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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Research Project #431907

Research Project: Coordinated Development of Genetic Tools for Pecan

Location: Fruit and Tree Nut Research

Project Number: 6042-21220-014-02-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Sep 1, 2016
End Date: Aug 31, 2021

As more pecan trees are introduced into areas with high salinity soil, inadequate availability of water, and disease pressures, the development of genetic tools that can help mitigate these environmental and horticultural constraints is critically needed. This project is a request for funding to develop genetic tools for pecan trees that are essential to address many of the constraints on pecan nut production. The introduction of pecan trees into different environmental areas, such as the desert southwest, requires different genetic traits for pecan than those in the more humid environments of the traditional growing regions of the Southeast and South-Central United States. The identification of desirable traits such as efficient nutrient uptake/transport, disease resistance, salinity tolerance, drought tolerance, insect resistance, size control, and nut quality need to be identified in existing pecan genotypes. A current genome wide association study for pecan is in progress that utilizes high throughput sequencing technologies to detect high-density genome-wide markers for a large number of samples. The genome-wide marker data have the potential for detecting loci responsible for environmental adaptation through association analysis between marker genotypes and agro-ecological characteristics. The data from this study will allow broad details to be gleaned along with predicting the environmental adaptation ability of trees through genome-wide prediction. The development of genetic markers from these populations with detailed phenotypes is necessary and will benefit pecan producers by development of novel cultivars through breeding technologies and by facilitating the making of the best specific crosses. A marker assisted breeding technology for pecan will greatly benefit the pecan industry by decreasing the time for development of novel cultivars. If the genetic marker associated with a phenotype is known then this trait can be introduced by breeding technologies. The use of molecular technologies can verify the inclusion of these genetic markers that are linked to specific traits and verification of these markers will ultimately decrease the time required for selection. The development of genetic markers with specific traits has the potential to influence economics of pecan production. Development of trees with key traits will be more advantageous. For instance, trees that are better suited for specific environments may yield higher nutritional quality pecan nuts and may require less input by growers. This would provide an economic advantage to the pecan grower and would be more environmentally friendly.

1. Complete genomic sequence of multiple reference pecan trees that captures of the genetic diversity of the pecan genome. We will deploy a combined Illumina based short read sequencing and Pacific Biosystem’s long read sequencing to achieve MB scale contiguity for the inbred reference tree 87MX-3-2. For positioning and validation of these MB sized pieces to form pseudomolecules, we will use low pass resequencing to type SNPs in a reference pecan F2 population and use linkage information to position these large contigs of the genome sequence. We will then add to this genome assembly dense RNA-seq data sets from multiple tissues to provide accurate annotation of the gene compliment. Based on the success of generating the inbred reference sequence, we will sequence the genomes of several key cultivars with diverse genetic backgrounds from the USDA breeding program, using a similar methodology. 2. Identification of molecular mechanisms, and the genetics that control horticultural traits such as flowering, germination, nutrient transport, disease resistance, and nut quality. Based on the ongoing research to perform genome wide association from diverse pecan genotypes to pecan agronomic phenotypes, we expect to broadly identify regions of the genome linked to specific traits of interest. As part of this project, we will further localize these traits using deep re-sequencing of linked cultivars and natural accessions paired with transcriptomic studies to better understand these molecular mechanisms in order to incorporate these into genomic assisted pecan breeding. 3. Phenotypic descriptor development, data collection and delivery. Existing phenotypic data will be integrated into GRIN-Global, the database of the National Plant Germplasm System. Additional phenotypic descriptors will be developed for targeted parameters, especially focusing on tree architectural traits. Establishment of a database and web portal suitable for storing, analyzing and visualizing the genomic, phenotypic and marker-trait data information generated from this projects. 4. Develop and/or establish Carya mapping populations contrasting for key traits, genotyping progenies and phenotypic data collection. Developing high-density SNP-based linkage maps in pecan will enable identification of molecular mechanisms and corresponding genes impacting agriculturally-relevant traits for which phenotypic data will be collected including seed germination, flowering time and amount, nutrient transport, disease resistance and nut quality. This will allow for identification of useful alleles for specific phenotypes. 5. Development of marker systems for use in cultivar verification and eventually marker assisted breeding for both rootstock and cultivar development. Generate SNP genotyping platforms suitable for high throughput genotyping to characterize pecan cultivars and initiate marker-assisted selection strategies in pecan.