The traditional orange carrot is the richest plant source of provitamin A in the US diet and one of the most widely consumed and nutritious vegetables in the world. In spite of the known health benefits attributable to carrots and other vegetables, the 2010 Dietary Guidelines for Americans indicated that vitamin A is under-consumed, and overall vegetable consumption is less than 40% of that recommended by nutritionists. The carrot industry needs breeding stocks and genomic tools that can be used to develop carrots with improved field performance to better withstand biotic and abiotic stress, and improved flavor and appearance to better meet consumer needs and develop new products. Given these critical consumer and carrot industry needs, the long-term goals of this project are, 1) to generate genotyping and genomic resources for carrot germplasm, and use a database platform to deliver phenotypic and genotypic information for carrot stakeholders to tap into the breadth of carrot genetic diversity, and establish a science-based foundation for long-term carrot improvement ��� as measured by more economical carrot production with a smaller environmental footprint, and by increased per capita carrot consumption; 2) to provide stakeholders with carrot germplasm from advanced breeding pools developed from diverse carrot germplasm in our previous SCRI research from plants with favorable phenotypes for traits important for growers and consumers that will help speed the delivery of new carrot cultivars adapted to meet future challenges; 3) to perform transdisciplinary research, using carrot as a model, to better understand how new traits can influence consumer and market value of carrots, with results that can be applied to other specialty crops; and 4) to recruit and train students and postdoctoral scholars, and inform and engage the public, as we undertake these goals

The demand for natural pigments, such as anthocyanins, for use as a food colorant continues to grow in the US and worldwide, with the US being the largest consumer and producer. However, the production and use of anthocyanins (ANT) is challenging due to lower stability, non-uniform yield, and challenges to match the desired hues, which leads to higher prices and non-stable market availability. Purple carrot is one of the most used source of anthocyanins as a natural food dye since it contains large quantities of acylated anthocyanins which imparts higher heat-, light- and pH-stability, enhancing their shelf-life. Despite these advantages, anthocyanins are largely extracted from non-uniform purple carrot cultivars not specifically bred for ANT extracts, which limits the ability of the colorant industry to standardize and optimize anthocyanin yield and stability. Genetic and genomic resources and knowledge of carrot ANT content and profiles are developing rapidly. However, these resources have not been translated to a practical application. The objectives of this project are: (1) Deliver genotyping and phenotyping capacity to select carrot cultivars that can maximize anthocyanin yield and stability; (2) Identify the molecular mechanisms involved in the synthesis of anthocyanins and phenolic acids in carrot roots in response to external factors; (3) Evaluate extraction efficiency across genotypes, and identify anthocyanins and phenolic acid composition that contributes to ANT extracts increase of shelf life and stability. The outcomes of this project will facilitate the establishment of innovative solutions to improve and standardize ANT yield, product performance and stability; which are critical steps to sustain the growing demand of ANT extracts from purple carrots. This AFRI proposal addresses Program Area Priority Code: A1103, ����������������Foundational Knowledge of Plant Products���������������.

VacciniumCAP: Leveraging genetic and genomic resources to enable development of blueberry and cranberry cultivars with improved fruit quality attributes. The proposed project provides a coordinated trans-disciplinary research team that will develop DNA and precise high-throughput phenotyping tools (Obj. 1) to routinely and efficiently use to select cultivars with improved fruit quality traits (Obj. 2, 4) that can positively affect profitability across multiple primary systems including production, processing/distribution and consumers/market (Obj. 2-3). Such a coordinated genomics-based approach has been successful in other fruit crop groups such as the Rosaceae, but is currently lacking in Vaccinium.

The Dietary Guidelines for Americans 2015 (DGA) has constructed recommendations for fruit and vegetable consumption based on their inherent 1) nutrient content, and 2) presence of bioactive compounds with recognized benefits for prevention of chronic diseases. However, with a large disparity between guidance and consumer behavior, increasing production alone cannot deliver the benefits of fruit and vegetable consumption required for a healthy population. With this in mind, we propose a novel approach to improve our population������������������s aptitude to meet dietary recommendations. Our strategy delivers more from the current consumption patterns by providing a path to improve and diversify fruit and vegetable products and, by extension, servings. This disruptive approach will provide a map of genetic factors that improve micronutrient and bioactive density and bioavailability in a strategic set of fruits and vegetables that are already commonly consumed, and will allow for development of products that are more effective at delivering the requisite nutrients and bioactives per serving. Combined with novel ingredient technologies and translation to a broader array of consumer product platforms (snacks, beverages, cereal), our effort will help diversify fruit and vegetable products available for consumers to meet DGA guidance. To validate this approach, preclinical and clinical assessments that apply advanced metabolic fingerprinting will be used to compare new products and platforms to standard fruit and vegetable recommended servings to ensure enhanced delivery of fruit and vegetable nutrients and bioactive phytochemicals. Establishment of the equivalency of this approach to deliver fruit and vegetable servings in a different way will set the stage for broader adoption by the industry and consumers. Our approach is novel in that it is one of the first to truly leverage delivery (bioavailability) as a differentiating trait to target in breeding of improved fruits and vegetables and development of more effective products. We have high throughput capacity and experience to screen for these traits across unique germplasm collections of highly consumer relevant fruits and vegetables (blueberry, spinach and banana) from our own collections and from key industry partners (General Mills and Dole Foods). We also have unique expertise in ingredient technology to capture and deliver fruit/vegetable micronutrients and phytochemicals as ingredients suitable for new product formats. With the capability to effectively test their equivalency in humans, our transformative approach has the potential to make meaningful advances in delivering materials to help consumers meet dietary guidelines for fruit and vegetable consumption.

Overall project objectives are 1) to phenotype diverse carrot germplasm and breeding stocks to discover variation for traits important for improving carrot disease and pest resistance, reliable crop production and tolerance to environmental stress,enhanced consumer quality, and superior color and nutritional value; 2) to develop an expanded carrot genomic database for breeders; 3) to initiate development and evaluation of breeding pools from diverse gerrnplasm and breeding stocks that include alleles for improved crop production and consumer quality traits; and 4) to evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions.

Given the low sequencing depth coverage used in this study, the linkage map has very low resolution across the 48 blueberry homologous chromosomes, which limits QTL analysis. The genotyping technology that we propose to use in this project will provide high sequencing coverage that will enable us to accurately estimate allele dosage and employ advanced computational tools developed to construct linkage maps for autopolyploid species, like blueberry.

In order to have an ideal plant for mechanical harvest we have to pyramid a set of desirable genes into an already superior cultivar with decent flavor and yield. Since these traits are controlled, by different genes, which most likely are unrelated and complex, we need to focus on one trait at a time per bi-parental population to identify gene(s) underlying controlling each trait. In the case of blueberry and thanks to the works that have been done previously (M Mainland and J Ballington, Pers. Comm.), we have a wealth of phenotypic information about these traits in different genetic backgrounds. However, our knowledge about the genetics underlying each phenotypic observation is very limited due to the lack of genomics information in previous research. With the advent of next generation sequencing technologies in recent years, genotyping thousands of individuals by sequencing, or developing genetic markers in a short period is no longer insurmountable. In the recent past genotyping was expensive and phenotyping was easier to do, resulting in a focus on phenotyping. Now genotyping is no longer a limitation but precise phenotyping is a limiting factor in all plant, animal and human genetics studies. To tackle the problems that we are facing today, with regard to amenability of blueberries to mechanical harvest, we need to define a multidisciplinary approach among plant breeders, plant physiologists, plant molecular biologists and agricultural and biological engineers. From breeding stand point, we need to focus on mapping the gene(s) for firmness, late ripening to extend the production season, pillar or broomy tree architecture, easy detachment of the fruit, fruit size, high anthocyanin content, and high soluble solid content. Conventional breeding will remain in the core of our breeding program, but identification of QTLs will help developing molecular markers for each trait and genomic selection in early generations to speed up the breeding program by marker-assisted selection. This is a multiyear project starting in spring 2016 and ending by summer 2021, however it has been budgeted for one year in order to develop the populations and do preliminary parental genotyping surveys. We will resubmit the proposal in subsequent years to have continuity of the project. The populations and the parental genotype data that will be collected in the first year will provide preliminary data to seek more funding from USDA and other institutions. In the first year, we are going to develop mapping populations by crossing, germinating seed and transplanting the seedlings in to 4-Inch pots; we will extract DNA, run molecular markers to genotype parental cultivars and to investigate their polymorphism rate. In the second year (2017) we will start genotyping two populations. By Oct 2017, we should have all seedlings transplanted into the Ideal Tract Farm in Castle Hayne. In years 3 - 5, we collect phenotypic data on fruit firmness of the population and finish the QTL mapping. As the plants grow more each year in subsequent years, we can collect more fruit from each plant and our data will be more accurate as we progress.

We propose to use high molecular weight gDNA to create long-insert PacBio libraries for sequencing at DHMRI on the Sequel system. The data will be used to construct a high-quality draft genome for pineapple, clone MG-2. In order to get a chromosome-scale assembly, we will use the Hi-C sequencing technology available through Phase Genomics. Utilizing PacBio in combination with Hi-C technology is the highest standard in genomic assembly and will allow us to build a complete and accurate reference genome that can confidently be used for future pineapple studies. PacBio iso-seq data will be used to annotate the genome and locations of gene families involved in flower induction, fruit development and bromelain biosynthesis.

The overall goal of this project is to identify and coordinate research priorities and breeding trait targets based on the various industry sectors and further integrate genomic/phenotypic data to develop a sustainable technical platform to accelerate and increase the efficiency of cultivar development and adoption. The potential of genomic approaches to enhance crop improvement, particularly through genomic selection, is enormous. Genomics research has not yet been translated into routine practical breeding application in cranberry or blueberry breeding. Their shared ancestry can be harnessed to leverage knowledge and resources across commodity boundaries via comparative genomics. This project will also identify priorities for extension activities that are integrated with identified research priorities to enable dissemination and rapid adoption of research results. A large research community currently working on cranberry and blueberry will be united for the first time to work towards the development of coordinated research objectives that will lead to application for a future SCRI-NIFA CAP grant proposal and empower research towards accelerated development of novel germplasm to meet industry and consumer needs.