Statement of Work Zeng genotyping project.doc

UNITED STATES DEPARTMENT OF AGRICULTURE

AGRICULTURAL RESEARCH SERVICE

CGRU

SPECIFICATIONS

Cotton FY24 Statement of Work (SOW) Project: Genotyping Genetic Populations of Within-Boll Yield Components by Whole Genome Sequencing

GENERAL INFORMATION

1.0 Scope of Work:

Increase of cotton yield is always a top priority in cotton breeding programs. Breeding for genetic improvement of yield through yield components has reached a plateau because some key components are highly affected by environmental conditions. Breeding for increasing yield by within-boll yield components can be an effective approach with a determination of genetic mechanisms underlying the relationships of these yield components to the lint yield. Genotyping mapping populations by whole genome sequencing will help us determine the molecular mechanisms underlying these phenotypic relationships. At least 1,000 plants in the genetic populations need to be analyzed by sequencing. The goal of this project is to improve cotton yield and promote profits of cotton producers.

2.0 Background:

Within-boll yield components include seed weight, seed number per boll, lint weight per seed, seed surface area per seed, lint weight per seed surface area, and lint number per seed surface area. The phenotypic relationships of these components to lint yield are often complicated overlapped among themselves. Genotyping of genetic populations by whole genome sequencing can reveal the genetic basis of these relationships and help us determine the components most contributing to yield. It is required that appropriate methodologies are applied to generate accurate and reliable genotyping and reveal the genetic mechanisms. Continuity in protocols from our previous work to the next will be desired for a high efficiency and reliability of this work. The vendor, Novogene, Inc., has been the source to provide service to us and our cooperators such as Cotton Fiber Bioscience Laboratory for whole genome sequencing of cotton years in the past.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

Prospective Vendor will perform DNA sequencing: Each F2 plant along with the parents will undergo WGS (Whole Genome Sequencing) with 10 X coverage, generating approximately 25Gb of data per sample. Prospective Vendor provides a deep sequencing that align with our goal and budget.

4.0 Place of performance:

Company Address: 2921 Stockton Blvd. Suite 1810, Sacramento CA 95817 VAT number: GB 273975163 Phone: 916-252-0068(toll free) Fax: 916-252-0068 5.0 Government Furnished:

The government agency performs planting of the genetic populations in fields, sampling tissues, and preparing DNA samples. The agency checks samples for number count and packing and submit the exact number of DNA samples to the vendor.

The shipping dock is open Monday through Friday, 8:00am to 4:30pm

6.0 Deliverables / Schedule:

Milestone Deliverable

Reporting requirement:

Key Deliverables

Timeline and milestone were defined as above No later than three months after contract award

7.0 Travel:

No travel is required for this service.

8.0 Contractor’s Key Personnel:

Novogene:

Matt Colucci, MSc | LinkedIn

Regional Sales Manager, Southeast | Novogene Southeast

Novogene USA Inc. | Novogene Website

Cell: 401-533-1752 [Eastern Time Zone] | Matthew.Colucci@novogeneusa.com Texas A&M:

Charlie Johnson

Texas A&M AgriLife Genomics & Bioinformatics Service

Phone: 979-862-3262 txgen@ag.tamu.edu charlie@ag.tamu.edu 9.0 The contractor required to perform measurements:

Whole genome sequencing with 10X coverage