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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

2015 Annual Report

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]

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
In support of Objective 1, ARS scientists at Beltsville, Maryland, screened 18 different accessions of diploid strawberry for flowering habit (remontancy) and ability to produce flowers and fruit at moderately elevated temperatures. A dayneutral octoploid dessert strawberry accession, Seascape, was screened under the same conditions for comparison. Two of the accessions did not flower under any of the conditions tested. The remaining accessions flowered under short days and long days when grown at 25°C days and 20°C nights. None of the accessions produced quality fruit at the higher temperature. One accession that appeared to be more tolerant to the higher temperature is being tested further. In support of Objective 2, ARS scientists at Beltsville, Maryland, created a new late-season strawberry plant. Consumers demand strawberries all year long. To help meet this demand, farmers who grow only the spring-fruiting strawberry types extend their harvest season for as many weeks as possible by raising varieties that fruit both early and late in the spring strawberry season. The newly-created late-season strawberry plant identified this year shows resistance to fruit decay in the field and after harvest and has high yield of large attractive fruit with excellent flavor. This plant will be tested further to determine if its performance is consistently superior and if it should be released as a named variety to help extend the spring strawberry season for farmers. In support of Objective 3, ARS scientists at Beltsville, Maryland, created several repeat-fruiting strawberry types that will be easy to propagate from plant parts. In order to increase their stocks of strawberry plants for sale to farmers, strawberry nurseries need varieties that can be propagated easily from plant parts. One of the hurdles to creating repeat-fruiting strawberry varieties that are easy to propagate is that the genes that control these two traits trend very strongly not to be inherited together. Thousands of seedlings were searched yearly to identify a few that have both desirable traits, and were selected even though their fruit quality and disease resistance are marginal compared with once-fruiting varieties. The few that were identified this year will be bred with once-fruiting strawberry plants to create repeat-fruiting seedlings that can be propagated easily and have fruit quality and disease resistance on par with once-fruiting strawberry varieties. In support of Objective 1, ARS scientists at Beltsville, Maryland, created several primocane-fruiting raspberry plants and one primocane-fruiting raspberry plant with significantly smaller and softer spines. The identification of these seedlings in the early stages of the work demonstrates the validity of the approach taken to generate raspberries with these highly desirable traits. This work will be continued in search of a completely spine-free primocane-fruiting seedling. In support of Objective 4, ARS scientists at Beltsville, Maryland identified over twenty different mutants with visible phenotypes in runnering, flower development and morphology, leaf structure, plant architecture, fruit characteristics, and fertility. In addition, mutants with delayed runnering, increased yield, and increased thermotolerance were identified. The genetics of these mutant traits is currently being investigated. These mutants will allow identification of genes involved in these traits, and support the development of molecular markers that breeders can use to screen for these traits in the laboratory. A large number of plants in the mutant population have become part of a TILLING population that will allow scientists to find plants with a mutation in their gene of interest.

1. DNA tools to develop strawberry varieties with extended fruiting time. Breeding of strawberries, a fruit that has many valuable nutritional properties, is slow in part because seedlings derived from breeders’ crosses must be grown to maturity for evaluation of many traits, including whether the plant will produce fruit spring through fall, or just a condensed crop in the spring. The breeding process would be more efficient and greatly accelerated if a breeder could test potential parent plants and the resulting seedlings and know with confidence which seedlings would have a certain desired trait. A DNA based method, called “marker assisted breeding” is available to accomplish this, but requires DNA “markers” that can be used by the breeder to identify the parent plants and seedlings with the desired trait. ARS scientists at Beltsville, Maryland, and Corvallis, Oregon, together with researchers at the University of Michigan and University of Minnesota, discovered markers that can be used to select seedlings that produce strawberry fruit from spring through fall. Strawberry breeders worldwide will use these markers to more efficiently develop improved repeat-fruiting strawberry varieties that growers can use to reduce the economically damaging effects of weather extremes such as spring frosts and summer heat waves.

2. Characterization of genes in the diploid strawberry genome. The diploid strawberry genome was sequenced several years ago and the genes were identified by computer based on the data available at the time. A substantial amount of new data based upon gene expression was obtained as part of this project and utilized to refine sequence data of previously identified genes. As part of a collaborative effort with scientists at the University of Maryland and Towson University, ARS scientists in Beltsville, Maryland, used computational tools to refine gene sequences and deposit the new information on a publicly available website, the Genome Database for Rosaceae. This accomplishment will benefit scientists and breeders working with plants in the Rosaceae family to find and study their gene of interest.

3. DNA tools to more efficiently develop superior raspberries. Breeding of raspberries, a fruit with many valuable nutritional and health-promoting properties, is slow in part because seedlings derived from breeders’ crosses must be grown to maturity for evaluation of many characteristics. The breeding process would be more efficient and greatly accelerated if a breeder could test a small seedling and know with confidence what characteristics that seedling will have if grown to maturity. A DNA based method, called “marker assisted breeding” is available to accomplish this, but requires DNA “markers” that can be used by the breeder to identify the parent plants and seedlings with the desired trait. ARS scientists at Beltsville, Maryland, and Corvallis, Oregon, and scientists at the University of Georgia and Clemson University developed 351 easy-to-use DNA-based “markers” to help select raspberry seedlings with desirable characteristics. The new markers were developed from the DNA sequences of 3,507 raspberry genes. The markers and gene sequences were deposited in a public database for use by geneticists and breeders worldwide to associate the markers with desirable traits for use in breeding.

Review Publications
Harshman, J.M., Lewers, K.S., Jurick II, W.M., Walsh, C.S. 2014. Selection efficiency for raspberry postharvest shelf life affected by storage temperature and harvest season. HortScience. 49:311-319.
Castro, P., Lewers, K.S., Weebadde, C., Wang, D., Hancock, J., Stewart, P., Bushakra, J., Finn, C.E., Luby, J. 2015. Genetic mapping of day-neutrality in cultivated strawberry. Molecular Breeding. 35(2):79-94.