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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Research Project #435799

Research Project: Improving Fruit Crop Traits Through Advanced Genomic, Breeding, and Management Technologies

Location: Innovative Fruit Production, Improvement, and Protection

Project Number: 8080-21000-029-000-D
Project Type: In-House Appropriated

Start Date: Nov 14, 2018
End Date: Apr 26, 2023

Objective 1. Identify and functionally analyze genes regulating plant architecture, abiotic stress tolerance, fruit quality, and disease resistance. [NP301, C1, PS1A, PS1B; C3, PS3A, PS3B] Sub-objective 1a. Identify and functionally analyze genes regulating plant architecture in temperate, deciduous fruit crops and rootstocks. Sub-objective 1b. Identify and functionally analyze genes regulating dormancy, cold hardiness, drought, disease resistance in apple and stone fruit crops. Sub-objective 1c. Identify and functionally analyze genes regulating fruit development traits in stone fruits. Objective 2. Develop and optimize advanced methods for tissue culture propagation and genetic transformation of temperate, deciduous fruit crops. [NP301, C1, PS1A, PS1B; C3, PS3A, PS3B] Sub-objective 2a. Optimize tissue culture production of apple, pear, and stone fruit scion and rootstock genotypes. Sub-objective 2b. Develop transgenic and gene edited lines and field plantings of fruit crops for functional analysis of genes that regulate important traits identified in Objective 1. Sub-objective 2c. Develop CRISPR technologies for modifying important functional traits in fruit crops. Objective 3. Use standard and rapid cycle breeding systems to generate advanced lines of germplasm for the apple and stone fruit breeding community and industry. [NP301, C1, PS1A, PS1B; C3, PS3A, PS3B] Sub-objective 3a. Use early-flowering apple and stone fruit rapid breeding systems to introgress and or pyramid economically-important traits, such as disease resistance, from wild species and known sources of established cultivars, into commercial germplasm. Sub-objective 3b. Utilize rapid breeding system to eliminate transgenes from Agrobacterium-based-CRISPR transformation of fruit crops. Sub-objective 3c. Establish field plantings of select lines of stone fruit and apple germplasm developed through classical and transgenic technologies that exhibit economically-desirable traits.

This project leverages plant breeding, genomics, genetics, molecular biology, and biotechnology strategies to address fundamental problems facing tree fruit production. The variety development and basic research activities are synergistic as the germplasm developed through the breeding efforts serve as a critical resource for identifying the genetic basis for complex traits. Many of the objectives proposed will use the unique transformation technologies developed by the investigators coupled with available genome sequences for several tree fruit species. These transformation systems have been used to develop FasTrack technology to shorten the breeding cycle for fruit tree species. Plums and pears transformed with the poplar FLOWERING LOCUS T produce flowers within the first year of growth and can be hybridized to achieve generation cycles of one to two years. Biological processes under study will include flowering time/dormancy, tree architecture, and fruit development. Regulation of flowering time in peach will be investigated using genetic, molecular and deep sequencing-based strategies. An extreme late blooming trait that avoids spring frost will be combined with commercial quality traits through conventional breeding. Tree architecture, specifically the regulation of TAC1, LAZY1, and LAZY2 expression by light, gravity, and the circadian clock, will be carried out via gene expression studies along with promoter swap experiments to determine the functional consequences of mis-expressing each gene. Collectively, these data will provide important practical information about how light regulation of IGT genes contributes to tree shape. We will continue to characterize previously created plum and apple PpeDRO1 over-expression transgenic lines and RNAi silencing lines to evaluate the impacts of over- or loss- of DRO1 function on root system architecture. In pear, we will leverage our biotechnology system to functionally characterize putative apple dwarfing/precocity genes and assess their potential to confer these traits in pear rootstocks. To study how fruit tissue determination is achieved, we have begun transcriptome-based comparisons of different fruit types, tissues, and developmental times to identify gene networks that specify properties of fleshy versus non-fleshy tissues during and after fruit set. Technology to engineer and breed for stoneless fruits will be tested using a combination of biotechnology and conventional breeding. A novel super sweet trait in peach/nectarine that confers extremely high brix (20o–30o) will be bred to develop commercial quality super sweet varieties. Methods for gene editing will be developed for plum and pear via isolation and use of novel promoters. Lastly, the research unit will continue to pursue national and international release of the transgenic plum ‘HoneySweet’ that is resistant to Plum Pox Virus (PPV). Collectively, these efforts will fill in key knowledge gaps about fundamental fruit tree developmental processes, provide new technologies for developing fruit tree germplasm with economically important traits, and lead to the development of new fruit varieties with superior traits.