PT Sampoerna Agro Tbk Sampoerna Strategic Square North Tower, 28th Floor Jl. Jend. Sudirman Kav. 45 Jakarta, Indonesia,12930 Development of Marker Assisted.

Slides:



Advertisements
Similar presentations
Linkage and Genetic Mapping
Advertisements

Planning breeding programs for impact
Fall 2014 HORT6033 Molecular Plant Breeding INSTRUCTOR: AINONG SHI HORT6033 web site:
Potato Mapping / QTLs Amir Moarefi VCR
Frary et al. Advanced Backcross QTL analysis of a Lycopersicon esculentum x L. pennellii cross and identification of possible orthologs in the Solanaceae.
Association Mapping as a Breeding Strategy
An Introduction to the application of Molecular Markers
Qualitative and Quantitative traits
SNP Applications statwww.epfl.ch/davison/teaching/Microarrays/snp.ppt.
ASSOCIATION MAPPING WITH TASSEL Presenter: VG SHOBHANA PhD Student CPMB.
Genomic Tools for Oat Improvement
Pepper Mapping & Major Genes Mapping of chlorophyll retainer (cl) mutation in pepper The Pun1 gene for pungency QTL mapping for fruit size and shape.
Genome Structure/Mapping Lisa Malm 05/April/2006 VCR 221 Lisa Malm 05/April/2006 VCR 221.
Genetic Basis of Agronomic Traits Connecting Phenotype to Genotype Yu and Buckler (2006); Zhu et al. (2008) Traditional F2 QTL MappingAssociation Mapping.
Discovery of a rare arboreal forest-dwelling flying reptile (Pterosauria, Pterodactyloidea) from China Wang et al. PNAS Feb. 11, 2008.
Bob Weaber, Ph.D. Cow-Calf Extension Specialist Assistant Professor Dept. of Animal Sciences and Industry
QTL Mapping R. M. Sundaram.
Chapter 7: Molecular markers in breeding
Dr. Almut Nebel Dept. of Human Genetics University of the Witwatersrand Johannesburg South Africa Significance of SNPs for human disease.
Biology and Bioinformatics Gabor T. Marth Department of Biology, Boston College BI820 – Seminar in Quantitative and Computational Problems.
The role of parallel genetic changes in domestication: Fruit size in the plant family Solanaceae Matt Robinson.
Mining SNPs from EST Databases Picoult-Newberg et al. (1999)
Positional Cloning LOD Sib pairs Chromosome Region Association Study Genetics Genomics Physical Mapping/ Sequencing Candidate Gene Selection/ Polymorphism.
Human Migrations Saeed Hassanpour Spring Introduction Population Genetics Co-evolution of genes with language and cultural. Human evolution: genetics,
PLANT BIOTECHNOLOGY & GENETIC ENGINEERING (3 CREDIT HOURS)
A multi-state, multi-institution project, funded by USDA/CSREES dedicated to the genetic improvement of US wheat through research, education and extension.
Quantitative Genetics
Review Session Monday, November 8 Shantz 242 E (the usual place) 5:00-7:00 PM I’ll answer questions on my material, then Chad will answer questions on.
GENOMIC MAPPING FOR DROUGHT TOLERANCE IN SORGHUM Introduction Drought is a major abiotic factor limiting crop production. Sorghum is one of the most drought.
Geuvadis RNAseq analysis at UNIGE Analysis plans
Module 7: Estimating Genetic Variances – Why estimate genetic variances? – Single factor mating designs PBG 650 Advanced Plant Breeding.
Methods of Genome Mapping linkage maps, physical maps, QTL analysis The focus of the course should be on analytical (bioinformatic) tools for genome mapping,
Outline of Barley CAP Approach Breeding lines from 10 breeding programs are phenotyped (over 40 traits) in collaborative trials and individual breeder.
SNP Haplotypes as Diagnostic Markers Shrish Tiwari CCMB, Hyderabad.
© 2010 by The Samuel Roberts Noble Foundation, Inc. 1 The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA 2 National Center.
Fig. S1 The non-metric multi-dimensional scaling of 24 double haploid (DH) lines (colored in grey) in the background of 225 DH lines (colored in blue)
Pea plants have several advantages for genetics.
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.
Quantitative Genetics
North Carolina State University Oat Maker Development Peter Maloney Jeanette Lyerly Paul Murphy Gina Brown-Guedira USDA-ARS Crop Science Department 840.
Finnish Genome Center Monday, 16 November Genotyping & Haplotyping.
Gramene: Interactions with NSF Project on Molecular and Functional Diversity in the Maize Genome Maize PIs (Doebley, Buckler, Fulton, Gaut, Goodman, Holland,
INTRODUCTION TO ASSOCIATION MAPPING
QTL Associated with Maize Kernel Traits among Illinois High Oil × B73 Backcross-Derived Lines By J.J. Wassom, J.C. Wong, and T.R. Rocheford University.
Data Management for Integrated Breeding
Marker Assisted Selection in Tomato Pathway approach for candidate gene identification and introduction to metabolic pathway databases. Identification.
The International Consortium. The International HapMap Project.
Software and Databases for managing and selecting molecular markers General introduction Pathway approach for candidate gene identification and introduction.
Use of breeding populations to detect and use QTL Jean-Luc Jannink Iowa State University 2006 American Oat Workers Conference Fargo, ND24 July 2006.
Fast test for multiple locus mapping By Yi Wen Nisha Rajagopal.
Lecture 22: Quantitative Traits II
Association Mapping in European Winter Wheat
Genetic mapping and QTL analysis - JoinMap and QTLNetwork -
Comparative mapping of Brassica oleracea using sequence-based markers derived from other Brassica relatives and transcriptome sequences generated from.
Moukoumbi, Y. D1. , R. Yunus2, N. Yao3, M. Gedil1, L. Omoigui1 and O
Plant Breeding Approach
The is a Critical Resource for Developing and Refining Trait-Predictive DNA Tests Cameron Peace, Daniel Edge-Garza, Terry Rowland, Paul Sandefur.
Association between SSR markers and
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.
Genome Wide Association Studies using SNP
Introduction to bioinformatics lecture 11 SNP by Ms.Shumaila Azam
Genome-wide Association Studies
General Animal Biology
Department of Crop and Soil Science
AGEseq: Analysis of Genome Editing by Sequencing
Linkage analysis and genetic mapping
General Animal Biology
Evan G. Williams, Johan Auwerx  Cell 
LECTURE 5: Microevolution Part 3 Mendelian Genetics
Presentation transcript:

PT Sampoerna Agro Tbk Sampoerna Strategic Square North Tower, 28th Floor Jl. Jend. Sudirman Kav. 45 Jakarta, Indonesia,12930 Development of Marker Assisted Selection through association mapping in Oil Palm Javier Herrero, PhD

Background  THE FACT: Nowadays African oil palm (Elaeis guineensis Jacq.) is the major source of vegetable oil. The application of genomic knowledge and tools in oil palm breeding is highly suitable due to the crop’s long generation cycle and large space requirement for field testing.  OBJECTIVE: As part of Sampoerna Agro breeding program improvement. AIMS to improve and accelerate its oil palm breeding process Molecular breeding laboratory (Palembang) Biotechnology Department (Vitoria, Spain) Research collaboration

Background  THE CHOICE: CANDIDATE-GENE ASSOCIATION MAPPING DEFINITION: “Association mapping is a statistical method to analyze the effects of existing alleles of candidate genes based on linkage disequilibrium (LD) and allows the discovery of strong associations between specific allele marker-trait expression in a set of genotypes, instead of in a designed mapping population” (Breseghello and Sorrells 2005; Ingvarsson 2005; Zhu et al., 2008). It involves finding marker-trait associations

Phenotypic data Interesting traits Candidate genes (CG) ASSOCIATION Phenotyping PLANT MATERIAL: Derived from Dura x Pisifera selected parents. Samples are selected based on 8 interesting traits. Extensively characterized (10 years). Every trait consists of average taken from 17 progenies with 2 GT which are segregated as best and worst performance. Set of 250 Genotypes (GT)

Genotypic data Interesting traits Candidate genes (CG) PhenotypingGenotyping Identification of trait-specific CG: Two contrasting bulks PER trait 1 1 BSA-cDNA-AFLP Quantitative trait loci VS Annotated sequences mEgCIR0059 linked to a QTL for MF in Lg 16 with high homology to a Transcription factor (Auxin Response factor) 2 2 Co-location analysis 3 3 Known genes DATABASES PUBLICATIONS With relevant biological meaning and related to the trait ASSOCIATION Set of 250 Genotypes (GT) Direct homology search

Genotypic data Interesting traits Candidate genes (CG) PhenotypingGenotyping Identification of trait-specific CG: ASSOCIATION Set of 250 Genotypes (GT) Total = 188 potential candidate genes BSA-cDNA-AFLPCo-location analysisKnown genes *Example CG database

Genotyping Interesting traits Candidate genes (CG) Phenotyping Genotyping Identification of CG (3 aproaches): 1.BSA-cDNA-AFLP. 2.Co-location analysis. 3.Known genes. ASSOCIATION Amplicon sequencing in Set of GTs (ION Torrent) Set of 250 Genotypes (GT) filter and separate output amplicon sequencing Identification of CG’s allele patterns in the GTs ASSOCIATION MAPPING Statistical analysis ASPAM software Pool of PCR products

…… Amplicon processing 1. Identification of allelic diversity for each CG. 2. Assignation of allele composition to each GT bp 187 bp Via Clustal: 2 SNPs. Pattern 1: 99 GTs Pattern 2: 60 GTs Sequence SELECTION PATTERN – GT association Short sequences and sequencing errors are discarded. Example: One batch consisted of 52 candidate genes in 250 bar-coded genotypes sent for sequencing using the ION Torrent system. It separates per CG and GT via several steps of local BLAST CG GT *OUTPUT = 5 million sequences. *Desired output product. *Example of CG sequence analysis. Alignment file of repeated patterns.

Association Pat S1 S2 S3 S4 Code Cultivar $ BN BW CPO HT FN FW MF OWM / / / / / …………… *Example for a particular CG “Pattern Code Trait File”. ASPAM generates SAS files for Pattern and SNP analyses. Association Mapping STSTISTICAL ANALYSES mixed-model approach Stich et al. (2008) Pattern/SNPs GT/CODETrait/Phenotype 1. Identification of significant associations. 2. Effects of specific allel combination on traits (So far, 89 CG analyzed). 3 3 PATTERN – GT – TRAIT association

Results Table b): Pattern analysis.Table a): Example for Results of SNP analysis. b): CG INFLUENCES traits BN, CPO and OWM with indicates significances (0,0063, 0,0024 and 0,0058, respectively) with 5 patterns. For CPO Allele 1 (present in 55 GTs) yields the highest value with 4,5 (Ton/he), which is significantly better than that of pattern 2. a): SNP 1 of a specific CG has a significant effect on BW and HT. Level 2 of S1 (present in 11 GTs) leads to a significant higher bunch weight and Height increment than Level Significant effects for 12 CG alleles on trait expression for 7 different characters were identified. (So far, 89 potential CGs analyzed OUT OF 188). 127 Significant effects for 12 CG alleles on trait expression for 7 different characters were identified. (So far, 89 potential CGs analyzed OUT OF 188).

SUMMARY Interesting traits Candidate genes (CG) Phenotyping Genotyping Identification of CG (3 aproaches): 1.BSA-cDNA-AFLP. 2.Co-location analysis. 3.Known genes. Alleles of CG / Allele composition of GT Effects of specific allel combination on traits ASSOCIATION Amplicon sequencing in Set of GTs (ION Torrent) Set of 250 Genotypes (GT) Data Analysis (Association Mapping) Data Analysis (Association Mapping) Phenotypic values of 8 interesting oil palm traits: BN, BW, FN, FW, HI, MF, OWM & CPO

What’s next? Interesting traits Candidate genes (CG) Phenotyping Genotyping ASSOCIATION Association Mapping MORE TRAITs!! Sh gene Virescens Drought Tolerance Fertilizer efficiency MORE TRAITs!! Sh gene Virescens Drought Tolerance Fertilizer efficiency MORE CGs!! Involved in the desired trait performance MORE CGs!! Involved in the desired trait performance Obtained CGs WITH SIGNIFICANT EFFECTS Design of allel-specific primers GENOTYPING & VALIDATION (in independent set of Genotypes) Selection of parents with useful alleles GERMOPLASM Increment (New varieties) GERMOPLASM Increment (New varieties) MAS Model Building (New crosses) MAS Model Building (New crosses) Plant material selection:

Thanks for your attention Terima kasih