STATEMENT OF WORK.docx

STATEMENT OF WORK (SERVICES) (SOW)

GENERAL INFORMATIONTitle of Project:

Characterization and Utilization of Genetic Diversity in Soybean and Common Bean and Management and Utilization of the National Rhizobium Genetic Resource Collection.

Statement of Need and Purpose:

The purpose of this request is to purchase sequencing services which will be used to help facilitate further genotyping of soybean and common bean populations and breeding lines created by soybean and common bean collaborators and our lab for the purposes to map genes/genomic regions controlling protein and oil content and to characterize breeding lines.

Background Information and Objective:

Soybean and common bean are among the most important crops in the U.S., with an annual value of $34 and $2 billion, respectively. These crops are important sources of protein for animal feed or human food. Soybean is also an important source of oil and a top U.S. export commodity. To cope with biotic and abiotic stress that cause >20% yield loss and demands for enhanced quality, breeders need to discover genes from new resources and develop approaches to accelerate the breeding processes. Molecular genotyping and sequencing of populations and individuals is critical to determine the novelty and positions of genes in the genome and assist selection. This research and goals are relevant to the NP301 Action Plan, Component 1. Crop Genetic Improvement; Problem Statement 1A: Trait discovery, analysis, and superior breeding methods.

Period of Performance:

Work must be done within 60 working days after receiving and QC of samples.

SCOPE OF WORKGeneral Requirements:

Sequencing of our 440 soybean samples must have a minimum of 20 Gb of data for each sample, which is about 20x coverage of the WGS. For the WHOLE genome library preparation, the DNA fragment length should be approximately 350bp to obtain 150 PE reads. Guarantee library preparation, and data quality (Q30 for ≥ 85%) for each sample that passes QC. SNP + InDel + SV +CNV calls among all samples are called, i.e by aligning the WGS of each sample to the Wm82a2v1 assembly (available at https://data.jgi.doe.gov/refine-download/phytozome?genome_id=275&_gl=1*1iczlxw*_ga*MTI4OTk5NDI3MS4xNzAxOTY4ODI2*_ga_YBLMHYR3C2*MTcwNjYzMTg1OS40LjEuMTcwNjYzMTkzOC4wLjAuMA..&expanded=Phytozome-275 ) individually, then combine all the aligned files to jointly call SNP + InDel + SV +CNV. The SNPs, indels, SV and CNV should be annotated using gff3 files associated with the Wm82a2v1 assembly ( the gff3 files are also available at the same site of the assembly). For SNP and single-base Indel annotations, the mutation type (non-synonymous or synonymous or stopgain/stoploss, etc.), position, reference allele, alternative allele, gene ID should be included; For Indels of more than 2 bases, genomic regions, locations, reference and alternative Indel alleles, and gene IDs should be included. For SV annotation, the SV genomic region, gene ID, location, type, and size should be included. For CNV annotation, the genomic region, location, type and size of the CNV and gene ID should be included.

Delivery Requirements:

The delivery should include:

1. Sequence reads and BAM files.

2. Files containing SNPs, InDel, SV and CNVs among genotypes as well as files with annotations for SNPs, Indels, SV and CNVs.

3. Description of the sequencing protocols, data analysis procedures, software used and parameters.

4. Summary of the sequencing results and data analysis results.

5. The above data or information shall be available for download by us on the website or FTP site or sent to us via hard drive.

DELIVERY OR DELIVERABLES

Assays and related reagents