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.
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.
Tomato flavor has become an important trait for targeted crop improvement. Because of the historical emphasis on yield and other agronomically important traits, many modern tomato varieties have lost their rich flavor, leading to consumer dissatisfaction. While volatile compounds play an important role in defining the distinct tomato flavor, little is known about their biochemical pathways, making it difficult to build a desirable volatile profile. Identifying the genes involved in volatile production can help us better understand the biochemistry as well as accelerate the breeding process. This study focuses on two consumer-desired volatiles, 1-nitro-2-phenylethane and phenylacetaldehyde, and has mapped a novel QTL on chromosome 8 by combining results from linkage mapping and GWAS (genome-wide association study). A cluster of Amino Acid Decarboxylases (AADCs) were identified as the candidate genes underlying this QTL and a total of four SV haplotypes of the AADC cluster were found in the Varitome collection. Among these haplotypes, Type III was lost during domestication and is a likely beneficial allele to increase the concentrations of phenylacetaldehyde and 1-nitro-2-phenylethane in tomato fruits. Preliminary data of transgenic plants created by CRISPR/Cas9 suggested a positive involvement of this AADC locus in volatile production. Enzymatic analysis of the AADC proteins and incorporation of the beneficial allele into modern tomato varieties is in progress. The outcome of this study will provide breeders valuable tools to facilitate the selection process for better tomato flavor. Characterization of volatile pathways will also give us insights on plant secondary metabolite biosynthesis and the evolution history during adaption and domestication. This research is funded by NSF IOS 2151032.
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.
