Skip to main content
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

2016 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
In support of Objective 1, ARS scientists at Beltsville, Maryland, identified one diploid strawberry accession as having low fertility due to a pollen defect, one chemically induced mutant that shows faster recovery of photosynthesis from heat stress than wild type, three chemically induced mutants that exhibit loss of runnering, six chemically induced mutants that affect flower development or senescence affecting fertility, one chemically induced mutant involving leaf structure and one chemically induced mutant involving overall leaf angle. This collection of germplasm will enable researchers to identify genes that are useful in breeding new traits and enhancing the development of molecular markers for breeding superior varieties of commercial strawberry. In support of Objective 1, ARS scientists at Beltsville, Maryland, evaluated 74 of the 90 named strawberry plants maintained in Oregon at the National Clonal Germplasm Repository (NCGR) that have a genome much simpler and easier to study than that of commercial strawberry. Evaluations at Beltsville were conducted 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. These findings will aid in selecting a subset of accessions to further study mechanisms of flowering at high temperatures in the context of these simple genomes. In support of Objective 1, ARS scientists at Beltsville, Maryland, determined that the allele conferring repeat-fruiting in commercial strawberry is dominant. A single genomic region was found responsible for controlling the trait in multiple genetic backgrounds, but no previous study was able to determine “gene action,” whether the repeat-fruiting gene is dominant or recessive, i.e., needed in one copy or two in order to pass the trait to progeny. Knowledge of gene action is key to determining a breeding approach to incorporate repeat fruiting into strawberry breeding programs around the world. In support of Objective 2, ARS scientists at Beltsville, Maryland, identified B1806, a once-fruiting strawberry breeding selection with exemplary fruit quality and extraordinarily long shelf life. This year the cooperating nursery reported that daughter plants from that selection tested virus-free, so that the nursery will have plants available February 2017 for confirmation testing by ARS scientists and cooperators. B1806 could be available for release as early as June 2018. With at least a two-week shelf life, this selection has the potential to augment strawberry supplies to Mid-Atlantic distributors unable to meet demand with reduced supplies from drought-stressed California. In support of Objective 2, ARS scientists at Beltsville, Maryland, identified two strawberry breeding selections as possibilities to release as varieties. Both are resistant to anthracnose and botrytis, the two major strawberry diseases of the world. They also are tolerant to rain damage, an important advantage in many years. Both selections received above-average scores in all categories used to evaluate potential varieties. In support of Objective 3, ARS scientists at Beltsville, Maryland, identified a strawberry selection, B1915, that, when used as a parent in cross pollinations for repeat fruiting, consistently confers a desirable plant growth habit to the resulting seedlings. From these resulting seedlings, ARS scientists identified 17 promising repeat-fruiting breeding selections with the desired open habit, good runner production for nursery propagation, and attractive fruit. This is a breakthrough from the bushy plants with short fruiting trusses currently in our repeat-fruiting breeding population. In support of Objective 3, ARS scientists at Beltsville, Maryland, determined that strawberry varieties cannot use full sunlight and prefer instead about 50% to 75% full sunlight. This may explain why strawberries perform so well under low tunnels even though the temperatures under the tunnels are similar to temperatures outside tunnels. In support of Objective 3, ARS scientists at Beltsville, Maryland, have determined the environmental and cultural conditions that consistently support or fail to support disease expression for three fruit rot diseases when the strawberries are grown under low tunnels. This knowledge allows testing strawberry breeding selections for resistance to these diseases individually and sequentially in a single growing year from the same planting. In support of Objective 4, ARS scientists at Beltsville, Maryland, determined using chemically induced mutants, that runnering in diploid strawberry is regulated by more than a single gene. This information is important for the identification of the genes that are involved in determining whether the plant produces either a runner or a branch crown and is fundamental to developing the means to control this process in commercial strawberry. In support of Objective 4, ARS scientists at Beltsville, Maryland, showed that a mutant plant selected as being tolerant to high temperature as a germinating seedling is not, as a mature plant, more tolerant to chronic moderately elevated temperature. This finding illustrates that it will be necessary to develop alternative approaches to selecting or screening for plants that are thermotolerant during flowering or fruiting.


Accomplishments
1. DNA tools to develop better raspberries. Breeding of raspberries, a fruit which has 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 traits, including fruit quality. The breeding process would be greatly accelerated, and would be much more efficient, if a breeder could test a small seedling and know with confidence what traits that seedling will have if grown to maturity. This research reports the analysis of 3,507 raspberry genes and the discovery of 351 potential DNA markers by a collaborative team including ARS scientists at Beltsville, Maryland. Results indicate that further analysis will provide many more markers. The gene sequences and markers will be deposited in a public database. Raspberry breeders and geneticists worldwide will use them.

2. Naming of genes in Rosaceae family plants. Sequencing of the genomes of several members of the Rosaceae family (strawberry, apple, peach, black raspberry) has revealed a high level of synteny in these plants and has enabled the identification of homologous genes for useful traits within members of the family. A standardized gene naming system was developed by an international consortium that includes ARS researchers at Beltsville, Maryland. The standardization of gene names will facilitate the exchange of information among different laboratories and enable comparative genomic analyses for assigning putative gene function.


A collaboration was established with the College of Agriculture, Urban Sustainability and Environmental Sciences (CAUSES), University of the District of Columbia, Washington, DC to identify strawberry varieties suitable for urban roof-top production. Strawberry varieties growing under low tunnels, at the Beltsville Agricultural Research Center in Beltsville, Maryland, also are growing on a University of the District of Columbia (UDC) rooftop production location near Beltsville. Similar data will be collected at both locations to determine and compare yield and fruit quality of these varieties to determine suitability for urban production. A University of the District of Columbia student will be trained in data collection and analyses for the project. A female minority graduate student, whose thesis research was performed at a USDA laboratory, was awarded a PhD in chemistry from the University of Maryland. An undergraduate student from the Texas A&M was recruited and accepted in a USDA intern program targeting students from Hispanic Serving Institutions. The student was trained in methodology for plant breeding and horticulture.


Review Publications
Bushakra, J., Lewers, K.S., Staton, M.E., Zhebentyaeva, T., Saski, C.A. 2015. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). Biomed Central (BMC) Plant Biology. 15:258-269.
Song, C., Ring, L., Hoffman, T., Slovin, J.P., Schwab, W. 2015. Acylphloroglucinol biosynthesis in strawberry fruit. Plant Physiology. doi:10.1104/pp.15.00794.
Jung, S., Bassett, C.L., Bielenberg, D.G., Cheng, C., Dardick, C.D., Main, D., Meisel, L., Slovin, J.P., Troggio, M., Schaffer, R.J. 2015. A standard nomenclature for gene designation in the Rosaceae. Tree Genetics and Genomes. 11:108.
Sooriyapathirana, S., Mookerjee, S., Weebadde, C.K., Finn, C.E., Lewers, K.S., Bushakra, J., Luby, J.J., Stewart, P., Neils, S., Hancock, J.F. 2015. Identification of QTL associated with flower and runner production in octoploid strawberry (Fragaria × ananassa). Journal of Berry Research. 5:107-116. doi: 10.3233/JBR-150095.