USDA CENTRAL SMALL GRAIN GENOTYPING LAB, MANHATTAN KS

Laboratory Instrumentation

  • Ion Proton

    Ion Proton Sequencer
    Ion Proton Next Generation Sequencer.
  • LGC Oktopure Robot

    LGC Oktopure DNA Extraction Robot
    Used for semi-automated DNA Extraction.
  • ABI 3730 DNA Analyzer

    ABI Sequencer
    Used for SSR and STS marker assays.
  • Ion CHEF

    Ion CHEF
    For emulsion PCR and sequencing chip loading prior to next generation sequencing on our Ion Proton.
  • Ion Proton OT2

    OneTouch 2
    For emulsion PCR and sequencing using next generation sequencing technology.
  • 7900HT Fast RealTime PCR

    7900 Fast RealTime PCR System
    For RT-PCR and KASP SNP analysis.
  • Sequenom Mass Array

    sequenom sequenom
    Multiplex SNP genotyping of 30-40 SNPs for 384 samples per run.
  • Plate Centrifuge

    centrifuge
    Can spin 4 deepwell plates at a time. We have two of these.
  • Freeze Dryer

    freeze dryer
    Dries 18 deepwell plates in 2 days for DNA isolation.
  • PCR Machines

    PCR machines
    10 PCR machines with single and dual 384-well blocks for marker analysis.
  • Pipetting Robot

    robot
    Beckman Biomek NXp for liquid handling during DNA isolation and PCR setup.
  • Liquid-dispensing Robot

    robot
    Formulatrix Mantis for liquid handling during assay setup.
  • Spectrophotometer

    spectrophotometer
    Quantifies 96 well plate samples of DNA and RNA.
  • Tissue Grinder

    tissue grinder
    Grinds two 96-deepwell plates of plant tissue in 5 min for DNA isolation.

Contact Us For Genotyping Services

Please contact either Dr. Bai or Dr. St. Amand prior to planning any genotyping service request. We can assist you in selecting markers, reserving time for your work, and all other planning.

General: Dr. Guihua Bai <gbai@ksu.edu>
Technical: Dr. Paul St. Amand <pst@ksu.edu>
USDA Genotyping Lab
3402 Throckmorton Hall
785-532-7350

Genotyping Services

The USDA Central Small Grain Genotyping Center (CSGGC) in Manhattan, KS, is one of four USDA Small Grain Genotyping Centers in the U.S. This Center offers collaborative genotyping services to regional breeders. We work very closely with both public and private hard winter wheat breeding programs in the Great Plains to conduct marker-assisted breeding for wheat cultivar development. The Center uses high-throughput SSR and SNP markers and breeder-friendly STS markers to genotype wheat samples. Selected information from this service is available to the public. We are committed to provide the genotyping service that our stakeholders need. Because of limited CSGGC budgetary resources, the number of data points for each breeding program depends on funding availability and number of samples sent from each program each year. Contact the lab for more specific information on data points assigned to each breeding program.

Sample turn-around time will vary with several factors including type of samples (seed or leaf tissue), type of markers to be analyzed (SSR, SNP or STS), availability of specific stock primers, the number of markers to be analyzed for each line, and the season in which samples are sent. Currently we accept both leaf tissue (fresh, freeze-dried, or oven-dried) and seed samples. Growing seedlings from seeds takes two extra weeks. Fresh leaf samples should be shipped on Dry Ice. SSR and STS markers are the preferred markers for genotyping; however, other markers can be used. Custom markers may need optimization before use for large-scale screening. Additionally, high-throughput techniques require that all samples in a 96-well plate or 384-well plate be tested with the same markers and not various combinations of markers within one plate. When the number of samples is fewer than 96, we recommend that reps, parents, and additional controls be analyzed so that the entire plate is full. The normal sample turn-around time will range from 4 – 10 weeks. Sample turn-around times can be shorter if advance notice is provided.

For genotyping of breeding materials, both the gene donor and background parents should be provided, along with information as to which parent is the gene donor. For unpublished markers, the appropriate primer sequences and PCR conditions must be provided to the Center at least one month prior to sample submission.

In addition to providing routine sample analysis, we work closely with breeding programs in the Great Plains Region. Our goals are to develop a new generation of DNA markers for agronomically important wheat traits and collaborate with breeding programs to design and conduct more extensive marker-assisted breeding projects in order to promote the quick release of new hard winter wheat cultivars or new germplasm with regional and world-wide impact.

Genotyping Data

Current and past genotyping data are password protected and available at the link below. Contact Dr. St. Amand for questions about your login ID and Password.

Data (password protected)

Ion Proton Sequencing

With prior approval, we can run GBS libraries on our Ion Proton sequencer. Up to 18 G of data may be obtained in a single run depending upon the library. Proton sequencing can take between 1 and 3 weeks to complete. For more information, please contact Dr. Guihua Bai.

Data from the Ion Proton Sequencer may be accessed by clicking the link. The correct user ID and password are required.


GBS Submission Form


Dr. Guihua Bai <gbai@k-state.edu>

Hard Winter Wheat Genetics Research Unit

3006 Throckmorton Hall

785-532-1124

Genotyping Lab Protocols

Our current laboratory protocols are available to anyone at the link below. These are updated frequently.

Lab Protocols

Released Cultivars

Wheat cultivars that have been developed using marker data from the USDA Central Small Grain Genotyping Lab.

Wheat Cultivars Using Marker Data

Genotyping Lab Markers

A table showing our most commonly used markers. This is useful for planning genotyping jobs or research projects. We have thousands of SSR markers and many more STS markers that we can use in any genotyping job. Contact us for custom, newer, or specialty markers.

Markers

Why Do Genotyping?

Our work greatly aids and improves new plant variety development. It also speeds variety releases. Here are some news articles from AgResearch Magazine on our lab and genotyping.

A Huge Plus for Breeders, Producers—and the Rest of Us

Diverse Wheat Tapped for Antifungal Genes

Annual Data Points

Every year we work closely with breeding programs in the Great Plains Region and also world wide. The data we generate are used for selecting new wheat cultivars & germplasm, for genetic mapping projects, or other research purposes. The table below outlines our annual production of marker data. A job year is Oct. 1 - Sept. 30. The count of scientists does not include those 15 or so participating in the regional performance tests. Plates hold 96 DNA samples. Standard markers are non-unique ABI, KASP, STS, SSR, CAP, and Gel markers. GBS markers are sequencing-based markers. Data points are 96 x plates x markers per job.


Job Year Scientists Jobs Plates Std. Markers Data Points Avg. DP/Job GBS UNEAK DP GBS Ref. DP
2006 8 24 92 175 36,404 1,517 . .
2007 8 40 139 433 57,744 1,444 . .
2008 11 84 431 847 189,216 2,253 . .
2009 9 36 301 214 89,280 2,480 . .
2010 7 16 108 192 60,864 3,804 . .
2011 8 24 289 299 93,984 3,916 . .
2012 16 38 108 1,559 266,304 7,008 . .
2013 14 45 161 567 141,888 3,153 . .
2014 13 28 123 472 109,536 3,912 . .
2015 8 21 89 286 82,080 3,909 . .
2016 11 39 111 357 70,464 1,807 8,915,819 71,041,844

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