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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

2017 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 identified several new diploid strawberry mutants with traits affecting plant architecture and fruit quality, including mutants with highly elongated inflorescences, mutants with abnormal branching patterns, and non-runnering mutants. In support of Objective 1, ARS scientists at Beltsville, Maryland, determined that molecular markers associated through multiple international studies with strawberry repeat fruiting do not accurately predict the phenotypes of progeny resulting from cross pollinations of two repeat-fruiting parents. A second independent genomic region controlling repeat fruiting was implicated. This information can be used by researchers to identify markers in the second region which, combined with the first markers, can be used to better match parental strawberries that will be more likely to yield repeat-fruiting offspring. 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 sent daughter plants to Beltsville to confirm identity and phenotype, but did not have enough virus-free plants to send cooperators. Additional plants will be available to send to cooperators Spring 2018. B1806 could be available for release as early as June 2019. With at least a two-week shelf life, this selection has the potential to augment strawberry supplies after field production ceases. In support of Objective 2, ARS scientists at Beltsville, Maryland, identified a late-season once-fruiting strawberry breeding selection for likely release as a cultivar. B2360 has significant resistance to anthracnose and botrytis, the two major strawberry diseases of the world. It also is tolerant to rain damage, an important advantage in many years. It has high yield of very attractive, uniformly-sized, sweet fruit with an excellent shelf life. B2360 received above-average scores for several years in all categories used to evaluate potential varieties. A nursery will be selected next to propagate B2360 for cooperator evaluations. This new late-season cultivar will help strawberry growers in the Northeast US to extend their production season into summer and bridge a potential production gap between strawberries and blueberries or raspberries. In support of Objective 3, ARS scientists at Beltsville, Maryland, determined the environmental conditions that control strawberry yield under low tunnels. For example, average bed temperature, not air temperature, and not the difference in temperatures between daytime and nighttime, four weeks (not three or five) prior to harvest determines yield. Strawberry yield increases steadily with 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. These findings will be useful for breeding repeat-fruiting cultivars and for developing best-management practices for growers. In support of Objective 4, ARS scientists at Beltsville, Maryland, determined that, contrary to the available scientific literature, at least two genes appear to be responsible for the loss of runnering in two non-runnering mutants of diploid strawberry, and that additional factors may also be involved in whether plants produce runners or not. These genetic experiments explain why it has not yet been possible to identify and clone the gene for runner production, which is critical to strawberry production. In support of Objective 4, ARS scientists at Beltsville, Maryland, in collaboration with an international consortium of scientists in academia and industry, completed a re-sequencing of the diploid strawberry genome using up-to-date long sequence read technology, producing a very high quality reference genome. Almost 1,500 new genes were discovered, and numerous large scale errors in the previous version have been rectified. The new sequence will benefit both basic and applied research. In support of Objective 4, ARS scientists at Beltsville, Maryland, in collaboration with scientists at the University of Minnesota developed a new separation and analysis system for identifying carotenoid pigments in small amounts of plant tissue using liquid chromatography/mass spectrometry. This work was required for further characterization of a diploid strawberry mutant defective in production of some carotenoids, which are known antioxidant pigments made by plants, fungi and algae, but not by most animals, but which are required for human health.

1. Strawberries perform better when grown 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 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. Higher temperatures found under low tunnels, especially in early spring and late fall, resulted in a much longer harvest seasons. Strawberry yield increased as light increased, and also with warmer temperatures up to about 28 degrees-Celsius, above which yields dropped due to excessive heat. Further test showed that yields were more strongly associated with soil temperatures than air temperatures. Growers will benefit from finding ways to keep the soil in the raised beds cool and maximizing the amount of 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. Creating new strawberries with better flavor and that fruit longer each year. Strawberries are very popular with consumers who would like to have them all year long and would like the strawberries they buy in supermarkets to taste better; therefore, breeders need a better understanding of how they can breed new strawberries that fruit all year long and taste sweeter and less tart. The genetics of repeat fruiting, sweetness and tartness were determined by studying how often each of these traits were inherited in the seedlings of a cross pollination between two strawberry plants. Sweetness was inherited independently from tartness so that no extraordinary methods should be needed by breeders to create new strawberries that are sweet and not too tart, and both these traits were controlled by multiple independent genes. In contrast, repeat fruiting in this study was found to be controlled by a single gene that was dominant over once-fruiting so that a breeder can expect that at least half of the seedlings from a cross-pollination with a repeat-fruiting strawberry and a once-fruiting strawberry should be repeat-fruiting. These results provide strawberry breeders with basic expectations from which they can more efficiently create improved strawberries.

Review Publications
Lewers, K.S., Fleisher, D.H., Daughtry, C.S. 2017. Low tunnels as a strawberry breeding tool and season-extending production system. International Journal of Fruit Science.
Castro, P., Lewers, K.S. 2016. Identification of quantitative trait loci (QTL) for fruit quality traits and number of weeks of flowering in the cultivated strawberry. Molecular Breeding. 36(10):138-156.
Darwish, O., Shahan, R., Liu, Z., Slovin, J.P., Alkharouf, N. 2015. Re-annotation of the woodland strawberry (Fragaria vesca) genome. Biomed Central (BMC) Genomics. 16:29.
Inostrozablancheteau, C., Aquea, F., Loyola, R., Slovin, J.P. 2013. Molecular characterization of a calmodulin gene, VcCaM1, that is differentially expressed under aluminum stress in highbush blueberry. Plant Biology. 15:1013-1018.
Vieira, P., Lakshman, D.K., Pandey, R., Slovin, J.P., Kamo, K.K. 2017. Symptom development in response to combined infection of in vitro grown Lilium longiflorum with the root lesion nematode Pratylenchus penetrans and soilborne fungi collected from diseased roots of field-grown lilies. Plant Disease. 101:1-8.