sensory quality, chemical content, and transcriptome profile on heat-tolerant lettuce, we grew two romaine lettuce cultivars with and without shading using 50% black shadecloth in 2018 and 2019. Shading reduced plant leaf temperatures, lettuce head fresh weights, glucose and total sugars content, and sweetness, but not bitterness, whereas it increased lettuce chlorophyll b content compared with unshaded controls. Transcriptome analyses identified genes predominantly involved in chlorophyll biosynthesis, photosynthesis, and carbohydrate metabolism as upregulated in unshaded controls compared with shaded treatments. For the tested cultivars, which were bred to withstand high growing temperatures, it may be preferable to grow them under unshaded conditions to avoid increased infrastructure costs and obtain lettuce deemed sweeter than if shaded.

Sitosterol-mediated Antioxidant Regulation to Enhance Heat Tolerance in Creeping Bentgrass

Heat stress symptoms in cool-season plants are characterized by loss of chlorophyll (Chl) and membrane stability, as well as oxidative damage. The objectives of this study were to determine whether foliar application of β-sitosterol, a naturally occurring plant metabolite, may promote heat tolerance by suppressing heat-induced leaf senescence as indicated by the maintenance of healthy turf quality (TQ), and Chl and membrane stability; and to determine its roles in regulating antioxidant metabolism in creeping bentgrass (Agrostis stolonifera). ‘Penncross’ plants were exposed to heat stress (35/30 °C day/night) optimal temperature conditions (nonstressed control, 22/17 °C day/night) for a duration of 28 days in environment-controlled growth chambers. Plants were foliar-treated with β-sitosterol (400 µM) or water only (untreated control) before heat stress, and at 7-day intervals through 28 days of heat stress. Plants treated with β-sitosterol had significantly greater TQ and Chl content, and significantly less electrolyte leakage (EL) than untreated controls at 21 and 28 days of heat stress. Application of β-sitosterol reduced malondialdehyde (MDA) content significantly at 21 and 28 days of heat stress, and promoted the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) from 14 through 28 days of heat stress. β-Sitosterol effectively improved heat tolerance through suppression of leaf senescence in creeping bentgrass exposed to heat stress in association with the alleviation of membrane lipid peroxidation and activation of the enzymatic antioxidant system.

A Consensus Genetic Map and Linkage Panel for Fresh-market Tomato

The first consensus genetic map in fresh-market tomato (Solanum lycopersicum) was constructed, combining genetic recombination data from two biparental F2 segregating populations derived from four different fresh-market tomatoes. Each F2 population was nominated by different academic tomato breeding programs located in major fresh-market tomato-producing areas of the United States, and chromosome-wide variation in recombination rates was observed between tomato populations based on the origin of their breeding programs. A consensus map constructed using 335 common single nucleotide polymorphism (SNP) sites found in both populations spanned 737.3 cM across 12 tomato chromosomes, with chromosome 2 containing more than 40% of the total SNPs and chromosomes 4, 5, 7, and 10 together representing less than 10% of the SNPs. There was a high degree of collinearity between the genetic and physical positions of those 335 SNP markers. The integration of 6553 SNP sites that were detected in either of the two populations with 335 common sites resulted in an extended consensus genetic map. The total length of the extended map was estimated to be 1997.9 cM, which was compatible with a previous estimate for large-fruited fresh-market tomato. A linkage panel for fresh-market tomato was also established using the combined dataset of the consensus map of 335 SNP loci and 73 SNP-genotyped core fresh-market tomatoes. An empirical genetic mapping study of the tomato brachytic trait using the linkage panel demonstrated the value of the consensus map and linkage panel for tomato research. The allelic information in the linkage panel will serve as a basis for SNP marker implementation, such as genotyping platforms and genomic association map, in tomato.

Novel Sources of Resistance to Fusarium oxysporum f. sp. lycopersici Race 3 Among Solanum pennellii Accessions

Fusarium wilt of tomato (Solanum lycopersicum), caused by fungal pathogen Fusarium oxysporum f. sp. lycopersici (Fol), is one of the most important diseases in tomato production. Three races of the pathogen are described, and race-specific resistance genes have been applied in commercial tomato cultivars for controlling the disease. Race 3 (Fol3) threatens tomato production in many regions around the world, and novel resistance resources could expand the diversity and durability of Fol resistance. The wild tomato species, Solanum pennellii, is reported to harbor broad resistance to Fol and was the source of two known Fol3 resistance genes. In this study, we evaluated 42 S. pennellii accessions for resistance to each fusarium wilt race. F1 plants, developed from crossing each accession with the Fol3 susceptible line ‘Suncoast’, were evaluated for Fol3 resistance, and BC1F1 plants were screened to determine the likelihood that Fol3 resistance was based on a novel locus (loci). Nearly all accessions showed resistance to Fol3, and many accessions were resistant to all races. Evaluation of F1 plants indicated a dominant resistance effect to Fol3 from most accessions. Genetic analysis indicated 24 accessions are expected to contain one or more novel Fol3 resistance loci other than an allele near the I-3 locus. To investigate genetic structure of the S. pennellii accessions used in this study, we genotyped all 42 accessions using genotyping by sequencing. Approximately 20% of the single nucleotide polymorphism (SNP) loci were heterozygous across accessions, likely due to the outcrossing nature of the species. Genetic structure analysis at 49,120 unique SNP loci across accessions identified small but obvious genetic differentiations.

Genetic Diversity and Population Structure of Chionanthus virginicus

The genus Chionanthus, known as fringetrees, is a member of the olive family (Oleaceae). Chionanthus virginicus is an understory tree or shrub with a wide range in forests of the eastern United States and is used as an ornamental tree that is known to be free of insects and disease in the wild. The species is tolerant of a wide range of environmental conditions, and there is interest in developing new cultivars with improved horticultural traits, such as tree form or upright growth habit and superior flowering display that are widely adapted. To identify genepools in the native range of C. virginicus for use in breeding programs, the genetic diversity and population structure were assessed for 274 individuals from 12 locations in four states (Florida, Maryland, North Carolina, and Texas) using 26 simple sequence repeats (SSRs). An average of 12.54 alleles/locus were detected, allelic richness averaged 2.80. Genetic differentiation was 0.11, indicating moderate differentiation among subpopulations. Despite the high genetic diversity and low population differentiation, Bayesian clustering analysis identified six genetic groups that match the geographic distribution of collection sites. Analysis of molecular variance indicated that most (82%) of the variation is explained within individuals, and 11% and 7% of the variation is due to differences among individuals within populations and among populations. Analysis of isolation by distance across all samples showed a weak positive relationship between geographic distance and genetic distance. The C. virginicus samples analyzed in this study indicate there is sufficient diversity for germplasm collection for use in breeding programs. Given the relatively moderate genetic differentiation, there are not likely to be unique islands of genetic diversity that may be missed when gathering parental materials for a breeding program

Floral Aromatics of Ptelea: Chemical Identification and Human Response

Many members of the citrus family (Rutaceae) are valued for the aromatic compounds emitted by their flowers. Ptelea species are unusually cold-hardy members of the Rutaceae, but conflicting descriptions of the fragrance of their unisexual flowers may discourage the use of these trees. We analyzed floral volatiles and human response to these chemicals to test the hypothesis that the fragrance of staminate and pistillate flowers of these species differs. Gas chromatography and mass spectrometry showed that most volatile chemicals emitted by flowers of Ptelea trifoliata and Ptelea crenulata are monoterpenes, sesquiterpenes, and esters. Most volatiles were emitted from flowers of both sexes, but ethyl benzoate and estragole were emitted only from pistillate flowers. When concentrations of aromatics differed between sexes, they were higher for pistillate flowers, except for cis-3-hexenyl butanoate and an unidentified terpene. For P. crenulata and P. trifoliata, respectively, 81% and 77% of survey responses were from volunteers who liked the fragrance. Panelists most frequently described the scent of flowers of P. crenulata of both sexes with the words citrus, lime, and sweet. Panelists distinguished between pistillate and staminate flowers of P. trifoliata, describing the odor of pistillate flowers most frequently with the words damp-earthy, spicy, and sweet; staminate flowers were perceived as light, fresh, grassy, and pleasant. This work represents the first analysis of floral volatiles of P. crenulata and resolves conflicting prior reports regarding the floral fragrance of P. trifoliata. We conclude that differences among people rather than the sex of flowers account for conflicting prior reports of floral fragrance. The scents of flowers of P. crenulata and P. trifoliata appeal to most people and are horticultural assets of these trees.

Fruit Qualities of Interspecific Hybrid and First Backcross Generations between Red Raspberry and Rubus parvifolius

Interspecific hybridization is useful in raspberry (Rubus idaeus L. ssp. idaeus) breeding to introgression of traits such as heat or cold tolerance, and excellent fruit qualities. Rubus L. wild species in Asia, including Rubus parvifolius L., have been attracting a great deal of attention as sources of new traits in breeding raspberry and blackberry (Rubus fruticosus Agg.). We previously developed and selected IPI-1 and IPI-3 first backcross (BC1) hybrids, [‘Indian Summer’ (R. idaeus ssp. idaeus) × R. parvifolius] × ‘Indian Summer’, as raspberry cultivars adapted to the warm climate in parts of Japan. In this study, we investigated the growth, morphological traits, and fruit qualities, such as sugar, organic acid, anthocyanins, and carotenoids, of each of these IPI lines over a 2-year period to discern their potential as commercial raspberry cultivars. IPI lines had the characteristic of primocane fruit with overflowing from side buds while the parent, IP-1 (‘Indian Summer’ × R. parvifolius), did not. IPI lines showed significantly lower values in anthocyanin content than red raspberry ‘Skeena’, while showing higher carotenoid contents. This study is the first research about fruit qualities such as anthocyanin and carotenoid content of BC1 hybrids using Japanese wild Rubus species.