SolCAPSolCAPSolanaceae Coordinated Agricultural ProjectSolanaceae Coordinated Agricultural Project

SNP Development for Elite Potato GermplasmSNP Development for Elite Potato Germplasm

David Douches Walter De Jong David Douches Walter De Jong Robin Buell Robin Buell David FrancisDavid Francis

John Hamilton Lukas Mueller John Hamilton Lukas Mueller AllenAllenVan DeynzeVan DeynzeFundingUSDA/AFRIThis project is supported by the Agriculture and Food Research Initiative Applied Plant Genomics CAP Program of USDA’s National Institute of Food and Agriculture.

What is SolCAP?What is SolCAP?

The SolCAP project is a The SolCAP project is a coordinated agricultural coordinated agricultural project project that links together people from public institutions, that links together people from public institutions, private institutions and industries who are dedicated to the private institutions and industries who are dedicated to the improvement of the improvement of the SolanaceaeSolanaceae crops: potato and crops: potato and tomato. tomato. 

Through innovative Through innovative research, education and extension research, education and extension the SolCAP project will focus on providing significant the SolCAP project will focus on providing significant benefits to both the consumer and the environment.benefits to both the consumer and the environment.

The SolCAP project is supported by the Agriculture and Food The SolCAP project is supported by the Agriculture and Food Research Initiative Applied Plant Genomics CAP Program of the Research Initiative Applied Plant Genomics CAP Program of the USDA’s National Institute of Food and AgricultureUSDA’s National Institute of Food and Agriculture

MinnesotaUniversity of Minnesota WisconsinUSDA/ARS University of WisconsinMichiganMichigan State UniversityOhio Ohio State University

Lead Institution: Michigan State University

OregonOregon State UniversityCedar Lake Research and ConsultingIdahoUSDA/ARS University of IdahoCaliforniaUC DavisCampbells R&D

New YorkCornell UniversityMarylandUSDA/ARS Beltsville

West VirginiaWest Virginia State UniversityNorth CarolinaNorth Carolina State UniversityFloridaUniversity of Florida

SolCAP Project ParticipantsSolCAP Project Participants

Commercial Solanaceae ProductionCommercial Solanaceae ProductionUS: $5.38 billion product value (1.6 million acres)US: $5.38 billion product value (1.6 million acres)

Potato Breeding Bottlenecks & ChallengesPotato Breeding Bottlenecks & Challenges

• Tetraploid geneticsTetraploid genetics• Narrow genetic baseNarrow genetic base• Small populationsSmall populations• Many pestsMany pests

• Multi-trait evaluationMulti-trait evaluation– QualityQuality– Resistance Resistance – AgronomyAgronomy

• Market differentiationMarket differentiation

Potato Breeding Bottlenecks & ChallengesPotato Breeding Bottlenecks & Challenges

• Lack of markers in elite germplasmLack of markers in elite germplasm

• Mostly a phenotypic based process • Market defining traits (CHO) difficult

to select for at early generation stages.

• Breeder needs to combine the

market-driven quality with the agronomic performance and host plant resistance needed by the growers.

The Potato Genome Sequencing ConsortiumThe Potato Genome Sequencing Consortium

• The Potato Genome Sequencing Consortium (PGSC) have collaborated to sequence the genomes of two species: Solanum tuberosum (RH) and Solanum phureja (DM1-3 516 R44).

• First potato genome assembly http://www.potatogenome.net

The Potato Genome Sequencing ConsortiumThe Potato Genome Sequencing Consortium

Whole genome shotgun sequencing – Hybrid approach using three sequencing technologies

Metrics: 850 Mb

• V3: 9,171 scaffolds (717.5Mb) & 58,998 contigs (9.7Mb)• N50 scaffold size: 1,318,511bp• N90 scaffold size: 253,760 bp

Available at:Potatogenome.net

Annotating the Potato GenomeAnnotating the Potato Genome

• Identified genes• Sequenced transcriptome from 29 different DM tissues• Analyzing the genes and their expression currently

In Solanaceae There is a Major GapIn Solanaceae There is a Major Gap Between Genomic Information and Breeding Between Genomic Information and Breeding

• Potato breeding are based upon phenotypes, not genotypes, despite the fact that they are being sequenced.

• Marker assisted breeding (MAB) is not widely practiced Marker assisted breeding (MAB) is not widely practiced due to a lack of genetic markers linked to traits of due to a lack of genetic markers linked to traits of interest.interest.

• SolCAP is providing translational genomics strategy.SolCAP is providing translational genomics strategy.

Primary Research ObjectivePrimary Research Objective

• To reduce the gap between genomics and breeding SolCAP will provide infrastructure to link allelic variation of SNPs in genes to valuable traits.

– Identify up to 10,000 SNPs for potato in elite germplasm

– Combine eSNPs w/ Illumina sequence-identified SNPs

– 75% of the SNP’s distributed throughout the genome

– 25% of the SNP’s targeted to candidate genes and genetic markers– Genotype germplasm panels and mapping populations with

Illumina Infinium platform

• Develop extensive sequence data of expressed genes, and identify SNP markers associated with candidate genes for CHO and vitamin biosynthetic pathways.

• Collect standardized phenotypic data of panel and 4x mapping population across multiple environments for potato.

• Address regional, individual program and emerging needs through a small grants program that supports SNP genotyping of additional mapping populations.

• Create integrated, breeder-focused resources for genotypic and phenotypic analysis by leveraging existing databases and resources at SGN and MSU.

Plan of WorkPlan of Work

1. Existing eSNPs from Kennebec, Bintje and Shepody ESTs

2. New Illumina GAII sequencer-identified SNPs from important processing cultivar transcriptomes:

Atlantic – high solids chip-processor Snowden – low reducing sugar storage chip processor Premier Russet – low reducing sugar; frozen proc.

Potato SNP Marker DiscoveryPotato SNP Marker Discovery

PotatoPotatoTotal # of Transcript Assemblies: 70,344Total bp length of Transcript Assemblies: 49,859,202Total # Transcript Assemblies w/ putative SNPs: 7,722Total bp length of Transcript Assemblies w/SNPs: 8,872,526Total # of putative SNP positions: 57,705

In SilicoIn Silico Sanger Identified SNPs (eSNPs) Sanger Identified SNPs (eSNPs)

TomatoTomatoTotal # of Transcript Assemblies: 48,945Total bp length of Transcript Assemblies: 33,916,704Total # Transcript Assemblies w/ putative SNPs: 5,198Total bp length of Transcript Assemblies w/ SNPs: 6,347,780Total # of putative SNP positions: 16,531

Sanger-derived Potato eSNPsSanger-derived Potato eSNPs

- Intra-varietal and inter-varietal - Bulk of sequence data from ESTs - http://solanaceae.plantbiology.msu.edu/analyses_snp.php

PotatoPotato

•Snowden•Atlantic•Premier Russet

TuberLeafFlowerCallus

cDNA Libraries for SequencingcDNA Libraries for SequencingUsing Illumina Genome Analyzer IIUsing Illumina Genome Analyzer II

•Isolate RNA from these 4 tissues•Pool in equimolar amounts•Construct normalized cDNA to reduce representation of

abundant transcripts

SNP WorkflowSNP Workflow

Library creation/QC GAII sequencing (single and paired end)

Data Collection

400

300

Analysis: transcriptome complexity SNP calling/validation

Assembly

Data Analysis of Illumina Data Analysis of Illumina cDNA Reads: PotatocDNA Reads: Potato

Sample Total Clusters Total ReadsPF Passed Clusters

% PF Passed Clusters

Total PF Reads

Actual Reads

Atlantic 1 7,601,277 15,202,554 6,382,748 83.97 12,765,496

Atlantic 2 10,544,542 21,089,084 9,252,168 87.74 18,504,336 30,185,186

Premier 1 7,812,394 15,624,788 6,652,121 85.15 13,304,242

Premier 2 11,678,379 23,356,758 9,999,926 85.63 19,999,852 31,949,096

Snowden 1 7,996,418 15,992,836 6,837,553 85.51 13,675,106

Snowden 2 11,781,671 23,563,342 10,393,322 88.22 20,786,644 33,288,120

De Novo Velvet Assemblies of Potato Illumina Sequences

Minimum contig length of 150bp:

Variety Total GbTranscriptome

Size (Mb)No.

Contigs N50 (bp)Maximum

Contig (Kb)

Atlantic 1.8  38.4 45215 1192 11.2

Premier  1.9 38.2 54917 826 6.6

Snowden  2.0 38.2 58754 775 6.9

• Atlantic:– 45214 contigs– 32520 align with GMAP(95%id, 50%cov)– 27106 align with GMAP(95%id, 90%cov)

• Premier:– 54917 contigs– 41497 align with GMAP (95%id, 50%cov)– 37297 align with GMAP (95%id, 90%cov)

• Snowden:– 58754 contigs– 44479 align with GMAP (95%id, 50%cov)– 40708 align with GMAP (95%id, 90%cov)

Alignment of S. tuberosum GAII-transcriptome contigs to the PGSC draft genome sequence from DM1-3 516 R44:

Velvet Assemblies of Potato Illumina Sequences

Query SNPs Filtered SNPs

Atlantic 224748 150669

Premier 265673 181800

Snowden 258872 166253

Identify intra-varietal SNPsIdentify intra-varietal SNPs

A/C SNP

Filtered SNP counts Filtered SNP counts

Filtering on SNP quality and 1 SNP/ 150bp window

Design SNPs for the Illumina Infinium PlatformDesign SNPs for the Illumina Infinium Platform

SNPs from:Final SNP 10K array content selected from 69,011 SNPs that pass the filtering and design criteria for the Infinium® platform using the following criteria:

-Read Depth: 20 reads min, 255 reads max-Biallelic based on all available sequence-Within exons (map to DM1-3 draft genome sequence); specifically, 50 bp from exon/intron junction-Max 1 SNP within 50 bp of candidate SNP-Preferred SNPs that were intervarietal

Candidate Genes For GenotypingCandidate Genes For Genotyping

-2009/10: a community call for genes to be placed on the potato and tomato platforms (assuming SNPs could be designed)

-Had strong response by the community; web page submissions, direct solicitations, email solicitations

~ 1800 sequences were identified by project personnel and the community for this targeted SNP discovery; note: represents redundant sequences

-In potato, > 700 candidate genes have a SNP that passes our filtering criteria

1065 candidates with no SNPs 160 candidates with 1 SNP 135 candidates with 2 SNPs 102 candidates with 3 SNPs 100 candidates with 4 SNPs 48 candidates with 5 SNPs 175 candidates with 6-10 SNPs 54 candidates with 11-31 SNPs

We want up to 5 SNPs per candidate gene.

SNPs found in candidate genesSNPs found in candidate genes

SNPs in some key candidate genesSNPs in some key candidate genes

Sucrose-phosphate-synthase 20

Soluble starch synthase 3, chloroplastic/amyloplastic 18

Acid invertase 16

Granule-bound starch synthase 2, chloroplastic/amyloplastic 10

Glucose-6-phosphate isomerase 10

Sucrose sythase 10

Isoamylase isoform 2 8

Sucrose transporter 8

Beta-amylase 6

Sucrose synthase 6

Granule-bound starch synthase 1 6

Phosphoglucomutase 6

Spacing and gene region coverageSpacing and gene region coverage

We expect approximately 25% of the SNPs will be mapped to candidate genes, 10% to SNPs from known genetic markers, and 65% to genes distributed across scaffolds, primarily those anchored to the DM1‐3 516R44 S. phureja draft genome.

2769 SNPs in candidate genes508 SNPs in genetic markers

6723 SNPs will come from throughout the genome

How much of the genome is represented? ~650 Mb of the genome will be covered (~850 Mb genome)

ValidationValidationHigh Resolution Melting• Tested: 48 primers• Validation (75%)• Problems with technical

replicates

GoldenGate Bead Express

96 x 480 samplesSelected 32 SNPs total per variety (96 total)

Validation rate ~85%

Illumina Output: GoodIllumina Output: Good

Premier Atlantic Snowden Rio Grande

BBBB 14 6 7 13

AAAA 17 5 6 21

hets 3 5 3BBBA 13 30 26

AABB 21 31 28AAAB 20 11 19

Total hets 57 77 76 59no data 6 6 6

nulliplex 31 11 13simplex 33 41 45duplex 21 31 28

SNP Validation: Dosage callsSNP Validation: Dosage calls

CrossDuplex x Duplex 10 10

Duplex x Nulliplex 2 4Duplex x Simplex 11 22

Nulliplex x Duplex 2Nulliplex x Nulliplex 28 28Nulliplex x Simplex 6 14

Simplex x Duplex 11Simplex x Nulliplex 8Simplex x Simplex 11 11

Simplex x Het 5 5Total 94

SNP segregation in 4x RussetSNP segregation in 4x Russet Mapping population (Premier x Rio Grande)Mapping population (Premier x Rio Grande)

Pair-wise Comparison of SNPsPair-wise Comparison of SNPs    Non-segregating Segregating SNPs (%)z

Cross Ploidy SNPs (%) I II

W2310-3 x Kalkaska 4X 22.4 37.6 40.0

MSG227-2 x Jacqueline Lee 4X 16.5 51.8 31.8

Atlantic x Superior 4X 5.9 51.8 42.4

Stirling x 12601ad1 4X 25.9 37.6 36.5

B1829-5 x Atlantic 4X 11.5 18.8 69.8

BER 63 x DM1-3 2X 79.3 20.7 0

BER 83 x DM1-3 2X 78.8 21.2 0

84SD22 x DM1-3 2X 46.0 54.0 0

MCR205 x DM1-3 2X 76.7 23.3 0

DI x DM1-3 2X 85 15 0

08675-21 x 09901-01 2X 53.8 46.2 0

RH x SH 2X 59 41 0

zI = segregation not dependent on scoring dosage; II = segregation dependent on scoring dosage

% Heterozygosity: 96 SNPs x 96 Potato lines% Heterozygosity: 96 SNPs x 96 Potato lines

Clone

Potato Panel SNP HeterozygosityPotato Panel SNP Heterozygosity

SNP Heterozygosity ExtremesSNP Heterozygosity ExtremesTetraploids Diploids

80-90% % Heterozygosity 50-60% % HeterozygosityAll Red 81.2 C5 52.9CF77154-1 83.5 84SD22 56.7CO95051-5W 84.7 MCD500036 69.4Snowden 84.7Atlantic 85.9 1-10% % HeterozygosityCO97215-2P/P 85.9 DM1-3 0

ber265857 5.9<50% % Heterozygosity CMM6-3 7.8

Chunshu No4 27.1 CMM 1T 8.2P1 28.2 CMM243503 8.2MSL512-6 44.7Inca Gold 47.1P2 48.2NDSU clone 4 48.2

Potato Germplasm PanelPotato Germplasm Panel

• Panel structure (350 clones)Panel structure (350 clones)– Top 50 N. American varieties

– Historical varieties

– Advanced US breeding lines

– Non-US germplasm

– Genetic stocks

• Population analysesPopulation analyses– Association mapping

– Historical relationship

– Hypothesis testing for trait

associations

– Parental selection

– Resolve population structure

• Phenotypic screening for Phenotypic screening for additional traits outside of additional traits outside of SolCAPSolCAP

• Phenotypic evaluation Phenotypic evaluation – Key traits: specific gravity,

sucrose, glucose, Vitamin C, maturity, tuber shape, tuber number, etc.

– Additional traits determined by breeding community

– Data curated at SGN

SNP comparison across potato germplasm SNP comparison across potato germplasm panel: resolving population structurepanel: resolving population structure

MSU Breeding Program varieties

Group Phureja clones clusters separately from elite germplasm

Wild species cluster separately from Phureja and Tuberosum

SNP Genotyping ConsortiumSNP Genotyping Consortium• Potato 10K (~9100 SNPs) Illumina Infinium chip• a core set of SNPs in standard germplasm panels in tomato and

potato. • Over 3000 genotyping samples were ordered• Consortium’s efforts resulted in securing a 24% discount per

sample beyond what would have been possible with one contributor ($85/sample)

• The barrier to entry for many institutions was lowered, as they were able to access this tool with only a 48 sample commitment. 

• Illumina saw orders from each of the

three major world regions.• More SNPs?

SolCAP SNP Genotyping SolCAP SNP Genotyping

• ~9100 SNPs for elite potato germplasm • 2010 SolCAP Goal:

1,152 potato x 9,100 SNPs• potato germplasm panel:350• 4x russet mapping population: 200• 2x mapping population: 160• Community SNP genotyping:

• 2 populations: 350

What makes up the Potato Germplasm Panel What makes up the Potato Germplasm Panel Phenotypic Evaluation?Phenotypic Evaluation?

• Clonal Study (CS)Clonal Study (CS)– 250 clones– 2 reps X 10 hills– OR, WI, NY

• Russet Mapping Population (MP)Russet Mapping Population (MP)– Rio Grande X Premier Russet– 200 progeny– 2 reps X 10 hills– ID, NC, MN

CS CS CSMP

MP

MP

States in blue = Participants in SolCAP

Potato Germplasm PanelPotato Germplasm Panel

• To be field tested 2 years X 3 major environments for To be field tested 2 years X 3 major environments for potato production. potato production.

• Evaluation of specific gravity, glucose and sucrose, chip Evaluation of specific gravity, glucose and sucrose, chip color, skin type, shape, vine maturity, tuber number, color, skin type, shape, vine maturity, tuber number, tuber shape, vitamin C, internal defects, bruising, tuber shape, vitamin C, internal defects, bruising, anthocyanins and biotic resistances. anthocyanins and biotic resistances.

Genotyping the core collections will Genotyping the core collections will impact strategies for translationimpact strategies for translation

• Potential translational approaches: Potential translational approaches: – 1) introgression from other populations (domesticated or wild) – 2) selection for coupling phase recombinants to establish

linkage blocks of favorable alleles (e.g. disease resistance loci)– 3) population development designed to maximize variation w/in

market classes– 4) association approaches– 5) whole genome approaches

• Other translational strategies will emerge under other Other translational strategies will emerge under other CAPs or through innovation in public research. CAPs or through innovation in public research.

Russet 4x Mapping PopulationRusset 4x Mapping Population

• Evaluate russet mapping population traits Evaluate russet mapping population traits (Yencho, Novy, Sowokinos, (Yencho, Novy, Sowokinos, Thill, Gupta, Haynes) (2009-2011)Thill, Gupta, Haynes) (2009-2011)

– Key traits: specific gravity, sucrose, glucose, Vitamin C, maturity, tuber shape, tuber number, etc.

• Genetic Mapping Genetic Mapping (Van Deynze, De Jong, Douches)(Van Deynze, De Jong, Douches)– Genotyping 9100 SNPs

• QTL Analysis QTL Analysis (Haynes)(Haynes)

– Identify markers associated with key traits

• MAS/MAB (Marker Assisted Selection / Breeding)MAS/MAB (Marker Assisted Selection / Breeding)– Validation of QTL in additional mapping populations– Use markers in new breeding populations

• Integrated, breeder-focused resources for genotypic and Integrated, breeder-focused resources for genotypic and phenotypic analysis at SGN and MSU. phenotypic analysis at SGN and MSU. – http://solcap.msu.eduhttp://solcap.msu.edu– http://solanaceae.plantbiology.msu.edu/http://solanaceae.plantbiology.msu.edu/– http://solgenomics.net/http://solgenomics.net/

Databases and ResourcesDatabases and Resources

SolCAP Education and Extension ObjectivesSolCAP Education and Extension Objectives

• Team-taught distance-learning graduate level course in translational genomics at Cornell University

• Yearly workshops for breeders to integrate genotype-based breeding strategies with elite germplasm

• Use eXtension.org to develop a Community of Practice for plant breeders, called Plant Breeding and Genomics, across all CAPs (Barley, Wheat, Conifer, RosBreed, Bean, Onion)

SolCAP PAA WorkshopSolCAP PAA Workshop

• August 15, 2010 Corvallis, Oregon

• Hands-on computer lab format

• Topics– Potato genome analysis: Robin Buell– Tetraploid QTL analysis: Christine Hackett– Use of Illumina Genome studio: Allen Van

Deynze

PB&GWorks Web communityPB&GWorks Web community

Target audience: The practicing plant breeder. 

Our long-term goal is to provide:

• Start-to-finish examples of marker-assisted selection applications

• Resource pages including protocols, software tutorials, and up-to-date contact information for companies offering genetic services

• Improved access to genetic resources through the "breeder's toolbox" 

http://pbgworks.hort.oregonstate.edu/http://pbgworks.hort.oregonstate.edu/

SolCAP has created PBGworks, a web community within the eXtension.org

Plant breeders, basic scientists, seed industry professionals, agricultural professionals, extension specialists and others can publish content and network.

Potato SNP Summary

•In silico Sanger eSNPs: potato: 57,705 eSNPs••~75,000 potato SNPs from 5.7 Gb of GAII transcriptome sequence (69,011 SNPs passed Infinium design)

•~650 Mb of the genome will be covered by SNPs

•Validation suggests SNPs can be called in broader germplasm

•Dosage reads of SNPs will optimize SNP genotyping of 4x mapping populations

•Reference Sequence of DM1-3 516R44 is permitting bioinformatic optimization of pipelines rather than relying on empirical validation.

Germplasm Panel SNP GenotypingGermplasm Panel SNP Genotyping

• SSR-based genetic map SSR-based genetic map – 2 years2 years– 200 markers200 markers

• 17 markers/chromosome17 markers/chromosome

– $5/ data point$5/ data point– Not dense enough for 4x Not dense enough for 4x

mappingmapping– Markers Markers maymay be linked to be linked to

traitstraits

• SNP-based genetic map SNP-based genetic map – < 1 week< 1 week– 9,100 markers9,100 markers

• >700 markers/chromosome>700 markers/chromosome

– < 2 < 2 ¢ ¢ / data point/ data point– Dense enough for 4x Dense enough for 4x

mappingmapping– Markers Markers areare in genes in genes– Markers robust enough Markers robust enough

for broader germplasmfor broader germplasm

Outcomes for Breeding from SolCAPOutcomes for Breeding from SolCAP

• A genome-wide set of markers and A genome-wide set of markers and bioinformatic tools accessible by bioinformatic tools accessible by breedersbreeders

– Breeders will access germplasm for crossing based upon SNP polymorphism and linked QTL of interest

– design crosses complementary for QTL and traits, and then use MAB in early generation selection.

• Better understanding of the allelic Better understanding of the allelic variation influencing CHOsvariation influencing CHOs

– Design crosses to create improved sugar and starch levels and starch quality.

– Crosses designed to manipulate and select variation within existing elite populations or introgress novel alleles from wild germplasm.

– More predictable and directed

breeding effort for processing and fresh market traits.

Outcomes for Breeding from SolCAPOutcomes for Breeding from SolCAP

Collaborators, OSUDavid FrancisMatt Robbins

Sung-Chur SimTroy Aldrich

Others:Michael Coe

Sanwen Huang

FundingUSDA/AFRIThis project is supported by the Agriculture and Food Research Initiative Applied Plant Genomics CAP Program of USDA’s National Institute of Food and Agriculture.

Collaborators, MSUDavid DouchesC Robin BuellJohn Hamilton

Kelly Zarka

Collaborators, CornellWalter De JongLucas MuellerJoyce van Eck

Collaborators, UCDAllen Van Deynze

Kevin StoffelAlex Kozic

Jeanette Martins

SolCAP AcknowledgmentsSolCAP Acknowledgments

Collaborators, Oregon State

Alex StoneJohn McQueen

Roger Leigh

Acknowledgments: PGSCAcknowledgments: PGSCBGI-Shenzhen, China (Sanwen Huang, Ruiqiang Li, Xun Xu, Wei Fan, Peixiang Ni, Hongmei Zhu, Desheng Mu, Bicheng Yang, Jian Wang and Jun Wang); Center Bioengineering RAS, Russia (Boris Kuznetsov); Central Potato Research Institute, India (Swarup Chakrabarti, V.U. Patil, Shashi Rawat and S.K. Pandey); Chinese Academy of Agricultural Sciences, China (Sanwen Huang, Zhonghua Zhang and Dongyu Qu); University of Dundee, United Kingdom (Dan Bolser and David Martin); ENEA, Italian National Agency for New Technologies, Energy and the Environment, Italy (Giovanni Giuliano and Gaetano Perrotta); Imperial College London, United Kingdom (Gerard Bishop); International Potato Center (CIP), Peru (Merideth Bonierbale, Marc Ghislain and Reinhard Simon); Institute of Biochemistry and Biophysics (PAS), Poland (Wlodzimierz Zagorski, Jacek Hennig, Pawel Szczesny, Piotr Zielenkiewicz and Robert Gromadka); Instituto Nacional de TecnologÌa Agropecuaria (INTA), Argentina (Gabriela Massa, Leandro Barreiro and Sergio Feingold); Instituto de Investigaciones Agropecuarias (INIA), Chile (Boris Sagredo, Alex Di Genova and Nilo MejÌa); Michigan State University, USA (Robin Buell, David Douches, Steven Lundback, Alicia Massa, and Brett Whitty); New Zealand Institute for Plant & Food Research, New Zealand (Jeanne Jacobs, Mark Fiers and Susan Thomson); Scottish Crop Research Institute, United Kingdom (Glenn Bryan, David Marshall, Robbie Waugh and Sanjeev Kumar Sharma); Teagasc Agriculture and Food Development Authority, Ireland (Dan Milbourne, Istvan Nagy and Marialaura Destefanis); Universidad Peruana Cayetano Heredia, Peru (Gisella Orjeda, Frank Guzman, Michael Torres, Tomas Miranda, German de la Cruz, Roberto Lozano and Olga Ponce); University of Wisconsin, USA (Jiming Jiang and Marina Iovene); Virginia Polytechnic Institute & State University, USA (Richard E. Veilleux); Wageningen University, The Netherlands (Bas te Lintel Hekkert, Christian Bachem, Erwin Datema, Jan de Boer, Richard Visser, Roeland van Ham, Theo Borm and Xiaomin Tang)

Funding at MSU for potato genomics: National Science Foundation

Visit us at http://solcap.msu.edu/

EXTRAS

Single-nucleotide polymorphism(SNP, pronounced snip)

SNP is a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome differs between members of a species

SNPs may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions between genes.

SNPs within a coding sequence may or may not change the amino acid sequence of the protein that is produced.

What is a SNP?What is a SNP?

Hawkeye Viewer – Visualizing SNPs

G/T SNP