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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Genetic Improvement for Fruits & Vegetables Laboratory » Research » Research Project #424143

Research Project: Strawberry, Raspberry, Blackberry: Crop Improvement through Genomics and Genetics

Location: Genetic Improvement for Fruits & Vegetables Laboratory

2018 Annual Report


Objectives
The overall goal of this project is to improve strawberry, raspberry and blackberry crops by better understanding and utilizing phenotypic traits. These include traits that will improve crop efficiency through increased production of marketable fruit and/or decreased requirement of inputs such as labor or pesticides. They also include traits that will negatively affect crop efficiency and have no immediate apparent commercial utility, but which will eventually have significant broader impact through increased understanding of basic function for these important fruit crops and other plants. The specific objectives of this project are: Objective 1: Identify or generate and characterize raspberry, diploid and octoploid strawberry, and tetraploid blackberry genotypes with beneficial or deleterious traits that affect repeat flowering and fruiting, resistance to abiotic stresses and diseases, or plant architecture. [NP301, C1, PS1A PS1B]. Objective 2: Develop and evaluate once-fruiting strawberry germplasm with high yield, excellent fruit quality, and resistance to Colletotrichum and Botrytis for performance under Mid-Atlantic growing conditions. [NP301, C1, PS1A] Objective 3: Develop and evaluate multiple-fruiting strawberry germplasm with open plant architecture, adequate runner production, high yield, and resistance to foliar and fruit rot diseases such as Colletotrichum and Botrytis for performance in the novel Beltsville low-tunnel production system. [NP301, C1, PS1A] Objective 4: Elucidate the functions or regulation of genes affecting traits that will improve strawberry production efficiency, such as flowering, fruiting, plant organ and flower development, or plant architecture. [NP301, C1, PS1B]


Approach
The diploid strawberry will be used as a model to better understand the genetic control of key production traits in the cultivated octoploid. Existing diploid germplasm will be evaluated, and novel diploid germplasm will be generated and characterized and compared with a few reference octoploid genotypes. Existing germplasm will be evaluated in growth chambers, under both ideal temperatures and higher stressful temperatures, primarily for the repeat-fruiting trait. The mutagen, ethyl methanesulfonate, will be used to generate plants with novel production phenotypes for further genetic study. The inheritance of selected novel traits with potential to affect crop productivity will be determined through testcrosses and segregation traits and molecular markers among progeny. Candidate genes will be identified by using whole-genome sequencing of bulked mutant DNAs and comparing the genome sequences of the mutant and the genotype from which the mutant was derived. The expression of candidate genes will be examined for developmental patterns and tissue localization. Transformed F. vesca plants will be produced that over-express the gene, or knock out gene expression, and promoter-reporter transformants also will be made and analyzed. Genes determined to be specifically induced at milestone developmental stages will be used as markers for which tissues and stages of reproductive development are susceptible to heat stress. Expression in specific cell types within an organ will be examined using RNA obtained using Laser Capture Microdissection. Traditional breeding methods will be used to develop improved octoploid strawberry cultivars. Cross-pollinations will be made that will result in seedlings that fruit once a year and others that will fruit multiple times a year. The genetics of repeat fruiting will be determined using the segregation ratios of these annually produced seedlings. Seedlings will be selected that have potential as cultivars and will be further evaluated in production systems appropriate for each type of fruiting pattern. Breeding goals will include improving yield, fruit quality and flavor, and disease resistance both in the field and after refrigerated storage. For the repeat-fruiting selections, additional emphasis will be placed on length of season and harvest efficiency. A novel low-tunnel production system will be used to evaluate these selections’ potential as cultivars while simultaneously providing a test environment to study the response of octoploid strawberries to environmental conditions including heat stress. Repeat-fruiting selections and cultivars will be evaluated weekly in the low-tunnel system for yield, fruit quality, and disease resistance from late winter to late fall. Environmental measurements, such as air and soil temperature, humidity, light, soil moisture, wind speed, and leaf wetness, will be made every 10 to 30 seconds and recorded throughout the year. Fruit production and environmental data will be analyzed through crop modeling to determine which environmental factors and what time period before harvest most strongly affect total fruit yield and the proportion of decayed fruit.


Progress Report
This is the final report for Project 8042-21220-254-00D, which terminated 25 February 2018. Over the five years of the project, progress was made under all four objectives, which fall under National Program 301, Component 1 (Crop Genetic Improvement), Problem Statement 1A (Superior new crops, varieties, and enhanced germplasm), and Problem Statement 1B (Innovative approaches to crop genetic improvement and trait analysis). Under Objective 1, strawberry plants that have a genome much simpler and easier to study than that of commercial strawberry, known as diploid strawberries, were studied as a genomic and genetic model for the commercial strawberry. Most of the 90 named diploid strawberry plants maintained in Oregon at the National Clonal Germplasm Repository (NCGR) were evaluated for flowering patterns while monitoring air and soil temperatures around the plants. Although evaluation at the NCGR showed 100% of the 90 named plants flowered continuously, evaluations at Beltsville identified many named strawberries that stopped flowering in the summer heat; only six continue to flower, emphasizing the effect of high temperature on strawberry fruit production. A set of diploid strawberry plants with novel phenotypes associated with production efficiency was derived from chemical mutagenesis, providing proof of concept for this genetics tool for strawberry. New mutant phenotypes generated included variations affecting vegetative plant propagation (important to commercial strawberry nurseries that sell plants to farmers), inflorescence length (important to growers who need easily picked fruit), petal retention on fruit (important to resistance to botrytis disease of fruit), pollen fertility (necessary for fruit production), fruit shape (important to consumer desire to purchase strawberries), petiole length, and leaf shape. The large number of DNA-based markers and the first genetic maps were developed for raspberry and are available for use in confirming cultivar identity, genetic studies, and raspberry breeding. A gene for repeat-fruiting in commercial strawberry was identified and shown to be dominant over the alternate gene for once-fruiting, information especially valuable to strawberry breeders in designing cross pollinations. Under Objective 2, an annual cycle of strawberry breeding progressed for the development of superior once-fruiting cultivars. The strawberry cultivar, ‘Flavorfest’, was found to be very productive with high disease resistance and fruit quality in the field. Demand for ‘Flavorfest’ plants continues to exceed supply. Specific strategies for improving flavor and shelf life were developed, incorporated into the annual breeding cycle, and made available to other strawberry breeders through scientific publication. Additional new strawberries identified in Project 8042-21220-254-00D will be released under its successor, Project 8042-21220-257-00D, Objective 1. Under Objective 3, the breeding cycle to develop repeat-fruiting strawberries was implemented annually and regularly adjusted for improving the efficiency of the process, including the further development of low tunnels in the breeding process. Specific aspects determined were appropriate planting date, the role of various environmental conditions in affecting yield and fruit quality, temperature management during the heat of summer and the frosts of fall, optimal irrigation and fertilizer methods, best cultivars to use as comparison to the breeding selections, methods of propagating breeding selections for further evaluation, and the discovery that repeat fruiting is controlled by more than the one gene currently known. Substantial progress was made in developing repeat-fruiting strawberry plants with an open architecture for easy harvest and which produced many stolons (runners) needed by strawberry nurseries to propagate plants for farmers. Although progress has been made for every important trait, an individual plant superior to existing repeat-fruiting cultivars for all traits has not yet been identified. This work will continue in the succeeding Project 8042-21220-257-00D, Objective 2. Under Objective 4, knowledge of strawberry genes and the strawberry genome was improved. Strawberry genes were identified that control the development of the strawberry flower parts that are important for its progression into the strawberry fruit in response to the naturally produced plant hormone, auxin. The progression from a flower to a fruit is a process that determines the quality of the resulting fruit for sale and consumption. The quality of the strawberry genome sequence was improved in terms of both quantity and quality (see accomplishments), and the names of genes in the genome were clarified to better compare location and sequence of genes with the same function in other important crops closely related to strawberry, such as apple, peach, cherry, almond, raspberry, and blackberry. The result of this increased and clarified genomic information allows progress by researchers working with one of these crops to be translated to the studies of researchers working with each of the other related crops. The genomic organization of the simple diploid strawberry is now used as the blueprint for studying the genomic organization of the commercial strawberry and all these other crop relatives.


Accomplishments
1. Environmental conditions controlling strawberry yield under low tunnels. Strawberries are economically valuable to farmers and are so popular with consumers that they expect to be able to buy strawberries all year long. In much of the U.S., traditional strawberries produce fruit only three to four weeks a year. To produce strawberry fruit for several months, farmers need to use a different kind of repeat-fruiting strawberry variety that fruits nearly all year long, and they need to grow them in a novel way that helps protect them from mid-summer outdoor conditions. Repeat-fruiting strawberries were grown in fields in two similar but slightly different ways (in raised beds and in raised beds under low tunnels) that were used to determine how day length, brightness, soil moisture, humidity and temperature affected strawberry yield. We determined that average bed temperature four weeks prior to harvest was predictive of yield. Strawberry yield increases steadily with bed temperature until an optimal temperature occurs then drops precipitously at higher temperatures, and the optimal temperature varies by cultivar. Strawberry plants utilize light more efficiently under low tunnels compared with open beds, partially explaining the increased yield and quality of strawberries produced under low tunnels. Of the cultivars tested, soil moisture increased berry size but not berry number. Growers will benefit from finding ways to keep the soil in the raised beds cool and maximizing the amount of diffused light. This information will be useful to strawberry farmers and to scientists studying ways to help farmers increase the length of the strawberry season to match consumer demand.

2. A high-quality sequence of the reference strawberry Fragaria vesca. Because the genome of the commercial strawberry is very complex, some genetic and genomic studies of important traits can be more easily revealed and understood when first studying the same traits in a wild strawberry relative, Fragaria vesca, with a much simpler genome. The genomic organization of the simple diploid strawberry has thus become a foundation for studying the genomic organization of the commercial strawberry. The existing draft sequence of the diploid strawberry, published in 2011, was greatly improved using the latest in fast-evolving technologies to sequence and organize genome pieces. The work resulted in a ~300-fold improvement in confidence of genomic organization, the addition of ~25 million base pairs of sequence, and the ability to recognize the likely function of 1,496 new genes. Accurate and complete genome sequence is critical to researchers working to understand and manipulate genes important for strawberry and fruit growth, fruit quality, and resistance to pests and environmental stress.


Review Publications
Lewers, K.S., Castro, P., Enns, J.M., Handley, D.T., Jamieson, A.R., Newell, M.J., Samtani, J.B., Flanagan, R.D., Smith, B.J., Snyder, J.C., Strang, J.G., Wright, S.R., Weber, C.A., Hokanson, S.C., Galletta, G.J. 2017. ‘Flavorfest’ strawberry. HortScience. 52(11):1627-1632.
Condori, B., Fleisher, D.H., Lewers, K.S. 2017. Relationship of strawberry yield factors with microclimate under open and covered raised-bed production. Transactions of the ASABE. 60(5):511-1525.
Edger, P.P., Vanburen, R., Colle, M., Poorten, T.J., Wai, C., Niederhuth, C.E., Alger, E., Ou, S., Acharya, C.B., Wang, J., Callow, P., Mckain, M.R., Shi, J., Collier, C., Xiong, Z., Mower, J.P., Slovin, J.P., Hytönen, T., Jiang, N., Childs, K., Knapp, S.J. 2017. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience. https://doi.org/10.1093/gigascience/gix124.