Transcriptomic responses underlying host-pathogen interactions between resistant and susceptible Prunus accessions and two Armillaria Root Rot fungi - Stephen Parris Fine mapping of Linkage Group 7 (LG7) Eastern Filbert Blight (EFB) Resistance in Hazelnut - Rion Mooneyham Estimation of Breeding Values to Improve Kernel Weight in Almond (Prunus dulcis) - Shashi Goonetilleke Alternative RNA Splicing Associated with Pecan Dichogamy - Xinwang Wang Alaska Can Grow More Than Giant Vegetables: The Potential of Rhubarb for Specialty Crop Producers - Carol Miles Utilization of Germplasm to Improve Illinois Horseradish - Alan Walters
Armillaria root rot (ARR) caused by Desarmillaria caespitosa and Armillaria mellea represents the main cause of premature stone fruit and nut tree decline in the United States. A. mellea is a primary concern for almond and peach growers in California, while D. caespitosa threatens peach production in the southeast region of the U.S. These fungi survive as facultative necrotrophs and colonize roots of several agriculturally important crops, including peach, almond, and sweet cherry. This colonization ultimately kills the woody roots and therefore host, severely limiting the tree’s lifespan and ability to provide a return on investment for the grower. Few management options are available to slow down ARR disease progression, and no management practice eliminates ARR fungi presence in an infested field. Additionally, most of the commercially available rootstocks are susceptible to infection, with only two peach/plum hybrid commercial rootstocks (Prunus umbellata × P. persica ‘MP-29’ and P. cerasifera × P. persica ‘Krymsk® 86’) showing partial resistance to ARR. The shared plum genetic background in these hybrids, paired with the lack of ARR resistance observed in peach germplasm suggests the source of resistance originated from plum. In this work, induced genetic responses in one susceptible accession, P. persica ‘Guardian®’, and two resistant accessions, P. cerasifera ’14-4’ and ‘MP-29’, when infected with D. tabescens and A. mellea were analyzed. Additionally, expression of genes encoding effectors and cell wall degrading enzymes (CWDEs) were investigated in the ARR fungi while infecting the three hosts. The results of the infection assays revealed unique responses between each of the three hosts in their progression of disease symptoms over time and in their transcriptomes while under infection by the two ARR fungi. Analysis identified key hub genes expressed by the two resistant Prunus accessions involved in the sensing and enzymatic degradation of chitin and the upregulation of GSTs, oxidoreductases, and transcription factors. Investigation of the ARR fungi transcriptomes similarly identified host-dependent expression of fungal effectors and CWDEs responsible for degrading the cell wall components cellulose, hemicellulose and pectin. Comprehensive analyses considering transcriptomes produced by both the host and pathogen during the infection course provides a deeper understanding of the factors driving resistant and susceptible responses to ARR infection, and their effects on the infecting pathogen’s gene expression.
Eastern filbert blight (EFB) disease caused by the fungal pathogen Anisogramma anomala (Peck) E. Müller is a major threat to Oregon’s hazelnut (Corylus avellana) industry. The Oregon State University (OSU) hazelnut breeding program has used ‘Gasaway’ as a source of resistance in many releases. Cultivars with ‘Gasaway’ resistance mapped to linkage group 6 (LG6) including ‘Jefferson’ and ‘McDonald’ have been extensively planted throughout Oregon’s Willamette Valley over the past decade. However ,‘Jefferson’ and ‘McDonald’ have exhibited small cankers in commercial orchards under high disease pressure. In New Jersey, cultivars with ‘Gasaway’ resistance develop large cankers. Thus, there are concerns about the long-term durability of ‘Gasaway’ resistance and the sustainability of Oregon’s hazelnut industry. The disease is also a main limiting factor to commercial hazelnut production in the eastern USA. New sources of resistance would be interesting, and a few major resistance genes have been mapped to LG7. Four populations were developed for fine mapping the LG7 resistance region using the ‘Ratoli’ (from Spain) and OSU 1166.123 (from Sochi, Russia) resistance sources. SSRs narrowed the resistance region to < 20 cM, and recombinant individuals were identified using 4-5 SSR loci within the region. Recombinants were inoculated with Anisogramma anomala in the greenhouse and in the field, and disease was evaluated 18 months later. A set of 22 new SSR markers were developed from di- and tri-nucleotide repeats between the flanking markers in the ‘Jefferson’ genome (v4). SSR markers were characterized using a diversity panel of 50 hazelnut accessions. To develop KASP/PACE primers for SNPs in the region, an initial set of 3000 SNPs was reduced to 100 using a SNP array. High density genetic linkage maps with new SSR and KASP markers were constructed for all four mapping populations. The results of this study will aid marker-assisted selection and the breeding of EFB-resistant cultivars with these new sources, and facilitate the pyramiding of R-genes in a single clonal selection for more durable resistance.
Improving nut and kernel quality traits is a high priority in almond breeding programs around the world. Almond has a long juvenile period and phenotypic selection for nut and kernel traits can only be conducted after three years from planting. In early stages of planting, individuals with desirable nut and kernel traits can be identified by marker-trait associations (MTAs) using molecular markers. Currently, MTAs are identified by quantitative trait locus (QTL) mapping using progeny from bi-parental crosses or association mapping panels. However, the efforts of identifying MTAs using current QTL detection methods are hampered either by unavailability of genomic information or required genetic linkage maps. In addition, most kernel traits have polygenic inheritance, and many genes and genomic regions affect genetic variations. In crop research, genomic selection would provide promising approach to accelerate the genetic gains and reduce the length of breeding cycle. Yet, application of genomic selection in almond breeding and research is limited. We present results demonstrating the predictive ability of whole-genome and pedigree-based models to identify elite candidate parents for almond kernel weight. In this work, we used ancestral pedigree and phenotypic data from 13,000 progeny that were derived from 57 parents and 291 families. Ancestral pedigrees were recorded from the available literature from the almond breeding programs in USA, Spain, Italy, France, and Australia. Average kernel weight was obtained for each progeny tree from 30 nuts. All parents were resequenced using whole-genome sequencing at a depth of 15x. Over 80k high quality, independent single-nucleotide polymorphisms were used to construct realised genomic relationship matrix and linkage disequilibrium (LD) regions were used to compute LD weights. Genomic best linear unbiased prediction (GBULP) using Asreml-R was used to predict genomic estimated breeding values (GEBV). Pedigree model derived from linear mixed model was used to predict individual tree effects (PEBV) to validate the predicted GEBVs. EBVs were compared using Pearson correlation coefficient (r) and elite candidate parents were selected based on the selection index. For kernel weight, both pedigree and genomic models resulted similar EBVs, and r was 0.97. A high level of correlation in EBVs obtained from two methods indicates the suitability of these models in estimating BVs for future predictions. Predicted elite candidate parents from this study can reduce the conventional breeding cycle of almond by 6 years. The constructed models mainly represent Australian context and multi-environmental trials are required to identify the broader applicability of these models.
Pecan (Carya illinoinensis), a North American native nut crop, exhibits two distinct flowering habits where male and female flowering occur at separate times. Trees that shed pollen before their pistillate flowers become receptive are classified as protandrous or type 1 (recessive homozygous, pp), while those with pistillate flowers receptive before pollen shed are protogynous or type 2 (dominant heterozygous, PP/Pp). Establishing commercial pecan orchards requires planting both types of pecan cultivars to ensure optimal pollination for maximum production. To investigate critical genes associated with pecan heterodichogamous flowering, we collected tissues from four stages (dormant buds, swollen buds, immature catkins, and immature pistils) of three genotypes (PP, Pp, and pp). Paired-end RNA sequencing at 125/150 bp read lengths was conducted on an Illumina platform. Clean and unique reads were mapped to an annotated 'Pawnee’ reference genome. Out of 32,267 annotated genes, over 5,000 (~15%) were identified to have alternative splicing events associated with pecan flowering dichogamy. We illustrate by three genes that present significant alternative splicing patterns associated with dichogamy genotypes, distinguishing the pp genotype from PP and Pp genotypes. These genes exhibited 6-18 nucleotide differences in RNA sequence between the pp genotype and PP/Pp genotypes, potentially resulting in an altered protein product with 2-6 amino acid differences between type 1 and type 2 genotypes. This study provides evidence for the prevalence of alternative RNA splicing in the transcription regulation of pecan dichogamy.
Specialty crop producers in Alaska need consistent, suitable crop and varietal options for successful commercial production, as food security is a major concern in this state that imports 95% of its food. The climate in much of Alaska is ideal for cool season, perennial corps that are winter hardy, such as Rhubarb (Rheum sp.). Rhubarb was brought to Alaska through several waves of immigration from regions extending from Russia through England and is now established throughout the state. Once a site for the National Plant Germplasm System (NPGS) Arctic and Subarctic Plant Gene Bank, the University of Alaska Fairbanks Matanuska Experiment Farm and Extension Center still maintains a collection of 41 accessions of Rheum sp. in the field. In addition, a new collection of heirloom rhubarb plants has been assembled by a local grower and maintained in large pots. In this project, we collected leaf samples from the heirloom collection plants for genotyping and phenotyping, as well as benchmark samples from plants remaining in the former germplasm collection, to provide an understanding of relatedness and desirable characteristics. A 5 cm square sample of leaf tissue was harvest from each plant, dried, and sent to a commercial laboratory for genotyping. Size and color of leaves and petioles, dates of emergence, plant vigor, and juice quality were measured on plants from the heirloom collection. Finally, surveys carried out of the last 12 years targeted a diversity of stakeholders (commercial producers, business owners, and the general public) to identify rhubarb quality expectations, including flavor, juice content, petiole color, and plant vigor. Based on genotyping results, plants not genetically redundant to those in the NPGS rhubarb collection currently located in Pullman, Washington, will be added to the collection. We present recommendations for variety suitability for different climate regions of Alaska based on the traits measured, taking into account varieties of rhubarb currently available wholesale to Alaska. Recommendations are also presented for further research into commercial production and added-value characteristics.
Horseradish (Armoracia rusticana, Brassicaceae) is an important specialty crop in Illinois, with most commercial production adjacent to St. Louis, Missouri in what is known as the Mississippi Bottoms. The continued development of new, improved horseradish cultivars is critical to sustain this important specialty crop industry, since horseradish clonal cultivars tend to "run out" and lose their productivity over a period of about 10 years. A small germplasm collection of clones from eastern Europe and Russia, as well as old cultivars no longer in wide use and other breeding materials that were saved from the breeding program has been maintained since the 1960s, first at University of Illinois until the early 2000s and now at Southern Illinois University-Carbondale. During the last 20 years, germplasm has been utilized from various sources to improve horseradish so this industry can sustain itself for the near future. The following examples are provided to illustrate the importance of new germplasm in new horseradish cultivar development. Accession 761A collected from Drążgów, Poland was instrumental in developing horseradish cultivars with tolerance to internal root discoloration which is caused by a soil-borne pathogen complex. The germplasm clone Czech has been very effective in transmitting its large root size trait to its resulting progeny and was used in many crosses made from 2005 to 2010. Many cultivars grown today have this germplasm source in their background. Another important clonal cultivar known as 9705 was widely grown during the 2000s and resulted from outcrossing accession 758A collected from Ribnica, Slovenia with an unknown male. Additionally, 315 is another very important cultivar that was the workhorse for the industry from 2005 to 2015 having lineage also from 758A. 15K was another industry workhorse in the late 1990s to early 2000s, and had its primary lineage traceable to 856A, an accession from the Czech Republic. These are a few examples of how germplasm sources have contributed to sustaining the Illinois horseradish industry and each will be discussed in further detail regarding their specific benefits. Moreover, most are still used in some capacity in the breeding program today.
The Power of Breeding and Genetics in Controlled Environment Horticulture - Krishna Bhattarai Novel Summer Squash: Breeding Tromboncino Types for U.S. Markets - James Myers Mapping QTL for Bacterial wilt resistance and plant height in Tomatoes - Dilip Panthee Effects of Prolonged Photoperiod on Chile Pepper Plant Architecture and Growth Habit - Shahab Nourbakhsh Seasonal Lettuce Germplasm Trials in Northeast Florida Hydroponics - Evelyn Fletcher Marker Development for Cadmium Accumulation in Spinach - Danyelle Forte
Controlled environment (CE) horticulture production has shown its potential to cope with the impact of climate change such as rising temperatures and declining water availability. Drives like “locally grown”, and “food miles reduction” favor CE-based food production which represents a $50 billion market for fresh, local, and sustainable food. CE production systems use advanced technology for climate control and mechanized growing practices for which infrastructure and software development have taken a good start. Contrastingly, the breeding and development of plants designed to best perform in CEs to reduce energy usage, allow automation, and increase profits are just beginning. The US CE producers can benefit from the breeding and development of new cultivars with modified stature that offer high-density planting and shortened crop cycles, ease in maintaining and harvesting, and allow automation. Utilization of plant genetics to breed for plant statures will increase crop diversity in CEs. Additionally, discovering new genetics in plant germplasms to enhance crop quality for nutrition, flavor, taste, color, and texture through breeding can meet consumer needs for fresh, high-quality, nutritious, and sustainably produced food. Several other opportunities exist where leveraging genetics to breed new crops that produce nutraceuticals, biofuel, macro and micronutrients, and bioactive compounds can sustain the CE horticulture industry, feed the increasing population, improve health, and cope with climate change.
Cucurbitaceae family squash and pumpkins are all New World domesticates from different parts of the Americas. While many types are eaten as winter squash at full maturity, others – termed summer squash – are used as vegetable where the immature fruit is eaten. The summer squash we are most familiar with belong to the species Cucurbita pepo. The immature fruit of C. maxima and C. moschata are sometimes used as summer squash and a few land race types have been developed mainly for summer squash use. ‘Tromboncino’ (also called Trombetta or Zucchetta Rampicante), is one such C. moschata summer squash from the Ligura region of Italy. It is most closely related to the butternut winter squashes. Originally domesticated in the tropical lowlands of Middle America, it is more tolerant of high temperatures, humidity and pest and diseases. Tromboncino is essentially a butternut squash with an extended neck that has been adapted to use as an immature vegetable but can also be used as a winter squash. The heritage varieties of Tromboncino are long-vined with prolific fruit production and produce few seeds. The seeds are found in a bulb at the end of the fruit, leaving a long seedless neck for culinary preparation. It has a firmer, meatier texture and a flavor profile that is more similar to a mature butternut squash. Tromboncinos are at their highest quality when used at 6-12" long, but they can be eaten at later stages until fully mature. The main breeding objective of the OSU vegetable breeding program was to develop a tromboncino type with better adaptation to the cool summers of Western Oregon, shift plant architecture to a bush plant habit while retaining prolificacy, and shorten fruit length for fresh market production. Another objective was to combine the tromboncino type with skin colors other than the traditional tan color of the heritage variety. We have been able to accomplish most objectives although the plant architecture is not yet comparable to the bush habit of C. pepo summer squash. Some types have dark green as well as yellow skin colors (conditioned by the precocious yellow gene). Two advanced lines are in the process of being released.
Bacterial wilt (BW) of tomatoes, caused by Ralstonia solanacearum, is a devastating dis-ease that results in large annual yield losses worldwide. Management of BW of toma-toes is difficult due to the soil-borne nature of the pathogen. One of the best ways to mitigate the losses is through breeding for disease resistance. Moreover, plant height (PH) is a crucial element related to plant architecture which determines nutrient management and mechanical harvesting in tomatoes. An intra-specific F2 segregating population (NC 11212) of tomatoes was developed by crossing NC 84173 (tall, BW susceptible) x CLN1466EA (short, BW resistant). We performed quantitative trait loci (QTL) mapping using single nucleotide polymorphic (SNP) markers and the NC 11212 F2 segregating population. The QTL analysis for BW resistance revealed a total of three QTLs on chromosomes 1, 2, and 3, explaining phenotypic variation (R2) ranging from 3.6% to 14.9%. Whereas, QTL analysis for PH also detected three QTLs on chromo-somes 1, 8, and 11 explaining R2 ranging from 7.1% to 11%. This work thus provides information to improve BW resistance and plant architecture-related traits in toma-toes.
This experiment sought to examine the effects of prolonged photoperiod and modified temperature and humidity in chile peppers, aiming to develop a protocol to accelerate their growth and enhance breeding efficiency. Four genotypes from three Capsicum species (C. annuum - Chimayo, Early Jalapeno; C. chinense - Orange Habanero; Chiltepin - C. annuum var. glabriusculum) were planted in two randomized flat trays per entry using SunGro propagation soil. After reaching the 2-3 leaf stage, they were transplanted into 8” pots, incorporating sterilized and LM-AP soil mixtures. The experimental population was grown in an improvised growth chamber with an average temperature of 25°C and humidity of 60% and exposed to a 20-hour daily cycle of 450 nm full spectrum LED grow lights and 730 nm Far Red LED grow lights and 4 hours of darkness. The control group grew in normal greenhouse conditions, exposed to normal daylight intensity and duration and an average temperature of 21°C and humidity of 40%. Weekly data recordings included plant growth measurements of plant height and leaf count. Basal branches were counted approximately 12 weeks after planting, and leaf widths were recorded 14 weeks after transplanting. Number of flowers and fruits were also recorded at 14 weeks after transplanting. Data were analyzed using RStudio, and Tukey HSD was used to detect differences between treatments and among genotypes. In terms of plant height, all experimental plants demonstrated a significant increase compared to the control group, both in absolute amounts and in rates, especially later in the growth stage. The leaf numbers in experimental plants were significantly lower than the control group, except for Orange Habanero, which showed no significant difference. Early Jalapeno, in both treatments, exhibited no significant difference in basal branches. In contrast, the remaining experimental plants displayed fewer or no basal branches compared to the control group. All experimental plants exhibited significantly wider leaves in comparison with the control group. While most experimental plants started flowering earlier, no significant differences were observed between numbers of flowers and fruits. The faster growth rates observed hold the promise of accelerated progress and improved efficiency in breeding initiatives, offering a fundamental shift in the way we approach crop development. Additionally, fewer number of basal branches may have implications for machine harvestability, as fewer basal branches is considered a desirable trait for machine harvesting.
The Hastings Agricultural Extension Center adopted the lettuce variety trials in 2018 for the demonstration of alternative row crops. Within the Tri-County Agricultural Area (TCAA), the term "alternative" refers to any crops outside of the traditional rotations - potatoes and cabbage. While these crops are the staple of the community, the acreage has been reduced due to tight profit margins and competitiveness for chipping contracts. Lettuce, along with artichokes and pumpkins, have been one of the newly adopted commodities for North Florida. What initially began as field trials expanded into the controlled systems of protected agricultural and hydroponics. Three seasons of germplasm trials with 14 newly developed lines in the hydroponic towers were conducted in Hastings to evaluate their soilless potential. Under 20% shade, lettuce was grown in the Verti-Gro system with 40% perlite, 30% coconut coir and 30% peat moss. These trials were also home to many field tours for the community, and opportunities for local growers to witness and observe their growth habits. Data evaluations included marketability, timing (if observed) of bolting, tip burn, and head weights. Weights ranged from 0.10 - 0.85 kg, with Botrytis and Sclerotinia being the most common disease pest identified. Since the trials began, our lettuce acreage has increased from 15 to 100 in the county, including two organic growers and one conventional, and with opportunities for more research to benefit these diversified growers.
I am a lecturer and academic advisor for the Soil, Water and Ecosystem Sciences Department. My research and extension background included alternative crop assessments for Florida growers, insecticide fate and transport in citrus and phosphorus nutrient management in artichokes. These... Read More →
California is the largest spinach producing state in the USA, accounting for 75% of hectares planted. The major production area is the Salinas Valley, which is known to have geogenic cadmium soils. Spinach is a hyperaccumulator and its affinity for divalent cations, like zinc and iron, likely contributes to the accumulation of Cd. Cadmium has known adverse health effects in humans, so California’s Office of Environmental Health Hazard Assessment’s (OEHHA) set a limit of 4.1 ug Cd per day by consumption. Consequently, growers do not produce spinach on high cadmium soils, limiting their ability to rotate crops throughout the valley. Even so, a few fresh leaf market spinach samples with foliar concentrations of Cd above the limit have been reported.
Our long-range objective is to develop improved fresh market spinach germplasm that restricts Cd uptake while maintaining nutritional quality. We have observed phenotypic variation for foliar cadmium concentration in a wide diversity of spinach germplasm with over 500 accessions originating from 42 countries, showed that greenhouse evaluations in high Cd soil largely reflected phenotypic performance in the field, and developed populations segregating for Cd uptake. We have also developed a hydroponic system that reflects field and greenhouse Cd uptake, but that is more controlled and scalable. Our current objectives are to identify quantitative trait loci (QTL) in the spinach genome associated with Cd accumulation. We have developed a biparental mapping population for genetic mapping by crossing high and low individuals which was evaluated in hydroponics earlier this year and will be evaluated in field conditions this fall. Markers tagging major QTL loci will be developed into high-throughput KASP markers for routine use in breeding.
Safeguarding Herbaceous Ornamental Plant Diversity: The Ornamental Plant Germplasm Center - Yu Ma SNP-Enabled Genetic Diversity and Population Structure of Gladiolus (Gladiolus ×hybridus) Cultivars - Marie Abbey Development of Genetic Fingerprinting of Azalea Cultivars Using SSR Markers - Seth Wannemuehler A Chromosome-Scale Haplotype-Resolved Reference Genome of Lantana camara and Insights into Unreduced Female Gamete Production - Brooks Parrish Identification of Flowering Dogwood QTLs for Bract Color using a Pseudo-F2 Population - Trinity Hamm Evaluation of Hibiscus cannabinus as an Alternative Fiber Crop for Florida: Identification of Valuable Traits and Germplasm for Cultivar Improvement - James Webb
Ornamental crops play an indispensable role in enriching our daily lives, offering not just visual delight but also therapeutic benefits. Moreover, the floriculture industry stands as a pivotal pillar within the nation’s agriculture sector, experiencing a substantial 16% increase in sales from 2019-2022, marking it as one of the fastest-growing industries. Safeguarding ornamental plant diversity has become more crucial than ever to sustain this industry and ensure its continued growth and resilience in the face of climate changes and evolving consumer preferences. Located in Columbus, OH, the Ornamental Plant Germplasm Center (OPGC) is one of 20 gene banks in the U.S. National Plant Germplasm System. Established through a cooperative effort between the USDA-ARS and The Ohio State University, it began operations in 2001. The center’s main goals are to acquire, document, maintain, characterize, and distribute herbaceous ornamental genetic resources and associated information for conservation, and to enhance scientific research as well as the floriculture and nursery industry. Current priority genera include Begonia, Coreopsis, Lilium, Phlox, Rudbeckia, and Viola. Since the OPGC began operation, 7350 accessions have been acquired, representing significant diversity within the 432 genera and over 2000 species of herbaceous ornamentals conserved. More than 13,000 germplasm items have been delivered free of charge to researchers, breeders and educators around the world. This presentation will outline the core functions of OPGC, including its germplasm collection, conservation techniques, and collaborative research initiatives.
Studies on genetic diversity and population structure provide important insights for determining ancestry and target trait enhancement in breeding programs. Gladiolus(-i), Gladiolus ×hybridus (Iridaceae), is a tetraploid, asexually-propagated, herbaceous perennial floricultural crop. Gladioli have tall flower stalks which make them ideally suited for cut flowers (floral design) and annual garden plants. Gladiolus is an important cut flower crop (in the top 5) for floral design. The purpose of this study was to analyze the genetic diversity of cultivated gladiolus germplasm to determine ancestry and relatedness. In this study we examine 549 unique gladiolus cultivars using DNA marker-based analysis. Samples were collected from the public (University of Minnesota) and private (Meyer, Otto) sector breeding programs in Minnesota and Europe. Population genetic diversity was analyzed using 17,556 single nucleotide polymorphism (SNP) markers developed by low-density DArTseq technology. Despite phenotypic differences, primarily in flower color or type (ruffled, etc.), the genetic diversity of gladiolus cultivars is low. The heterozygosity value was Ho=0.09 and the Fischers (FHOM) inbreeding coefficient was FHOM=0.40. SplitsTrees showed no differentiation, the average minor allele frequency (MAF) and polymorphism information content (PIC) was MAF=0.12 and PIC=0.15. The lack of significant genetic diversity among cultivars as well as breeding programs demonstrates a narrow germplasm base for this important cut flower crop. We discuss our findings and recommend ways to use these conclusions to improve future genome-wide association studies (GWAS) as well as increase efficiency and diversity in breeding goals.
Marie Abbey is a researcher at the University of Minnesota Horticultural Science department. She has studied perceptions of biotechnology, invasive plant species, and aquaponics. Her current research is in flower breeding and molecular genetics.
Azaleas (Rhododendron spp.) are economically important ornamental flowering shrubs in landscapes around the world with thousands of cultivars representing many species of Rhododendron. Because azalea is an asexually propagated crop, potential discrepancies in plant identity may occur throughout the propagation pipeline, which can lead to mislabeling during propagation and commercialization processes. For example, the University of Minnesota (UMN) cultivar ‘Electric Lights Double Red’ is currently being propagated but flower morphology of the propagules differed from the original plant leading to uncertainty of propagule identity. Previous studies have identified DNA markers, specifically simple sequence repeats (SSRs), capable of differentiating azalea hybrid offspring from different species of the section Pentanthera. This study aims to leverage these previously developed SSR markers to authenticate the identity of breeding germplasm at the UMN and uniquely fingerprint other cultivars on the market. The evaluated azaleas pedigrees include up to 15 different species of deciduous azalea. Therefore, a total of 15 SSR markers that amplified fragments from several species of section Pentanthera were selected for this study. DNA was extracted from lyophilized leaf samples of 139 azalea cultivars using a Qiagen DNeasy Plant Pro Kit. Preliminary analysis of the azalea DNA using the selected SSR markers has identified the presence of 16 expected unique cultivars and 3 pairs of previously known duplicates. The outcome of this research will demonstrate the feasibility of providing azalea breeders, growers, and producers a marker-based system for assuring cultivar trueness-to-type and protection of intellectual property.
This comprehensive study unveils the first annotated, haplotype-resolved, chromosome-scale reference genome of Lantana camara, alongside insights into candidate genes for unreduced female gamete production through ovary transcriptome sequencing. L. camara, a native of the Caribbean, plays a dual role as a valued ornamental plant and a challenging invasive species. The absence of a high-quality genomic resource has previously limited the exploration of its ornamental and invasive characteristics. This work closes this gap by delivering a critical genomic resource for L. camara, essential for ornamental breeding programs and invasive species management. The genome of a diploid L. camara breeding line UF-T48 was assembled de novo, utilizing HiFi and Hi-C reads, achieving phased genome assemblies with a BUSCO score of 97.7% and LAI score of 19.37, indicating high quality. This assembly resolved all 22 chromosomes into pseudochromosomes, with an average length of 117 Mb, and annotated 83,775 protein-coding genes, laying a foundational step for Verbenaceae family genomic research. Simultaneously, this research delves into the plant’s reproductive biology, specifically targeting the mechanism of unreduced female gamete production, a trait that has played an important role in the evolution and spread of lantana, contributed to the plant’s invasiveness, and and complicated the development of sterile triploids. By aligning RNA-seq data to the reference genome, we identified differentially expressed genes associated with cell division and meiosis, crucial for understanding the genetic underpinnings of unreduced gamete production. These findings not only enhance the genetic comprehension of L. camara but also provide invaluable genomic resources for future genetic studies, conservation efforts, and breeding strategies aimed at producing non-invasive sterile cultivars. This pioneering genomic and transcriptomic analysis marks a significant leap forward in researchers’ ability to manipulate L. camara for both horticultural innovation and environmental management.
Flowering dogwoods (Cornus florida L.), known for their showy spring display and year-round appeal, are extensively planted as ornamental trees. In 2019, dogwoods ranked third in value for deciduous flowering trees in the U.S., generating more than $31 million in wholesale and retail sales. Tennessee is vital to this industry. The state leads the country in the number of dogwood plants sold, with almost double the number of trees sold as the next top producing state in the country. The showy bracts of dogwoods are modified leaves with a spectrum of color ranging from white to red, with many intermediate colors and patterns. Cornus florida ‘Cherokee Brave’ with deep pink bracts and ‘Appalachian Spring’ with creamy white bracts are two popular cultivars. Partially phased reference genomes have recently been assembled and annotated for these cultivars, ranging from 1,253 to 1,266 Mbp in length with 28,558 to 28,768 annotated protein coding genes. With these newly annotated genomes providing greater context, a QTL analysis was conducted using a pseudo-F2 population of ‘Cherokee Brave’ × ‘Appalachian Spring’ which segregates for bract color. Genotyping was completed using double-digest restriction-site associated DNA sequencing (ddRADseq) with PstI and MspI. With increasing demand for high-throughput phenotyping, six different phenotypic methods were utilized to determine which method was optimal for QTL detection. The phenotyping methods included: 1) manual characterization into binary classes (white or pink); 2) manual characterization into five classes (white, light blush, medium blush, pink, red); 3) colorimeter readings; 4) image analysis using full inflorescence; 5) image analysis using bracts detached from inflorescence; and 6) one bract per inflorescence. QTLs were identified using all phenotyping methods. The QTLs identified here will be used as the foundation for developing a marker assisted selection system for bract color in flowering dogwoods.
Hibiscus cannabinus, commonly referred to as Kenaf, is an annual warm-season plant that can thrive in the Southeastern United States. It serves as a vital source of natural fiber with diverse applications, such as biocomposites, paper pulp, textiles, industrial absorbents, animal bedding, and potting medium. A set of 86 accessions of Hibiscus cannabinus, acquired from USDA-GRIN, underwent evaluation in Central Florida for various parameters, including plant height, basal width, stem width 50 cm above the plant base, stalk fresh weight, stem fresh weight, stalk dry weight, leaf dry weight, bast weight, and core weight. Significant variations were observed among accessions for all the measured variables. Notably, stalk dry weight emerged as the key trait of interest, representing the plant portion with desirable fibers for various applications. The top Duncan grouping for stalk dry weight comprised eight accessions: PI 329191 (18-85), PI 639889 (18-157) known as "Whitten," PI 270111 (18-55) known as "G-32," PI 603071 (18-152) known as "Dowling," PI 638930 (18-154) known as "74200 I4," PI 638932 (18-156) known as "Yue 74-3," PI 270106 (18-50) known as "G-14," and PI 468077 (18-137). Out of the 86 USDA-GRIN accessions examined, these eight have been identified as the top-performing choices for field production in Central Florida. Furthermore, these selected accessions are deemed desirable parents for future cultivar improvement endeavors, aiming to develop enhanced cultivars of Hibiscus cannabinus specifically tailored for production in Central Florida.
Breeding for Photoperiod Insensitive and Indeterminate Flowering Habit in Pigeonpea - Diego Viteri Breeding for Improved Tomato Flavor - Denise Tieman Genome-Wide Association Study Identifies Key SNPs Associated with Mineral Element Accumulation in Spinach (Spinacia oleracea) - haizheng xiong Comparative Analyses of Tissue-Specific Transcriptome Responses to Salt Stress in Lettuce Roots and Leaves - Modan Das QTL Mapping Of Horticulturally Important Plant Architectural Traits In Cucumber (Cucumis sativus L.) - Thi Nguyen Screening Sweetpotato Germplasm for Resistance to Meloidogyne incognita - Phillip Wadl Variation for Non-Acclimated and Acclimated Heat Tolerance Among Potato Germplasm: Indication of Separate Genetic Control - Jiwan Palta
Friday September 27, 2024 2:29pm - 4:00pm HST
Coral 1
Pigeonpea [Cajanus cajan (L.) Mill.] is an important legume consumed in the Caribbean basin. Cultivars with indeterminate flowering habit have sensitivity to the photoperiod in Puerto Rico. The objectives of this research were to: (1) develop two breeding lines with indeterminate flowering habit that can be planted year-round, and (2) evaluate their agronomic performance. IIPG-7 and IIPG-11 breeding lines, derived from the bi-parental cross ‘ICPL 86012’/‘Guerrero’, were developed by pedigree and bulk breeding methods. Both breeding lines, their parents, and cultivars checks were tested in field trials in Isabela and Lajas, Puerto Rico in 2022 and 2023. IIPG-7 and IIPG-11 were early genotypes that initiated flowering between 73-84 days after planting (dap), and reached harvesting maturity at 121-127 dap compared with indeterminate cultivars ‘Ariel’, ‘Blanco Yauco’, ‘Kaki’, ‘Pinto Berrocales’, and ‘Super Pinto’ that initiated flowering between 91 to 102 dap and reached maturity at 138-148 dap. These cultivars had seed yield values over 1,000 kg/ha while IIPG-7 and IIPG-11 produced between 721 to 1,010 kg/ha under short day conditions in both locations. In contrast, IIPG-7 and IIPG-11 were the only indeterminate genotypes that initiated flowering between 42-88 dap, reached maturity between 88-172 dap, and seed yields varied from 626 to 2,449 kg/ha under long day conditions in Isabela and Lajas. These new breeding lines can be used to develop pigeonpea cultivars with insensitivity to the photoperiod.
Consumers are dissatisfied with the flavor of modern commercial tomatoes; however, modern tomato varieties have many desirable agronomic traits such as shelf life, disease resistance and yield. The flavor deficiency in modern tomatoes is due to a cumulative loss of superior alleles affecting flavor volatiles while breeding for other traits. The lack of breeder focus on the consumer is largely due to the genetic complexity of the tomato flavor phenotype as well as a lack of a simple assay that can define consumer preferences. Tomato flavor is a result of interactions between sugars, acids and aroma volatiles, with volatile compounds giving the tomato fruit its characteristic aroma and flavor. We have quantified 68 flavor biochemicals in over 700 tomato varieties, including modern, heirloom and ancestral tomato accessions. Over 160 of these varieties were evaluated by a large consumer panel for fruit flavor quality traits including overall liking. Genome Wide Association Studies (GWAS) identified genetic loci associated with altered levels of acids, sugars and aroma volatiles. We have used marker-assisted breeding to introgress loci associated with flavor biochemical levels from heirloom varieties into modern tomato varieties. Introduction of seven flavor loci affecting a variety of flavor volatiles into a modern tomato variety has resulted in altered flavor volatile profiles and improved flavor as assessed by a consumer panel.
Understanding the genetic basis of mineral element contents in crops is crucial for improving their nutritional value. This study conducted a comprehensive Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with the accumulation of 14 essential mineral elements in spinach (Spinacia oleracea). Utilizing a diverse collection of 281 spinach accessions, we assessed the content of Boron (B), Calcium (Ca), Cobalt (Co), Copper (Cu), Iron (Fe), Potassium (K), Magnesium (Mg), Manganese (Mn), Molybdenum (Mo), Sodium (Na), Nickel (Ni), Phosphorus (P), Sulfur (S), and Zinc (Zn), expressed in micrograms or milligrams per gram of dry weight (µg/gDW or mg/gDW). Genotyping revealed 83,952 SNPs across the spinach genome, analyzed using GAPIT3 and TASSEL5 software platforms. Statistical models employed included General Linear Model (GLM), Mixed Linear Model (MLM), FarmCPU, and BLINK within GAPIT, alongside SMR and GLM in TASSEL. Our analysis uncovered 33 significant SNP-trait associations distributed among the minerals: one for B, Cu, P, and K; two for Ca, Ni, Fe, Zn, and S; three for Mo and Mg; four for Na and Co; five for Mn. These findings highlight the genetic diversity influencing mineral nutrient accumulation in spinach and offer valuable markers for breeding nutritionally enhanced spinach varieties.
Dr. Ainong Shi is a faculty member in the Department of Horticulture at the University of Arkansas. His research laboratory specializes in plant breeding and genetics, particularly focusing on vegetable crops such as arugula, cowpea, and spinach for cultivar and germplasm development... Read More →
Lettuce is one of the most important leafy vegetable crops world-wide. Salt stress adversely affects lettuce production, leading to considerable yield losses. Understanding the molecular mechanisms underlying the salt stress response is essential for breeding and development of lettuce cultivars with improved salt tolerance. Thus, the objective of this research was to identify differentially expressed genes (DEGs) in lettuce root and leaf tissues under salt stress and non-salt stress conditions. We have compared two salt-stress tolerant and two salt-sensitive accessions from crisphead and leaf horticultural types. Differential gene expression was compared between salt-tolerant and salt-sensitive accessions from the same horticultural type to minimize the effect of horticultural types on the comparison. In the root samples of the salt-tolerant accessions, we identified 3,789 and 4,022 DEGs, while for the salt-sensitive accessions 9,030 and 9,945 DEGs were identified, for the crisphead and leaf types, respectively. In leaf tissues, we observed 5,683 and 9,445 DEGs in the salt-tolerant accessions and 5,836 and 10,172 DEGs in the sensitive accessions, respectively, for the crisphead and leaf types. Thus, the number of DEGs was higher in sensitive accessions of both root and leaf tissues, with a notably greater disparity in root tissues. Functional annotations of the DEGs indicated stress response as a common biological process in both root and leaf tissues. Protein phosphatase inhibitor and peroxidase were the most significantly enriched molecular function terms in roots, while chaperone and glycosyltranferase molecular function terms were most significantly enriched in leaves. Gene Ontology (GO) enrichment analysis determined that genes related to the organic substance biosynthetic process were most significantly enriched in roots, while genes related to photosynthesis, response to light stimulus, chlorophyll binding and regulation of the jasmonic acid-mediated signaling pathway were significantly enriched in leaves. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that plant hormone signal transduction, biosynthesis of secondary metabolites, and the MAPK signaling pathway were significantly enriched terms in both root and leaf tissues, while cysteine and methionine metabolism terms were most significantly enriched in roots and photosynthesis was most significantly enriched in leaves. Identification of the salt-stress responsive genes and the results on their expression patterns in salt-tolerant vs salt-sensitive cultivars obtained in the present study open the door for further functional analysis of these genes and their utilization in improving salt-stress tolerance in lettuce.
Cucumber (Cucumis sativus L.) is an economically important vegetable crop cultivated worldwide. Plant architectural traits, such as lateral branch number (LBN), vine length (VL), number of nodes (NN) and internode length (IL), may directly influence production practices, plant performances, fruit yield and quality. Despite their importance, investigation on the genetic basis of these traits in cucumber is limited. In this study, we conducted QTL mapping for VL, NN, IL and LBN using bi-parental F2, F2-derived F3 and recombinant inbred line (RIL) populations. There are significant positive correlations between LBN, VL and NN. Estimated board-sense heritability using entry-mean basis of the RIL population was high, ranging from 0.66 to 0.84. Two linkage maps were developed through genotyping-by-sequencing of 140 F2 individuals and Diversity Arrays Technology (DArTag) SNP genotyping of 135 RIL, containing 1912 and 334 SNP loci in seven linkage groups and spanning 1077 and 948 cM, respectively. QTL mapping analysis detected a total of 79 QTLs associated with the four traits in six environments or populations. Based on their physical locations, 66 QTLs were distributed in ten QTL clusters harboring four major-effect and six minor-effect QTLs. Each of the major- and minor-effect QTLs was supported by consistent and reproducible detection from at least three environments. Notably, major-effect QTLs for VL, NN and LBN were co-localized in two genomic regions on Chr1 (3.73 Mbp) and Chr6 (3.78 Mbp), and the major-effect QTL for IL was mapped in a 3.98-Mbp region on Chr5. These findings provide a framework for dissecting the genetic architecture of these complex traits, and valuable genetic information for cucumber breeders to employ molecular-assisted breeding approaches and develop improved varieties with enhanced productivity.
Several studies have documented variation in potato germplasm for heat tolerance of leaf tissue. Most researchers have relied on screening for heat stress by exposing excised leaf tissue (grown under non-stress condition) to a short-term (minutes-hours) of acute heat stress (37-55C). It is well known that plants vary in their ability to acclimate to heat stress know as priming. This priming can enable plant to survive subsequent temperatures that are lethal to plants grown under non-stress condition. Our recent studies show that potato plants under prolonged heat stress (35/25C, day/night, for 3-5 weeks) newly developed leaves (acclimated) can maintain health under heat stress by modifying anatomy and physiology. These results show that potato plants have the ability to acclimate to heat stress that results in increased heat tolerance. In the present study, we screened to potato germplasm for heat tolerance of leaf tissue before and after heat acclimation. Ion leakage after exposure of excised leaf tissue to 50C, was used as a screening assay and a reduction in this leakage was used to assess the heat acclimation ability. Wide variety of potato germplasm including commercial cultivars and accessions of various wild species were screened. Our result show significant genotypic variations in acclimated and non-acclimated heat tolerance. Furthermore, the heat acclimation ability appears to be independent of non- acclimated heat tolerance. For example, certain clones of the species Solanum commersonnii had similar non-acclimated heat tolerance but large variation in acclimated tolerance was found among various clones of this species. Similar results were obtained for different clones of Solanum microdontum and Solanum kurtzianum. As expected, the cultivars Zarewo, DTO and Papa Cacho were found to have higher non-acclimated heat tolerance than the others, but Papa Cacho had the highest heat acclimation ability. Our results suggest that non-acclimated heat tolerance and acclimated heat tolerance are under separate genetic control and that selection for both non-acclimated and acclimated heat tolerance may be useful for successful breeding for heat tolerance of potato leaf tissue.
