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.
Evaluation of Vegetable Soybean Breeding Lines for Yield and Related Traits - GuoLiang Jiang Could Broccoli's Ancestral Lineage Hold the Key to Increased Fatty Acid Content? - Alaina Kleine Characterization of A Novel Locus for Fruit Flavor Aroma in Tomato - Qian Feng Identification and Validation of Novel Resistance Loci to Fusarium oxysporum f.sp. lycopersici Race 3 in Tomatoes - Samuel Ipinyomi Enhancing Fusarium Wilt Race 2-Resistance and Brix Content in Watermelon through Genomic Selection - Anju Biswas Introgressing QTL from a Wild Relative to Improve Gummy Stem Blight Resistance in Watermelon - Cecilia McGregor Genome-wide association study reveals potential loci for powdery mildew resistance in the USDA core collection of Cucurbita pepo - Prerna Sabharwal BreedwithBIMS (Breeding Information Management System) for Crop Breeders - Ksenija Gasic
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.
Vegetable soybean (Glycine max), also known as edamame, is a specialty soybean that is harvested at R6 growth stage. Vegetable soybean has steadily increased in acreage and market demand although it is relatively new to North America. It is of significance to develop new cultivars that are more adapted to local environment and crop management system to promote specialty crop production and meet the market requirements. In this study, 14 genotypes of vegetable soybean, including 10 breeding lines and 4 check cultivars, were evaluated during 2020-2023 for potential uses as edamame. There were significant differences among genotypes in both fresh pod and mature seed yields, agronomic and seed composition traits investigated. The year effects and genotype x year interactions were also significant in most cases. Fresh pod yield averaged 11,227.5 kg ha-1, ranging 9,800.1 – 13,154.3 kg ha-1, and mature seed yield averaged 2,814.7 kg ha-1, ranging 2,029.2 – 3,175.2 kg ha-1. The average 100-seed weight of 14 genotypes was 26.9 g, ranging 23.1 – 30.1 g. Maturity averaged 153.3 days after planting, ranging 147.1 – 159.5 days. On a dry weight basis, seed protein, oil and sucrose contents averaged 43.5%, 18.7% and 5.0%, respectively. The estimates of broad-sense heritability were medium to high (66.82 – 94.90%) for most of the traits, while the heritability estimates for fresh pod yield and duration from flowering to maturity were relatively low (23.44% and 42.29%). Several breeding lines exhibited good yield, larger seed size, higher contents of protein, oil, oleic acid and sulfur-containing amino acids, suggesting the potential of release and commercial production.
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 →
In the pursuit of agricultural productivity, generations of breeding have often prioritized yield-related traits, inadvertently leading to the loss of desirable genetic traits linked to nutritional content. This phenomenon, known as the genetic lag effect, has implications for human health, particularly concerning the availability of essential nutrients such as omega-3 fatty acids. As omega-3 fatty acids are crucial for various aspects of human health, including heart health, cognitive function, and hormone regulation, it is imperative to explore alternative sources beyond traditional fish-derived options. The demand for plant-based alternatives is rising due to dietary preferences and concerns over fish oil production, emphasizing the need to investigate alternative sources of omega-3 fatty acids. Broccoli, with its rising consumption and rich nutritional profile, presents a promising avenue for addressing this need. For humans, the ideal ratio of omega 6 to omega 3, is 1:1. Yet, the American diet offers an astonishing 30:1 ratio! Broccoli has a ratio of 1:3 ratio. This is comparable to fish ranging from 1:1 to 1:7. Despite its potential, most broccoli breeding programs have focused primarily on grower-oriented traits rather than those beneficial to human health. Thus, there is an opportunity to enhance the nutritional content of broccoli, particularly its omega-3 fatty acid profile, to offer greater health benefits to consumers. This study investigates the omega-3 fatty acid profiles of 35 lines, 9 elite and 26 landrace broccoli cultivars, to address the pressing need for nutrient-rich foods. Our research employs lipid extraction from various tissues of broccoli plants, including bouquets, stems, and leaves. The lipid sample is screened using Gas Chromatography-Mass Spectrometry (GC-MS) for precise quantification and identification of fatty acids. Preliminary results reveal significant variation in omega-3 fatty acid content, specifically levels of alpha-linolenic acid (ALA) among the broccoli lines studied, highlighting the potential for breeding programs to select and develop varieties with enhanced nutritional profiles. By prioritizing consumer-oriented traits in crop breeding, such as omega-3 fatty acid content, we aim to contribute to developing biofortified broccoli varieties that offer sustainable and health-promoting dietary options. This research underscores the importance of diversifying food sources and prioritizing human health outcomes in agricultural practices to address evolving dietary needs and promote overall well-being.
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.
Fusarium wilt disease caused by the soil-borne pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is a major threat in tomato-producing regions that can lead to acute yield losses. Host resistance as compared to other control strategies provides an effective and reliable means to contain the spread of the pathogen. Given that genes that confer resistance to all the three known Fol races are single dominant genes, there is a risk of resistance breakdown by the mutating pathogen. Furthermore, in the face of imminent race 4 emergence, building a quantitative and durable resistance shield by pyramiding novel resistant genes in commercial cultivars becomes pertinent. S. pennellii has been previously identified as a repository for resistant genes to Fol3 and recently, two novel loci mapped at chromosomes 3 and 10 were identified from two accessions- LA 1522 and LA 750 respectively using bulk segregant analysis QTL seq. Preliminary analysis was conducted to develop molecular markers for both chromosomes and validate their co-segregation with the region of introgression associated with resistance. We found co-segregating markers for resistance harbored by chromosome 3 and designated the locus as I8. This marker therefore constitutes additional genomic resources for marker-assisted selection of this trait. Although we found markers that co-segregate with resistance on chromosome 10, we provide initial evidence that this resistance is the same with the I6 locus previously identified on chromosome 10 and derived from LA 716 while complementary phenotypic screens showed partial penetrance of this locus. Together, these resistance loci (I6 and I8) could constitute a qualitative shield against the pathogen in commercial cultivars. Efforts are underway to fine map these loci and characterize them under field conditions and against other previously known races.
Complex traits in plants are influenced by many genes, each having a small impact. Using marker-assisted selection (MAS) alone is not sufficient to improve these traits in elite cultivars. Genomic selection (GS) is a promising breeding approach for enhancing complex traits like resistance to Fusarium oxysporum f. sp. niveum (Fon) race 2 and increasing sugar levels (brix content) in watermelon. In our study, we wanted to see how well GS can predict disease resistance and sugar levels in an interspecific citron melon (Citrullus amarus) by cultivated watermelon (Citrullus lanatus) population. We created an F2:3 population by crossing USVL252-FR2 (resistant to Fon race 2, low brix; C. amarus) with ‘Sugar Baby’ (susceptible to Fon race 2, high brix; C. lanatus). We tested disease resistance in a growth chamber and measured sugar levels in a field trial using a randomized complete block design of the F3 families. We resequenced the DNA of 150 F2 plants to identify genetic differences. Disease response was assessed 28 days after inoculation, and sugar levels were measured with a brix meter to gauge sweetness. To predict disease resistance, we used two genomic models - Random Forest and GBLUP - which we found to be effective in previous studies. We compared the performance of univariate models (looking at disease and sugar levels separately) and bivariate models (looking at disease and sugar levels together) to identify the best approach for selecting superior cultivars based on these traits. We assessed model performance using ten-fold cross-validation. Our goal is to focus on these important polygenic traits and select superior genotypes early in breeding to develop watermelon cultivars with improved disease resistance and high sugar content.
Watermelon (Citrullus lanatus) is an economically important horticultural crop known for its sweet red flesh and is a popular summer snack. The southeastern US is an important production region for watermelon, but the hot and humid weather is conducive for the development of fungal diseases. Gummy stem blight (GSB), caused by three species of Stagonosporopsis; S. citrulli, S. caricae and S. cucurbitacearum, is an important disease that can cause severe yield losses worldwide under these favorable conditions. Currently, no resistant cultivars are available for this disease and management depends on preventative fungicide spay programs. Host resistance has been previously identified in C. amarus, an inedible crop wild relative of watermelon. However, different Stagonosporopsis spp. isolates elicit different responses in different resistant host genotypes which complicated resistance breeding. To address these issues, we (i) developed a point-of-care assay that can differentiate S. citrulli from the other two species and (ii) introgressed resistance QTL from wild C. amarus into cultivated watermelon. A dipstick-based DNA extraction method was coupled with an S. citrulli specific loop-mediated isothermal amplification (LAMP) assay to detect as little as 1 pg of DNA with real time fluorescence quantification and endpoint colorimetric detection formats. To address host resistance, we developed high throughput KASP markers spanning the QTL regions, and used marker assisted backcrossing to introgress QTL into the cultivar Crimson Sweet. Eight BC2F3 intogression lines were evaluated in the field for resistance to GSB. Two of the lines showed high levels of resistance to GSB under field conditions. KASP assays were also developed for background selection for known domestication alleles to accelerate selection for fruit quality traits. The developed detection assays, KASP markers and introgression lines can contribute to accelerated breeding for host resistance and general breeding efforts for GSB in watermelon.
Summer squash (Cucurbita pepo) is a significant vegetable crop in the United States with an annual value exceeding $216 million. The production of summer squash is significantly hindered by powdery mildew (PM), a fungal disease caused by Podosphaera xanthii. Management of PM relies on costly and routine application of fungicides. Moderate resistance to PM (designated PM0) in C. okechobeensis is widely deployed in commercial summer squash cultivars. However, it is important to expand the repertoire of alleles against PM in squash to complement and reduce the risk of PM0 resistance breakdown. In the current study, the USDA core collection of C. pepo (n= 207) was evaluated for PM resistance in Florida (greenhouse), New York (greenhouse), and Michigan (field) using a randomized complete block design across three reps, each with five plants. ‘Success PM’ (carrying PM0) and ‘Early Prolific’ Straightneck cultivars were used as resistant and susceptible checks, respectively. Pathogen inoculum was provided through naturally infected plants. At the 6th true-leaf stage, symptom severity data were collected on a scale of 0-100% based on visible pathogen sporulation on the surface of ‘top 4th leaf’, ‘bottom 4th leaf’, ‘stem above 4th leaf’, ‘stem below 4th leaf’, and ‘whole plant’. Across locations, ‘Success PM’ and ‘Early Prolific’ were consistently tolerant and susceptible, respectively. On the other hand, wide phenotypic variation was observed across the C. pepo core collection with accession 189 showing resistance across locations. The multi-location phenotype data was combined with genome-resequencing data (4 million SNPs) for the core collection to conduct a genome-wide association study using three statistical models (MLM, FarmCPU, and Blink). GWAS analysis for the FL dataset revealed significant genomic loci associated with PM resistance for ‘top 4th leaf’ (Chr 11 and 20), ‘stem above 4th leaf’ (Chr 4, 14 and 16), and ‘whole plant’ (Chr 13, 15, 18 and 20). Resistance loci for ‘top 4th leaf’ and ‘whole plant’ co-located on Chr 20, suggesting potential linkage/ pleiotropy for the two traits. For NY, significant hits for PM resistance were detected for the ‘top 4th leaf’ (FarmCPU: Chr 2, 4, 7, 13 and 19; Blink: Chr 3, 4, 5 and 19) and ‘bottom 4th leaf’ (Chr 6, 14 and 19). However, no significant GWAS hits were observed using MI data. The significant loci detected in this study will be validated and deployed in marker-assisted selection to improve PM resistance in squash.
With the continuous development of new scientific technology and methodology, breeding programs are both producing and utilizing a large amount of big data. This requires efficient management systems to keep track of various types of data such as performance, pedigree, geographical and image-based data as well as genotype data. Access to integrated breeding data in a database enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility by breeders. The Breeding Information Management System (BIMS) is a free, open-source, secure and online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data that has been available in several crop databases. But what about the crops that do not have a database? We report the utility of a new BIMS website (www.breedwithbims.org) that allows any crop breeders can use BIMS. One of the key features of BIMS is that users can import new trait data via an Android App called Field Book as well as historical data via templates. Field Book app allows breeders to collect phenotype data with less possibility of transcription errors. BIMS is also BrAPI compliant so that breeders can send and receive data from other BrAPI compliant resources including the Field Book App. Potential for streamlining data collection and management for vegetable crops will be presented.
