A BRIEF HISTORY OF GBS - · PDF file18.02.2014 · A BRIEF HISTORY OF GBS ... KEYS TO GBS DATA PRODUCTION 1. High quality DNA! 2. ... Andropogon gerardeii (big bluestem)-forage and

A BRIEF HISTORY OF GBS

Rob Elshire, Jeff Glaubitz and Katie Hyma

WHY DID WE DEVELOP GENOTYPING-BY-SEQUENCING?

Driven by the needs of the plant breeding and genetics researchers: Many markers scored quickly and cheaply.

To address the limitations of other genotyping platforms:• Cost• Throughput• Replicability• Marker Discovery Bias

GENOTYPING-BY-SEQUENCING FEATURES

• Reduced sample handling• Few PCR & purification steps• No DNA size fractionation• Efficient barcoding system• Simultaneous marker discovery &

genotyping• Scales beautifully

WHY ARE RESEARCHERS USING GBS?

• It is cheap.• Molecular biology is simple.• Produces heaps of markers.• Simultaneous discovery and genotyping.• It is robust.• Produces libraries ready to sequence on the

Illumina platform with no changes to the standard Illumina sequencing protocol or Illumina analysis pipeline.

KEYS TO GBS DATA PRODUCTION

1. High quality DNA!2. Accurate quantification. Use intercalating dye,

not spectroscopy.3. Accurate liquid handling.4. Careful titration.5. Random blank in each plate.6. Follow the protocol.

THE FUTURE OF GBS FOR MAIZE

GBS APPLIED TO MANY SPECIES AT THE INSTITUTE FOR GENOMIC DIVERSITY AT CORNELL

Barley landraces

Maize (Zea mays)

Andropogon gerardeii (big bluestem)-forage and hay

Brachypodium distachyon-model grass, biofuel crop

Rice (Oryza spp.)

Sorghum

Cucumber (cucumis sativus)

Squash (cucurbita spp.)

Soybean (Glycine max)

Potato (Solanumtuberosum)

Watermelon (Citrulluslanatus)

Pepper (capsicum annuum)

Pea (Pisum sativum)

Safflower (Carthamus tinctorius)

Hops (Humulus lupulus)-flavoring and stability in beer, herbal medicine

Chickpea (Ciser arietinum)

Sunflower (Helianthus annuus)

Horseradish (Armoraciarusticana)

Lentil (Lens culinaris)

Dioscorea (yam)

Cotton (Gopssypium spp.)

Arucariaangustifolia-seed crop, Brazil

Eucalyptus grandis-timber, pulp, riverbank stabilization

Jatropha curcas-biofuel crop

Cashew (Anacardiumoccidentale)

Willow (Salix purpurea)

Spruce (Picea spp.)

Blue catfish (Ictalurus furcatus)-Largest species of catfish in the US, primarily in the Mississippi river drainage

Gulf killfish (Fundulus grandis)-Indicator to test effects of the Deepwater Horizon oil spill

Blackstripe topminnow (Fundulusnotatus)-conservation

Mexican Tetra (blind cave fish)Astyanaz mexicanus

Verticillium dahliae(shown infecting potato tuber)

Cattle (Bos taurus) Sus scrofa (boar, pig)

Catchfly (Silene latifolia)

Neurospora spp.

Chickadee

Iris spp.

GBS STRENGTHS AND WEAKNESSES