Allele Survey - North American Oats Nick Tinker et al. Agriculture and Agri-Food Canada.

Slides:

Advertisements

Similar presentations

Frary et al. Advanced Backcross QTL analysis of a Lycopersicon esculentum x L. pennellii cross and identification of possible orthologs in the Solanaceae.

Advertisements

Increasing grain yield and improving BYDV tolerance in oat: Past, Present and Future Frederic L. Kolb 1 and Jean-Luc Jannink 2 1 Dep. of Crop Sci., Univ.

ASSOCIATION MAPPING WITH TASSEL Presenter: VG SHOBHANA PhD Student CPMB.

Centre for Genetic Resources, the Netherlands Traditional breeding: limitations Bert Visser Copenhagen, 13 december 2005.

Fingerprinting and Markers for Floral Crop Improvement James W. Moyer Dept. of Plant Pathology North Carolina State University, Raleigh, NC

Molecular Marker Development and Utilization at Ottawa - Within AAFC Integrated Oat Improvement Project Presented by Steve Molnar VIII International Oat.

Molecular Mapping of Seed Tocopherols in Soybean HEINRICH S. WOHLESER 1, YUKIO KAKUDA 2, and ISTVAN RAJCAN 3 1 University of Guelph, Department of Plant.

Genetic Basis of Agronomic Traits Connecting Phenotype to Genotype Yu and Buckler (2006); Zhu et al. (2008) Traditional F2 QTL MappingAssociation Mapping.

Dr. Graham Scoles Dr. Brian Rossnagel Crop Molecular Genetics Lab Department of Plant Sciences Barley and Oat Breeding Program Crop Development Centre.

Chapter 7: Molecular markers in breeding

DNA polymorphisms Insertion-deletion length polymorphism – INDEL Single nucleotide polymorphism – SNP Simple sequence repeat length polymorphism – mini-

Trends in Conservation and Utilization of Oat Genetic Resources

1.Generate mutants by mutagenesis of seeds Use a genetic background with lots of known polymorphisms compared to other genotypes. Availability of polymorphic.

PCR-Based Markers for Oil,  -glucan, and Protein Content Steve Molnar, Winson Orr, Julie Chapados, Anissa Lybaert, Ismahane Elouafi, Shan He, Charlene.

Piyaporn Phansak 1, Watcharin Soonsuwan 1, James E. Specht 1, George L. Graef 1, Perry B. Cregan 2, and David L. Hyten 2 1 Department of Agronomy and Horticulture,

Getting Biodiesel From Jathropa The jatropha seeds, commonly known as the physic nuts, contain up to 40% oil. The jatropha oil can be used directly as.

PLANT DEVELOPMENTAL MUTANTS AS MODELS FOR CROP SYSTEMS BIOLOGY STUDIES FACCIOLI P., BALDASSARRE V., PAGANI D., STANCA A.M., TERZI V. CRA-CPG Genomic Research.

PLANT BIOTECHNOLOGY & GENETIC ENGINEERING (3 CREDIT HOURS)

How Much Do You Remember???. Character A heritable feature.

A multi-state, multi-institution project, funded by USDA/CSREES dedicated to the genetic improvement of US wheat through research, education and extension.

Genetic Diversity of the Phaseolus acutifolius A. Gray Collection of the USDA National Plant Germplasm System Using Targeted Region Amplified Polymorphism.

Identification of molecular markers for aluminium tolerance in diploid oat through comparative mapping and QTL analysis 1 Eastern Cereal and Oilseed Research.

Dorrie Main, Jing Yu, Sook Jung, Chun-Huai Cheng, Stephen Ficklin, Ping Zheng, Taein Lee, Richard Percy and Don Jones.

GENETIC FINGERPRINT ESTABLISHED FOR THE SELECTED ALFALFA GENOTYPES USING MOLECULAR MARKERS.

Creating a Kinship Matrix using Microsatellite Analyzer (MSA) Zhifen Zhang The Ohio State University.

Module 7: Estimating Genetic Variances – Why estimate genetic variances? – Single factor mating designs PBG 650 Advanced Plant Breeding.

Using mutants to clone genes Objectives 1. What is positional cloning? 2.What is insertional tagging? 3.How can one confirm that the gene cloned is the.

Natural Variation in Arabidopsis ecotypes. Using natural variation to understand diversity Correlation of phenotype with environment (selective pressure?)

Howard Hughes Medical Institute-NMSU Research Scholar

POOL Database and Information Service July 27, 2006 Jitka Deyl Agriculture and Agri-Food Canada Agriculture et Agroalimentaire Canada.

Oat Molecular Toolbox: Toward Better Oats Nick Tinker, 2014-March-5 Agriculture and Agri-Food Canada.

Abstract Maize, (Zea mays L. ssp., corn) Abnormal Chromosome ten (Ab10) is an uncommon variant of chromosome 10. Ab10 causes a segregation abnormality.

APPLICATION OF MOLECULAR MARKERS FOR CHARACTERIZATION OF LATVIAN CROP PLANTS Nils Rostoks University of Latvia Vienošanās Nr. 2009/0218/1DP/ /09/APIA/VIAA/099.

Molecular identification of living things. Molecular Markers Single locus marker Multi-locus marker RFLP Microsatellite DNA Fingerprinting AFLP RAPD.

Jing Yu 1, Sook Jung 1, Chun-Huai Cheng 1, Stephen Ficklin 1, Taein Lee 1, Ping Zheng 1, Don Jones 2, Richard Percy 3, Dorrie Main 1 1. Washington State.

1 Gene Therapy Gene therapy: the attempt to cure an underlying genetic problem by insertion of a correct copy of a gene. –Tantalizingly simple and profound.

American Oat Workers Conference, Fargo 2006 Towards a Global Strategy for the Conservation of Oat Genetic Resources Federal Centre of Breeding Research.

Announcements: Proposal resubmission deadline 4/23 (Thursday).

Agriculture and Agri-Food Canada Agriculture et Agroalimentaire Canada 2006 Molecular Mapping of the Dw6 Dwarfing Locus in Oats Abstract In crosses involving.

1 International Consultation on Pro-poor Jatropha Development, Rome, Apr 08HY Genetic Markers for Jatropha Biodiversity Evaluation and Breeding Introduction.

Genotyping and association analysis of Gossypium hirsutum lines for resistance in Reniform Nematodes Megha V. Sharma*, Stella Kantartzi, David Weaver,

Pea plants have several advantages for genetics.

Oat Molecular Markers: Status and Opportunities Howard W. Rines USDA-ARS and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul,

Experimental Design and Data Structure Supplement to Lecture 8 Fall

Quantitative Genetics. Continuous phenotypic variation within populations- not discrete characters Phenotypic variation due to both genetic and environmental.

Complex Traits Most neurobehavioral traits are complex Multifactorial

Quantitative Genetics

North Carolina State University Oat Maker Development Peter Maloney Jeanette Lyerly Paul Murphy Gina Brown-Guedira USDA-ARS Crop Science Department 840.

INTRODUCTION TO ASSOCIATION MAPPING

UNIT 9: INHERITANCE PATTERNS

Pure Lining Breeder Seed for Molecular Variety ID in Oat AOWC, July 23, 2006, Fargo Brian Rossnagel, Peter Eckstein, Tom Zatorski & Graham Scoles Crop.

1 DNA Polymorphisms: DNA markers a useful tool in biotechnology Any section of DNA that varies among individuals in a population, “many forms”. Examples.

Mapping and cloning Human Genes. Finding a gene based on phenotype ’s of DNA markers mapped onto each chromosome – high density linkage map. 2.

Gramene V. 211 Gramene Diversity Gramene Genetic Diversity database contains SSR and SNP allelic data and passport descriptions for rice, maize and wheat.

Use of breeding populations to detect and use QTL Jean-Luc Jannink Iowa State University 2006 American Oat Workers Conference Fargo, ND24 July 2006.

Simple-Sequence Length Polymorphisms SSLPs Short tandemly repeated DNA sequences that are present in variable copy numbers at a given locus. Scattered.

Marker Assisted Selection in Soybean Brian Diers University of Illinois.

Advances in Breeding for Winter Hardiness in Oats P. V. Maloney 1, J. H. Lyerly 1, D. R. Wooten 1, J. M. Anderson 3, D. P. Livingston III 2, G. Brown-Guedira.

Oat Molecular Toolbox: Toward Better Oats Nick Tinker, 2014-March-5 Agriculture and Agri-Food Canada.

Simple-Sequence Length Polymorphisms

T3/Tutorials: Data Submission

Molecular Marker Characterization of plant genotypes

Comparative mapping of the Oregon Wolfe Barley using doubled haploid lines derived from female and male gametes L. Cistue, A. Cuesta-Marcos, S. Chao, B.

Genotyping module.

Introduction to bioinformatics lecture 11 SNP by Ms.Shumaila Azam

DNA Polymorphisms: DNA markers a useful tool in biotechnology

Loss of Heterozygosity and Microsatellite Instability at theMLL Locus Are Common in Childhood Acute Leukemia, but not in Infant Acute Leukemia by Julie.

Barley (Hordeum vulgare subsp. vulgare)

Presentation transcript:

Allele Survey - North American Oats Nick Tinker et al. Agriculture and Agri-Food Canada

Markers are boring.

Germplasm is exciting!  Germplasm is defined by alleles  Markers are our best window into the alleles that define germplasm. – through linkage analysis – through surveys and diversity analysis – Through association analysis  We still need more markers in oat  And we need information about them

SOAP  “Standard Oat Allele Panel” –(for North America)  Selected by collaborators following AOWC meeting in Wilmington 2002  Stay tuned for Global Oat Allele Panel and new DArT markers

Why ?  Common point of reference for marker screening  Share biological materials (seed, DNA)  Collect orthogonal data  Share common and relevant data

How ?  10 breeders / adaptation regions  Nominate “current germplasm representing packages of alleles giving adaptation to your region and/or unique quality”  Used (or will be used) extensively in crossing  3 to 5 representative genotypes per region  Narrowed down by avoiding co-ancestry  Re-increased from single seed of representative breeders line(s)

Lines 1-18 (note duplicates)

Lines

Why Common markers?  So we don’t all report results using different markers if common markers are available.  Share technology, materials, experience  Collect orthogonal data  Share common and relevant data  Select optimum markers for further work  Use for predicting MAS feasibility –(is a marker polymorphic in your material?)  Potential use in association analysis

Orthogonal is Nice Markers Germplasm M1M2M3M4M5M6P1P2P3P4P5 VAAABBAB VBBAABBA VCCDEFGA VDABAABA VEAAADFG VFBADCAT VGTARBAB Phenotypes

….This is Not Markers Germplasm M1M2M3M4M5M6P1P2P3P4P5 VA???BAB24??2723 VB???BBA VC???F??????? VDABA?BA43? VEAA??FG4343??? VFBA??AT7663??? VGTA??AB4675??? Phenotypes

Marker screened in SOAP  SCARs (Molnar and Orr) – 50  Other misc. (Wight) - 5  New SSR markers (Wight) – 12  Jannink - SSRs, SCARs – 12  Approx 80 Primer pairs = 200 polymorphic bands = 100 loci ?  To do: –other SSRs, AFLP? RFLP? DArT

How to record the data ?  Some markers defined and mapped  Others new, un-mapped  Anticipate need to share screening results and screening methods...  Future need for others to contribute directly to online database?

Welcome to GELATO! (Diane Bergeron et al. poster)

GELATO  Demo: avena.agr.gc.ca/gelato  Freestyle web based marker scoring  Record what you see (“Virtual Lite-Brite”)  Clickable grid – any cell can be a “band” –Black (present), white (absent), pink (unknown)  Optional: Paint bands from same locus  Stored in a relational database  Query data in the same format  Generate “virtual gels”

Simple SCAR marker

Complex, multi-locus (avenin)

Microsatellite

The following is more of an inventory than an analysis...  Extract data from Gelato  Each band as a character  200 polymorphic bands  (Locus-based extraction in progress)  Make numerical data set 1=absent, 2=faint, 3=present

41 entries 250 “bands” Present Faint Absent

Cluster analysis (markers and varieties) – Average linkage – Pearson-r

Zoom on varieties Note: Paired lines = alternate seed sources Most lines un-related Some known relationship: Medallion Ronald Jay Sesqui ? Kanota = oddball

Cluster – zoom on markers

Add phenotypic data First year of replicated tests Ottawa (Yan) Saskatoon (Rossnagel)

Data Unification and Distillation Engine

Information systems for crop performance data Information systems for crop performance data N. A. Tinker and W. Yan 647–662 Biplot analysis of multi-environment trial data: Principles and applications Principles and applications W. Yan and N. A. Tinker 623–645 Can J. Plant Sci. 86 (July 2006)

Conclusions  SOAP Seed and DNA available NOW  SOAP survey will be published and shared  Planned repository –GELATO + GrainGenes ?  Also coming (and related): –GELATO –DUDE –OatGenes –SCAR markers (Molnar) –DArT markers and extended global panel

Thanks ! Doers:  Charlene Wight  Jitka Deyl  Shan He  Diane Bergeron  Hai Pham  Klaus Jakubinek  Winson Orr  Julie Chapados Dreamers  Steve Molnar (AAFC)  Weikai Yan (AAFC)  Art McElroy  Judith Fregeau-Reid  Brian Rossnagel SOAP panel Development:  Deon Stuthman, Howard Rines, Steve Harrison, Ron Barnett, Jennifer Mitchell-Fetch, Herb Ohm, Mike McMullen, Fred Kolb, Heidi Kaepler, and many others who provided seed….