Kuliah Internasional dan symposium

Genomics using domestic animals as genetic models

Sebagai tindak lanjut dari Kuliah Internasional untuk mahasiswa pasca sarjana yang telah diselenggarakan pada tahun lalu, Fakultas peternakan IPB bekerja sama dengan Swedish Agriculture University dan Linkoping University,  Swedia akan mengadakan  Genomics using domestic animals as genetic models Informasi tentang perkuliahan ini adalah sebagai berikut:

Pengajar :

1. Professor Göran Andersson, Ph.D

Dept. Animal Breeding and Genetics
Swedish University of Agricultural Sciences (SLU)
P.O. Box 597, S-75124 Uppsala, Sweden

2. Prof. Dominic Wright

Dept. Animal Breeding and Genetics

Linkoping University, Swedia

3. Mia Ollson,

Dept. Animal Breeding and Genetics
Swedish University of Agricultural Sciences (SLU)
P.O. Box 597, S-75124 Uppsala, Sweden

4. Maria Wilbe,

 Dept. Animal Breeding and Genetics
Swedish University of Agricultural Sciences (SLU)
P.O. Box 597, S-75124 Uppsala, Sweden

Tempat :

Departemen Ilmu Teknologi Peternakan, Fakultas Peternakan IPB, Kampus IPB Darmaga, Bogor

Waktu :

Mulai 7- 17 Maret 2011 (perkuliahan 7-10 Maret; 14-16 Maret, di luar waktu ini diperuntukkan untuk tugas mandiri), pada tanggal 17 Maret akan diadakan symposium

Materi Pekuliahan :

1. Genetika kuantitatif
2. Genetika molekuler
3. Teknologi reproduksi

Diharapkan setelah mengikuti perkuliahan ini mahasiswa dapat memahami tentang seluk beluk animal genomics dan mengidentifikasi gen gen yang berperan dalam ekspressi sifat sifat produksi dan reproduksi yang komplek

 Sistem Pekuliahan :

1. Kuliah (presentasi materi)
2. Latihan dan pendalaman materi dengan menggunakan komputer 
3. Diskusi kelompok
4. Penyusunan topik penelitian
5. Presentasi topik penelitian

Peserta Perkuliahan :

Mahasiswa pascasarjana IPB (S2 dan S3) diutamakan major Teknologi produksi ternak, nutrisi, biologi, bioteknologi dan reproduksiserta major lain yang bidangnya berhubungan dengan topik perkuliahan.

Persyaratan : 

1. Mendaftarkan diri ke Sekretariat Program pascasarjana Ilmu Ternak, Fakultas Peternakan IPB atau mengirim email ke Prof. Dr. Ir. Ronny Rachman Noor MRur.Sc ( ronny_noor@yahoo.com Alamat e-mail ini diproteksi dari spabot, silahkan aktifkan Javascript untuk melihatnya  ) dengan  menyertakan CV paling lambat hari Selasa  tanggal  1 Maret  pukul 14.00 wib.  catatan : pengumuman peserta terseleksi akan dilakukan pada hari Kamis , tanggal 3 Maret 2011 melalui website LPPM IPB
2. Mengikuti materi perkuliahan secara penuh dan membawa laptop yang memiliki fasilitas koneksi ke internet.

Biaya Perkuliahan :

Free

Bahasa Pengatar :

Inggris

Mengingat  keterbatasan tempat (hanya untuk 25 mahasiwa) dimohon agar mahasiswa dapat segera mendaftarkan diri dengan menyertakan CV.  Calon Peserta akan diseleksi berdasarkan CV calon peserta.  Kami akan menutup pendaftaran apabila jumlah peserta telah memenuhi quota.

Format CV

Curriculum Vitae Calon Peserta Kuliah internasional Animal Genomic

Name                                                               :

Place and Date of Birth                                       :

Gender                                                             : Male/Female

Working Unit                                                    :

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email *)                                                           :

Program                                                           : Master / PhD

Major                                                                :

Research Topic                                                   :

Publication  (last 5 years)                                    :

*) it is required for sending course material

 Course description

Genomics using domestic animals as genetic models

Course description: Participating students will obtain theoretical and practical knowledge in domestic animal genomics and bioinformatics.

Course contents: Lectures, computer exercises, group discussions and seminars

–Gene and genome structure: Organization of genes and genomes in eukaryotes. The structure and function of chromatin and description on how the chromatin structure is regulated.

Mechanisms underlying genome plasticity and the role of DNA transposons and retrotransposons

–Genotype-environvent interactions; description on how the genes within the genome interacts and controls the phenotype. Describe how gene interactions controls complex traits. Discussion on systems biology and biological interactions.

–Gene expression: The role of transcription factors in regulated transcription and their roles in development and cellular phenotype.

– The principles for epigenetics: Definition of epigenetics and description on how epigenetic mechanisms control chromatin structure and gene expression

– The sequencing of complete genomes using next-generation sequencing techniques: The concepts of genome biology, the techniques used when performing large-scale sequencing and how to find relevant information like regulatory elements, genes and selective sweeps in the genome. 

– Genetic variation and mutations: How does variation occur and which forces are acting on variation? What types of mutations exist at the molecular and functional level. Here the students also get introduced to the concept how to correlate phenotypes with genotypes, the usage of genetic markers and the most commonly used molecular techniques.

– Genetic Association studies: These lectures deal with how genetic markers can be used in association studies. General principles of the laboratory work will be discussed and also calculations of allele frequencies, Odds ratio, p-value and correction of multiple testing. The students will use a computer program that analyses microsatellites (Genetic Profiler) installed on their own computers. They will analyse affected and unaffected dogs to learn how to evaluate whether a genetic marker is associated with a disease/trait or not.  Freely available statistical programs will be used to evaluate the statistical significance of the results.

– Molecular techniques: The most commonly used molecular techniques (standard and advanced PCR, sequencing, techniques for analysis of gene expression, gel-electrophoreses, are presented with much time to discuss the students own laboratory issues. 

– Conservation genetics: This part of the course brings up the basic concepts in population genetics and how to use genetics as a tool when working with endangered species and threatened populations. The knowledge can easily be translated into the preservation of domesticated species, their special characteristics and economical values. The students are given a case of national importance and relevant for conservation of domesticated species to discuss. Authentic genetic data will be interpreted and guided by questions prepared by the teacher.

– Introduction to Genome browsers – Ensembl and UCSC: This part of the course deal with how to browse genes and genomes with Ensembl genome browser and UCSC genome browser.  Genome browsers are software system, which produces and maintains automatic annotation on selected eukaryotic genomes. It performs automatic analysis of new genome data and maintains analysis and annotation on the current data. The students will get a walk through the main pages of the Ensembl browser and UCSC genome browser and learn how to navigate and use it. The students will also learn how to design primers by using the program Primer 3.

–Genetic mapping of complex traits:

Understand the principles for genetic mapping techniques including linkage mapping, IBD-mapping, genome-wide association and QTL-mapping. Use of high density genome-wide SNP-arrays.

Discussion about the techniques applicability in genetic studies using domestic animals. Computer exercises in QTL mapping.

Dates: March 7th to March 17th 2011

Prerequisites: Background in Biology, Genetics and Molecular Biology.

Lecturers:

Mia Olsson, MSc, PhD student in domestic animal genomics. Uppsala University, Uppsala, Sweden

Maria Wilbe, MSc, PhD student in domestic animal genomics. Swedish University of Agricultural Sciences, Uppsala, Sweden

Dominic Wright, PhD in quantitative genetics. Linköping University, Linköping, Sweden

Prof. Göran Andersson PhD. Prof. In molecular genetics. Swedish University of Agricultural Sciences, Uppsala, Sweden

Sponsor: The Swedish Research Council

Course organizers:

Göran Andersson                                            Goran.Andersson@slu.se

Mia Olsson                                                      mia.olsson@imbim.uu.se

Maria Wilbe                                                    Maria.Wilbe@slu.se

Dominic Wright                                              Domwright@gmail.com

Heriberto Rodriguez-Martinez                        heriberto.rodriguez-martinez@liu.se

Ronny R. Noor                                               ronny_noor@yahoo.com

Schedule March 7 – March 17, 2011

Classes end no later than 17.00 every day

 Dominic Wright lecture outline

Lecture One: Principles of Genetic Linkage and Map Creation

• Background – Thomas Hunt and Alfred Sturtevant with the idea that mutations can be in linkage. Recombination between traits – crossing over during meiosis leading to disruption between traits. The use of number of recombinations to separate traits, distance in centimorgans.
• Genetic markers used for analysis, types of markers available. Crossing between two populations. The idea of a genetic map.
• Methods for measuring genetic distances. Use of three (and more) markers to establish gene order and distance (travelling salesman problem). Mapping functions (Kosambi, Haldane).

Practical One: Genetic Map construction.

• Use R (maybe crimap?) to perform a map construction on either a simulated or real (but limited) dataset.
• Try different methods of map construction. Counting the number of recombinations.

Lecture Two: Principles of QTL analysis

• Introduction to QTL analysis, definition of a QTL. Differences between Mendelian (simple) and quantitative (complex) traits.
• Crossing populations – types of QTL crosses (backcross, F2 intercross, advanced intercross, recombinant inbred lines).
• Measuring phenotypes and the regression of phenotypes on marker genotypes. Placing traits on the genetic map.
• Statistical methods for single marker analysis (T test!). Problems with this approach (close and distant linkage confounded with large and small effect size).
• Interval mapping and its advantages.
• Composite Interval Mapping, Multiple Interval Mapping and beyond. Introduction to these only!
•  Introduction to eQTL analysis and gene networks.
•  Advantages and disadvantages of QTL analysis.

Practical Two: QTL analysis in R

• Use of R/QTL to test mapping using an experimental dataset. Types of analysis.
• Preparation of a dataset. Plotting phenotypes, checking for outliers, data cleaning.
• Segregation distortion (possibly practical one?).
• Single marker analysis using regression.
• Interval mapping analysis using Haley-Knott regression and ML.
• LOD scores, plotting results.