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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

2014 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, together with scientists at the University of Maryland, characterized red, black, purple, and yellow raspberry fruit to understand how each responded to biotic and abiotic stress, specifically, how each deteriorated in storage with regard to color, firmness, fungal decay, juice leakage, sweetness, tartness, and antioxidant levels. Different raspberry color groups deteriorated differently from each other in storage, and different aspects of the weather prior to harvest, such as rainfall, humidity, and temperature, affected each raspberry color group differently during storage. The information will be used by raspberry growers and those who package and market raspberries. In support of Objective 2, development of once-fruiting strawberry varieties, ARS scientists at Beltsville, Maryland, have developed two new once-fruiting strawberry breeding selections to have tested by collaborators in other locations and production systems. In addition to resistance to diseases in the field and superior fruit quality, including exceptionally good flavor, these two selections feature a very long shelf-life of particular value to growers located far from their closest markets and also to consumers after purchase. In support of Objective 3, development of strawberry varieties that fruit multiple times a year, ARS scientists at Beltsville, Maryland, have recruited a U.S. manufacturer of agricultural plastics to produce three types of plastic film that will shield strawberry plants in the field from harsh infrared light in the hot summer months and, theoretically, allow fruit production through the summer. The yields and quality of fruit from strawberry plants grown under these three plastics will determine if strawberry breeding selections can be evaluated all summer long and if strawberry growers in climates with similarly hot summers can produce quality fruit for market for several months from spring through fall instead of just a few weeks in spring. Scientists in five other states have adjusted their research plans to determine if the ARS research at Beltsville can be adapted to their locations. In support of Objective 4, understanding gene function, ARS scientists at Beltsville, Maryland, together with scientists at the University of Maryland and Towson University obtained sequence data for genes turned on in tissue of 15 reproductive organs during strawberry flower development. Analysis of the sequence data showed that an unexpectedly large number of particular types of regulatory gene were expressed during the division process that leads to the production of pollen. Also, gene networks operating in the stem tip, which develops into the edible strawberry, were elucidated. In support of Objective 4, understanding gene function, ARS scientists at Beltsville, Maryland, together with scientists at the University of Maryland and Towson University updated the publicly available Strawberry Genomics Resources website with the new sequence data and analysis from developing flowers of the diploid strawberry, Fragaria vesca. This information can now be easily used by researchers interested in improving the important fruit crops in the Rosaceae plant family, including apples, peaches, and cherries, as well as strawberries, raspberries, and blackberries. In support of Objective 4, understanding gene function, ARS scientists at Beltsville, Maryland have annotated the genes encoding proteins involved in carotenoid biosynthesis in the Fragaria vesca genome and have investigated the expression of these genes in various plant tissues and in response to elevated temperatures. Carotenoids are yellow, orange, and red pigments known to be important scavengers of dangerous forms of reactive oxygen in cells, and may be involved in protecting reproductive tissues such as pollen from abiotic stresses that decrease yield.

1. Understanding repeat fruiting in blackberry. Developing new varieties of thornless blackberries that produce fruit twice a year is a very slow process that could be accelerated with DNA-based tools. ARS scientists at Beltsville led a collaboration that identified pieces of DNA present in both seedlings and adult plants that were associated with thornlessness and repeat fruiting in blackberry. The pieces of DNA allow blackberry breeders to test a small seedling and know if it will be thornless and fruit twice a year when mature. This is the first report of the development of DNA-based tools for blackberry. Blackberry breeders and geneticists worldwide will use these and other newly discovered DNA pieces to more efficiently develop improved varieties of blackberry, a heat-tolerant fruit with valuable nutritional properties.

2. Strawberry flower genes controlling development into fruit. Very little is known about what enables the center of the strawberry flower, which becomes the edible flesh of the strawberry, to be capable of responding to the plant hormone, auxin, so that it enlarges and becomes sweet, juicy, and colorful. The ability to respond to auxin is fundamental to all aspects of plant growth and development, and has been implicated in responses to abiotic stressors such as elevated temperatures. ARS scientists at Beltsville, Maryland, in collaboration with scientists at the University of Maryland and Towson University, identified genes controlling the development of the strawberry flower parts that are important for its development into the strawberry fruit in response to auxin. Knowledge of the identity of these genes will allow manipulation of plant responses to auxin to decrease the negative effects of abiotic stresses that affect crop yield, quality, and plant architecture.

Review Publications
Castro-Lopez, P., Stafne, E.T., Clark, J.R., Lewers, K.S. 2013. Genetic map of the primocane-fruiting and thornless traits of tetraploid blackberry. Theoretical and Applied Genetics. DOI:10.1007/s00122-013-2152-3.
Harshman, J.M., Jurick II, W.M., Lewers, K.S., Wang, S.Y., Walsh, C.S. 2014. Decay resistance to Botrytis cinerea and quality characteristics during storage of raspberry genotypes. HortScience. 49:311-319.
Darwish, O., Slovin, J.P., Kang, C., Hollender, C., Geretz, A., Houston, S., Liu, Z., Alkharouf, N. 2013. FveGD: an online resource for diploid strawberry (fragaria vesca) genomics data. Biomed Central (BMC) Plant Biology. 13:223.
Hollender, C.A., Kang, C., Darwish, O., Geretz, A., Matthews, B.F., Slovin, J.P., Alkharouf, N., Liu, Z. 2014. Floral transcriptomes in woodland strawberry uncover developing receptacle and another gene networks. Plant Physiology. DOI:10.1104/pp.114.237529.