Statement of Work.pdf

STATEMENT OF WORK

Background

• Pecan shuck decline is a physiological disorder affecting pecan trees, particularly those with heavy crop loads. It leads to premature blackening and splitting of the shucks, often resulting in reduced nut development or fruit loss. Although the precise cause remains uncertain, researchers attribute it to factors such as tree stress, water availability, and hormonal imbalances. This project aims to investigate the molecular mechanisms underlying pecan shuck decline by analyzing shuck tissue samples at various stages of the condition. RNA extraction and sequencing are being conducted to identify key genetic factors associated with the disorder, providing insights that may inform mitigation strategies. The study aligns with broader research initiatives in pecan tree health and is conducted within the framework of relevant agricultural research regulations in our breeding program.

Objectives

• Identify key genetic factors associated with shuck decline through RNA sequencing.

• Analyze gene expression patterns to better understand stress responses in pecan trees.

• Provide insights that could inform mitigation strategies for improving pecan tree health and productivity.

• Contribute to broader horticultural research by aligning findings with existing studies on tree physiology and disease management.

• The results from this project will help researchers and growers develop targeted approaches to reduce the impact of shuck decline, improving pecan crop yields and overall orchard sustainability.

Scope

• The work includes sample processing, library preparation, and sequencing

• Maintain a quality control (QC) process to verify sample integrity and sequencing performance.

• Provide timely updates on project progress, including reporting any technical issues that may impact data delivery.

• Ensure proper data storage, backup, and transfer to maintain the integrity of sequencing results.

Tasks or Requirements

• Sample Processing of 72 RNA samples (including RNA quality assessment and cDNA synthesis)

• Library Preparation (including fragmentation and adapter ligation, size selection, and quality control to ensuring libraries meet yield and concentration requirements for sequencing)

• cDNA sequencing using paried-end 150 base pair sequence reads to ~70 million read pairs per sample.

• Return of any remaining RNA samples to USDA

• Data delivery required on completion of contract over FTP, Globus Transfer, or Hard

Drive.

Deliverables or Delivery Schedule

• RNA Quality Control Report (including RNA integrity analysis and concentration)

• Library concentration and fragment size distribution report

• Raw Sequencing Data (FASTQ, BAM, or CSV files with relevant metadata)

• Detailed summary of workflow, troubleshooting logs, and QC validation

• Data delivery 60 days ARO